Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 14:21:27 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nv0_12601/04_2023/7nv0_12601_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nv0_12601/04_2023/7nv0_12601.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nv0_12601/04_2023/7nv0_12601_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nv0_12601/04_2023/7nv0_12601_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nv0_12601/04_2023/7nv0_12601_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nv0_12601/04_2023/7nv0_12601.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nv0_12601/04_2023/7nv0_12601.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nv0_12601/04_2023/7nv0_12601_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nv0_12601/04_2023/7nv0_12601_neut_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 55 5.49 5 S 66 5.16 5 C 6093 2.51 5 N 1701 2.21 5 O 2013 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 296": "OE1" <-> "OE2" Residue "A ARG 450": "NH1" <-> "NH2" Residue "B GLU 124": "OE1" <-> "OE2" Residue "B GLU 174": "OE1" <-> "OE2" Residue "D GLU 124": "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: 9928 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3162 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PTRANS': 15, 'TRANS': 414} Chain breaks: 2 Unresolved non-hydrogen bonds: 306 Unresolved non-hydrogen angles: 374 Unresolved non-hydrogen dihedrals: 252 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 7, 'PHE:plan': 5, 'GLU:plan': 13, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 185 Chain: "B" Number of atoms: 1864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1864 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 7, 'TRANS': 240} Chain breaks: 2 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "C" Number of atoms: 1902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1902 Classifications: {'peptide': 253} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 7, 'TRANS': 245} Chain breaks: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 35 Chain: "D" Number of atoms: 1888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1888 Classifications: {'peptide': 249} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 241} Chain breaks: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "P" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 512 Unusual residues: {'DOC': 1} Classifications: {'DNA': 24, 'undetermined': 1} Link IDs: {'rna3p': 23, None: 1} Not linked: pdbres=" DG P 24 " pdbres="DOC P 25 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "T" Number of atoms: 571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 571 Classifications: {'DNA': 28} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 27} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'TTP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.62, per 1000 atoms: 0.57 Number of scatterers: 9928 At special positions: 0 Unit cell: (121.632, 109.686, 115.116, 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 66 16.00 P 55 15.00 O 2013 8.00 N 1701 7.00 C 6093 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: 4.38 Conformation dependent library (CDL) restraints added in 1.4 seconds 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2250 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 29 helices and 13 sheets defined 22.5% alpha, 25.1% beta 24 base pairs and 45 stacking pairs defined. Time for finding SS restraints: 3.63 Creating SS restraints... Processing helix chain 'A' and resid 48 through 71 removed outlier: 3.676A pdb=" N GLN A 70 " --> pdb=" O ASN A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 94 Processing helix chain 'A' and resid 111 through 117 removed outlier: 4.036A pdb=" N GLU A 116 " --> pdb=" O TYR A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 144 No H-bonds generated for 'chain 'A' and resid 141 through 144' Processing helix chain 'A' and resid 174 through 188 removed outlier: 3.799A pdb=" N LYS A 179 " --> pdb=" O ARG A 175 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL A 181 " --> pdb=" O VAL A 177 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE A 184 " --> pdb=" O GLU A 180 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASP A 187 " --> pdb=" O GLU A 183 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N TYR A 188 " --> pdb=" O ILE A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 211 No H-bonds generated for 'chain 'A' and resid 209 through 211' Processing helix chain 'A' and resid 290 through 305 removed outlier: 3.925A pdb=" N VAL A 294 " --> pdb=" O ALA A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 325 removed outlier: 3.647A pdb=" N VAL A 322 " --> pdb=" O MET A 318 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ASP A 325 " --> pdb=" O LYS A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 346 No H-bonds generated for 'chain 'A' and resid 343 through 346' Processing helix chain 'A' and resid 360 through 366 removed outlier: 3.542A pdb=" N LEU A 365 " --> pdb=" O THR A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 377 Processing helix chain 'A' and resid 380 through 386 removed outlier: 3.609A pdb=" N LEU A 385 " --> pdb=" O ALA A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 399 Processing helix chain 'A' and resid 429 through 447 removed outlier: 3.899A pdb=" N GLN A 436 " --> pdb=" O TYR A 432 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU A 437 " --> pdb=" O SER A 433 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU A 438 " --> pdb=" O LEU A 434 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU A 442 " --> pdb=" O LEU A 438 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLN A 447 " --> pdb=" O ALA A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 496 removed outlier: 5.235A pdb=" N GLU A 490 " --> pdb=" O ALA A 486 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU A 491 " --> pdb=" O ILE A 487 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N THR A 494 " --> pdb=" O GLU A 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 19 Processing helix chain 'B' and resid 72 through 78 Processing helix chain 'B' and resid 141 through 151 Processing helix chain 'B' and resid 209 through 218 removed outlier: 4.526A pdb=" N PHE B 214 " --> pdb=" O ARG B 210 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LYS B 217 " --> pdb=" O ASN B 213 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N ALA B 218 " --> pdb=" O PHE B 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 15 No H-bonds generated for 'chain 'C' and resid 12 through 15' Processing helix chain 'C' and resid 72 through 81 removed outlier: 4.548A pdb=" N CYS C 81 " --> pdb=" O LYS C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 154 removed outlier: 4.107A pdb=" N HIS C 153 " --> pdb=" O ARG C 149 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE C 154 " --> pdb=" O ASP C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 217 No H-bonds generated for 'chain 'C' and resid 215 through 217' Processing helix chain 'C' and resid 219 through 221 No H-bonds generated for 'chain 'C' and resid 219 through 221' Processing helix chain 'D' and resid 10 through 18 Processing helix chain 'D' and resid 72 through 78 Processing helix chain 'D' and resid 141 through 148 Processing helix chain 'D' and resid 209 through 217 removed outlier: 4.649A pdb=" N PHE D 214 " --> pdb=" O ARG D 210 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LYS D 217 " --> pdb=" O ASN D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 221 No H-bonds generated for 'chain 'D' and resid 219 through 221' Processing sheet with id= A, first strand: chain 'A' and resid 201 through 203 Processing sheet with id= B, first strand: chain 'A' and resid 128 through 130 removed outlier: 6.376A pdb=" N ILE A 165 " --> pdb=" O ALA A 129 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 415 through 421 removed outlier: 6.660A pdb=" N LYS A 461 " --> pdb=" O ARG A 507 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N MET A 509 " --> pdb=" O LYS A 459 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LYS A 459 " --> pdb=" O MET A 509 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N VAL A 511 " --> pdb=" O THR A 457 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N THR A 457 " --> pdb=" O VAL A 511 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ILE A 513 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR A 455 " --> pdb=" O ILE A 513 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 59 through 61 Processing sheet with id= E, first strand: chain 'B' and resid 66 through 71 removed outlier: 6.900A pdb=" N GLU B 25 " --> pdb=" O MET B 40 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N MET B 40 " --> pdb=" O GLU B 25 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N CYS B 27 " --> pdb=" O GLN B 38 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLN B 38 " --> pdb=" O CYS B 27 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 203 through 208 Processing sheet with id= G, first strand: chain 'C' and resid 59 through 62 Processing sheet with id= H, first strand: chain 'C' and resid 26 through 30 Processing sheet with id= I, first strand: chain 'C' and resid 34 through 40 removed outlier: 4.731A pdb=" N LYS C 240 " --> pdb=" O THR C 224 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N THR C 224 " --> pdb=" O LYS C 240 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 203 through 208 Processing sheet with id= K, first strand: chain 'D' and resid 59 through 61 Processing sheet with id= L, first strand: chain 'D' and resid 66 through 71 removed outlier: 7.458A pdb=" N GLU D 25 " --> pdb=" O MET D 40 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N MET D 40 " --> pdb=" O GLU D 25 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N CYS D 27 " --> pdb=" O GLN D 38 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N GLN D 38 " --> pdb=" O CYS D 27 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS D 240 " --> pdb=" O THR D 224 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N THR D 224 " --> pdb=" O LYS D 240 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 203 through 207 376 hydrogen bonds defined for protein. 1017 hydrogen bond angles defined for protein. Warning, Cannot make NA restraints for OD residue Restraints generated for nucleic acids: 57 hydrogen bonds 114 hydrogen bond angles 0 basepair planarities 24 basepair parallelities 44 stacking parallelities Total time for adding SS restraints: 3.49 Time building geometry restraints manager: 4.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2259 1.33 - 1.45: 2177 1.45 - 1.57: 5527 1.57 - 1.69: 107 1.69 - 1.81: 109 Bond restraints: 10179 Sorted by residual: bond pdb=" C4' DOC P 25 " pdb=" C3' DOC P 25 " ideal model delta sigma weight residual 1.334 1.528 -0.194 2.00e-02 2.50e+03 9.44e+01 bond pdb=" C4' DOC P 25 " pdb=" O4' DOC P 25 " ideal model delta sigma weight residual 1.609 1.446 0.163 2.00e-02 2.50e+03 6.64e+01 bond pdb=" C4 DOC P 25 " pdb=" N4 DOC P 25 " ideal model delta sigma weight residual 1.494 1.335 0.159 2.00e-02 2.50e+03 6.34e+01 bond pdb=" C5 DOC P 25 " pdb=" C6 DOC P 25 " ideal model delta sigma weight residual 1.494 1.339 0.155 2.00e-02 2.50e+03 6.04e+01 bond pdb=" O4' DOC P 25 " pdb=" C1' DOC P 25 " ideal model delta sigma weight residual 1.268 1.421 -0.153 2.00e-02 2.50e+03 5.89e+01 ... (remaining 10174 not shown) Histogram of bond angle deviations from ideal: 97.07 - 104.48: 347 104.48 - 111.90: 4933 111.90 - 119.31: 3684 119.31 - 126.73: 4820 126.73 - 134.14: 215 Bond angle restraints: 13999 Sorted by residual: angle pdb=" O2A TTP A 901 " pdb=" PA TTP A 901 " pdb=" O5' TTP A 901 " ideal model delta sigma weight residual 109.50 122.69 -13.19 3.00e+00 1.11e-01 1.93e+01 angle pdb=" C ALA D 242 " pdb=" N ASP D 243 " pdb=" CA ASP D 243 " ideal model delta sigma weight residual 121.54 129.51 -7.97 1.91e+00 2.74e-01 1.74e+01 angle pdb=" C ALA B 231 " pdb=" N ASP B 232 " pdb=" CA ASP B 232 " ideal model delta sigma weight residual 121.54 129.35 -7.81 1.91e+00 2.74e-01 1.67e+01 angle pdb=" N PHE A 500 " pdb=" CA PHE A 500 " pdb=" C PHE A 500 " ideal model delta sigma weight residual 109.81 118.30 -8.49 2.21e+00 2.05e-01 1.48e+01 angle pdb=" O3' DA T 10 " pdb=" C3' DA T 10 " pdb=" C2' DA T 10 " ideal model delta sigma weight residual 111.50 105.85 5.65 1.50e+00 4.44e-01 1.42e+01 ... (remaining 13994 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.27: 5587 31.27 - 62.54: 420 62.54 - 93.81: 14 93.81 - 125.08: 3 125.08 - 156.35: 1 Dihedral angle restraints: 6025 sinusoidal: 2574 harmonic: 3451 Sorted by residual: dihedral pdb=" C2 TTP A 901 " pdb=" C1' TTP A 901 " pdb=" N1 TTP A 901 " pdb=" O4' TTP A 901 " ideal model delta sinusoidal sigma weight residual 301.68 145.33 156.35 1 2.00e+01 2.50e-03 4.60e+01 dihedral pdb=" O2G TTP A 901 " pdb=" O3B TTP A 901 " pdb=" PG TTP A 901 " pdb=" PB TTP A 901 " ideal model delta sinusoidal sigma weight residual -180.00 -64.13 -115.87 1 2.00e+01 2.50e-03 3.45e+01 dihedral pdb=" C5' TTP A 901 " pdb=" O5' TTP A 901 " pdb=" PA TTP A 901 " pdb=" O3A TTP A 901 " ideal model delta sinusoidal sigma weight residual 179.97 79.63 100.34 1 2.00e+01 2.50e-03 2.83e+01 ... (remaining 6022 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1150 0.058 - 0.116: 402 0.116 - 0.174: 90 0.174 - 0.232: 9 0.232 - 0.290: 5 Chirality restraints: 1656 Sorted by residual: chirality pdb=" CA THR C 219 " pdb=" N THR C 219 " pdb=" C THR C 219 " pdb=" CB THR C 219 " both_signs ideal model delta sigma weight residual False 2.53 2.24 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CB ILE A 166 " pdb=" CA ILE A 166 " pdb=" CG1 ILE A 166 " pdb=" CG2 ILE A 166 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CA LYS A 328 " pdb=" N LYS A 328 " pdb=" C LYS A 328 " pdb=" CB LYS A 328 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 1653 not shown) Planarity restraints: 1599 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG P 24 " -0.033 2.00e-02 2.50e+03 1.82e-02 9.93e+00 pdb=" N9 DG P 24 " 0.052 2.00e-02 2.50e+03 pdb=" C8 DG P 24 " -0.007 2.00e-02 2.50e+03 pdb=" N7 DG P 24 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DG P 24 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DG P 24 " -0.001 2.00e-02 2.50e+03 pdb=" O6 DG P 24 " -0.007 2.00e-02 2.50e+03 pdb=" N1 DG P 24 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DG P 24 " 0.005 2.00e-02 2.50e+03 pdb=" N2 DG P 24 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DG P 24 " -0.000 2.00e-02 2.50e+03 pdb=" C4 DG P 24 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT P 23 " 0.032 2.00e-02 2.50e+03 1.69e-02 7.12e+00 pdb=" N1 DT P 23 " -0.042 2.00e-02 2.50e+03 pdb=" C2 DT P 23 " -0.003 2.00e-02 2.50e+03 pdb=" O2 DT P 23 " 0.000 2.00e-02 2.50e+03 pdb=" N3 DT P 23 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DT P 23 " 0.005 2.00e-02 2.50e+03 pdb=" O4 DT P 23 " 0.006 2.00e-02 2.50e+03 pdb=" C5 DT P 23 " 0.002 2.00e-02 2.50e+03 pdb=" C7 DT P 23 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DT P 23 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET C 139 " -0.043 5.00e-02 4.00e+02 6.51e-02 6.77e+00 pdb=" N PRO C 140 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO C 140 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 140 " -0.036 5.00e-02 4.00e+02 ... (remaining 1596 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1288 2.74 - 3.28: 8533 3.28 - 3.82: 16466 3.82 - 4.36: 18498 4.36 - 4.90: 32052 Nonbonded interactions: 76837 Sorted by model distance: nonbonded pdb=" O LEU C 16 " pdb=" OG SER C 76 " model vdw 2.205 2.440 nonbonded pdb=" OG SER D 222 " pdb=" O LYS D 240 " model vdw 2.237 2.440 nonbonded pdb=" OG SER C 10 " pdb=" O ASN C 84 " model vdw 2.246 2.440 nonbonded pdb=" OG SER B 222 " pdb=" O THR B 224 " model vdw 2.272 2.440 nonbonded pdb=" OG SER C 134 " pdb=" O MET C 229 " model vdw 2.309 2.440 ... (remaining 76832 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'B' and (resid 1 through 121 or (resid 122 and (name N or name CA or name \ C or name O or name CB )) or resid 123 through 125 or (resid 126 and (name N or \ name CA or name C or name O or name CB )) or resid 127 through 129 or (resid 13 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 131 through \ 164 or (resid 165 and (name N or name CA or name C or name O or name CB )) or re \ sid 166 through 173 or (resid 174 and (name N or name CA or name C or name O or \ name CB )) or resid 175 through 255)) selection = (chain 'C' and (resid 1 through 54 or (resid 55 and (name N or name CA or name C \ or name O or name CB )) or resid 56 through 63 or (resid 64 and (name N or name \ CA or name C or name O or name CB )) or resid 65 through 94 or (resid 95 throug \ h 96 and (name N or name CA or name C or name O or name CB )) or resid 97 throug \ h 106 or resid 109 through 124 or (resid 125 through 126 and (name N or name CA \ or name C or name O or name CB )) or resid 127 or (resid 128 and (name N or name \ CA or name C or name O or name CB )) or resid 129 through 173 or (resid 174 and \ (name N or name CA or name C or name O or name CB )) or resid 175 through 185 o \ r resid 191 through 209 or (resid 210 and (name N or name CA or name C or name O \ or name CB )) or resid 211 through 255)) selection = (chain 'D' and (resid 1 through 54 or (resid 55 and (name N or name CA or name C \ or name O or name CB )) or resid 56 through 63 or (resid 64 and (name N or name \ CA or name C or name O or name CB )) or resid 65 through 94 or (resid 95 throug \ h 96 and (name N or name CA or name C or name O or name CB )) or resid 97 throug \ h 124 or (resid 125 through 126 and (name N or name CA or name C or name O or na \ me CB )) or resid 127 or (resid 128 and (name N or name CA or name C or name O o \ r name CB )) or resid 129 or (resid 130 and (name N or name CA or name C or name \ O or name CB )) or resid 131 through 164 or (resid 165 and (name N or name CA o \ r name C or name O or name CB )) or resid 166 through 185 or resid 191 through 2 \ 09 or (resid 210 and (name N or name CA or name C or name O or name CB )) or res \ id 211 through 254 or (resid 255 and (name N or name CA or name C or name O or n \ ame CB )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.090 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: 1.420 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 32.240 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6728 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 : 0.011 0.194 10179 Z= 0.666 Angle : 1.133 13.188 13999 Z= 0.615 Chirality : 0.061 0.290 1656 Planarity : 0.006 0.065 1599 Dihedral : 19.629 156.354 3775 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer Outliers : 1.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.56 (0.19), residues: 1158 helix: -3.60 (0.19), residues: 289 sheet: -2.05 (0.23), residues: 386 loop : -3.34 (0.22), residues: 483 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 300 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 310 average time/residue: 0.2525 time to fit residues: 104.3141 Evaluate side-chains 239 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 233 time to evaluate : 1.089 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0957 time to fit residues: 2.6590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 7.9990 chunk 90 optimal weight: 0.1980 chunk 50 optimal weight: 4.9990 chunk 31 optimal weight: 7.9990 chunk 61 optimal weight: 8.9990 chunk 48 optimal weight: 9.9990 chunk 94 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 57 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 ASN A 105 HIS A 191 ASN ** A 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 526 GLN B 65 ASN B 200 ASN C 65 ASN C 71 ASN C 84 ASN ** C 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 204 GLN D 49 GLN D 213 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6732 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 10179 Z= 0.267 Angle : 0.669 6.909 13999 Z= 0.359 Chirality : 0.044 0.151 1656 Planarity : 0.004 0.051 1599 Dihedral : 20.140 155.891 1774 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer Outliers : 3.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.32 (0.22), residues: 1158 helix: -2.32 (0.25), residues: 285 sheet: -1.33 (0.24), residues: 398 loop : -2.78 (0.24), residues: 475 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 236 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 24 residues processed: 255 average time/residue: 0.2292 time to fit residues: 80.2499 Evaluate side-chains 239 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 215 time to evaluate : 1.055 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1051 time to fit residues: 5.8714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 chunk 30 optimal weight: 10.0000 chunk 109 optimal weight: 8.9990 chunk 117 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 chunk 108 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 GLN ** C 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 213 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6731 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 0.039 10179 Z= 0.235 Angle : 0.629 7.385 13999 Z= 0.337 Chirality : 0.043 0.146 1656 Planarity : 0.004 0.047 1599 Dihedral : 19.853 149.710 1774 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer Outliers : 2.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.61 (0.23), residues: 1158 helix: -1.71 (0.28), residues: 286 sheet: -0.87 (0.25), residues: 398 loop : -2.41 (0.26), residues: 474 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 226 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 14 residues processed: 245 average time/residue: 0.2372 time to fit residues: 79.7386 Evaluate side-chains 230 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 216 time to evaluate : 1.030 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0936 time to fit residues: 3.9530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 10.0000 chunk 82 optimal weight: 9.9990 chunk 56 optimal weight: 10.0000 chunk 12 optimal weight: 30.0000 chunk 52 optimal weight: 6.9990 chunk 73 optimal weight: 0.8980 chunk 109 optimal weight: 4.9990 chunk 115 optimal weight: 8.9990 chunk 57 optimal weight: 7.9990 chunk 103 optimal weight: 4.9990 chunk 31 optimal weight: 7.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN A 291 GLN A 332 GLN B 71 ASN B 200 ASN C 38 GLN ** C 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6805 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.071 10179 Z= 0.367 Angle : 0.732 8.226 13999 Z= 0.385 Chirality : 0.046 0.212 1656 Planarity : 0.005 0.055 1599 Dihedral : 19.839 140.129 1774 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer Outliers : 3.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.55 (0.23), residues: 1158 helix: -1.81 (0.26), residues: 298 sheet: -0.80 (0.25), residues: 400 loop : -2.30 (0.27), residues: 460 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 224 time to evaluate : 1.053 Fit side-chains revert: symmetry clash outliers start: 32 outliers final: 20 residues processed: 242 average time/residue: 0.2424 time to fit residues: 80.2309 Evaluate side-chains 235 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 215 time to evaluate : 0.994 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1003 time to fit residues: 5.1540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 86 optimal weight: 10.0000 chunk 47 optimal weight: 6.9990 chunk 98 optimal weight: 9.9990 chunk 80 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 59 optimal weight: 9.9990 chunk 104 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 GLN ** C 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6816 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.057 10179 Z= 0.384 Angle : 0.744 13.141 13999 Z= 0.388 Chirality : 0.046 0.166 1656 Planarity : 0.004 0.052 1599 Dihedral : 19.852 140.971 1774 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer Outliers : 2.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.54 (0.23), residues: 1158 helix: -1.81 (0.26), residues: 307 sheet: -0.73 (0.25), residues: 398 loop : -2.33 (0.27), residues: 453 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 215 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 16 residues processed: 228 average time/residue: 0.2314 time to fit residues: 72.8749 Evaluate side-chains 221 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 205 time to evaluate : 1.281 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1293 time to fit residues: 6.9302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 0.9990 chunk 104 optimal weight: 0.2980 chunk 22 optimal weight: 9.9990 chunk 68 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 116 optimal weight: 20.0000 chunk 96 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 60 optimal weight: 0.4980 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 GLN ** C 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6688 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 10179 Z= 0.165 Angle : 0.581 10.124 13999 Z= 0.307 Chirality : 0.042 0.140 1656 Planarity : 0.003 0.047 1599 Dihedral : 19.662 147.956 1774 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer Outliers : 1.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.24), residues: 1158 helix: -0.99 (0.29), residues: 300 sheet: -0.34 (0.26), residues: 400 loop : -2.00 (0.28), residues: 458 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 238 time to evaluate : 1.078 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 243 average time/residue: 0.2473 time to fit residues: 80.9479 Evaluate side-chains 230 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 223 time to evaluate : 1.090 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0929 time to fit residues: 2.6558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 8.9990 chunk 13 optimal weight: 8.9990 chunk 66 optimal weight: 8.9990 chunk 84 optimal weight: 9.9990 chunk 65 optimal weight: 9.9990 chunk 97 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 115 optimal weight: 0.9990 chunk 72 optimal weight: 0.0570 chunk 70 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 overall best weight: 3.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN A 379 GLN A 444 GLN C 38 GLN ** C 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6765 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 10179 Z= 0.291 Angle : 0.675 11.626 13999 Z= 0.351 Chirality : 0.044 0.157 1656 Planarity : 0.004 0.037 1599 Dihedral : 19.635 140.458 1774 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer Outliers : 2.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.24), residues: 1158 helix: -1.11 (0.28), residues: 305 sheet: -0.33 (0.25), residues: 401 loop : -2.05 (0.28), residues: 452 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 212 time to evaluate : 1.124 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 12 residues processed: 225 average time/residue: 0.2442 time to fit residues: 75.5194 Evaluate side-chains 221 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 209 time to evaluate : 1.111 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1263 time to fit residues: 4.1813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 69 optimal weight: 7.9990 chunk 34 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 10 optimal weight: 0.0770 chunk 90 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 overall best weight: 1.9544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 GLN C 38 GLN ** C 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6715 moved from start: 0.3989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 10179 Z= 0.205 Angle : 0.616 11.106 13999 Z= 0.322 Chirality : 0.042 0.181 1656 Planarity : 0.003 0.036 1599 Dihedral : 19.533 142.911 1774 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer Outliers : 1.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.24), residues: 1158 helix: -0.78 (0.29), residues: 304 sheet: -0.18 (0.26), residues: 400 loop : -1.91 (0.29), residues: 454 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 219 time to evaluate : 1.180 Fit side-chains outliers start: 11 outliers final: 8 residues processed: 223 average time/residue: 0.2378 time to fit residues: 72.8290 Evaluate side-chains 217 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 209 time to evaluate : 1.093 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0948 time to fit residues: 2.9345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 107 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 chunk 46 optimal weight: 20.0000 chunk 84 optimal weight: 0.3980 chunk 33 optimal weight: 9.9990 chunk 97 optimal weight: 6.9990 chunk 70 optimal weight: 0.5980 chunk 113 optimal weight: 2.9990 chunk 69 optimal weight: 0.0980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 GLN A 444 GLN C 38 GLN ** C 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6630 moved from start: 0.4252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 10179 Z= 0.163 Angle : 0.584 9.390 13999 Z= 0.306 Chirality : 0.041 0.187 1656 Planarity : 0.003 0.031 1599 Dihedral : 19.309 144.753 1774 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.25), residues: 1158 helix: -0.32 (0.31), residues: 293 sheet: 0.03 (0.26), residues: 399 loop : -1.80 (0.28), residues: 466 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 228 time to evaluate : 1.125 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 231 average time/residue: 0.2325 time to fit residues: 74.1733 Evaluate side-chains 216 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 214 time to evaluate : 1.072 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1022 time to fit residues: 1.7297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 5.9990 chunk 79 optimal weight: 0.6980 chunk 119 optimal weight: 10.0000 chunk 110 optimal weight: 0.0010 chunk 95 optimal weight: 0.9980 chunk 9 optimal weight: 8.9990 chunk 73 optimal weight: 20.0000 chunk 58 optimal weight: 9.9990 chunk 75 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6669 moved from start: 0.4348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 10179 Z= 0.188 Angle : 0.604 9.233 13999 Z= 0.315 Chirality : 0.042 0.244 1656 Planarity : 0.003 0.027 1599 Dihedral : 19.240 140.019 1774 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.25), residues: 1158 helix: -0.25 (0.31), residues: 291 sheet: 0.15 (0.26), residues: 402 loop : -1.76 (0.28), residues: 465 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 213 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 217 average time/residue: 0.2322 time to fit residues: 69.3919 Evaluate side-chains 215 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 210 time to evaluate : 1.129 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1113 time to fit residues: 2.4355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 97 optimal weight: 0.0870 chunk 12 optimal weight: 0.0000 chunk 17 optimal weight: 30.0000 chunk 83 optimal weight: 0.7980 chunk 5 optimal weight: 10.0000 chunk 68 optimal weight: 0.1980 overall best weight: 0.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 GLN C 38 GLN C 44 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.195936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.156828 restraints weight = 12080.129| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 2.15 r_work: 0.3722 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6758 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 10179 Z= 0.180 Angle : 0.595 11.724 13999 Z= 0.311 Chirality : 0.041 0.206 1656 Planarity : 0.003 0.028 1599 Dihedral : 19.142 142.783 1774 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.25), residues: 1158 helix: -0.06 (0.31), residues: 294 sheet: 0.24 (0.26), residues: 404 loop : -1.75 (0.28), residues: 460 =============================================================================== Job complete usr+sys time: 2284.93 seconds wall clock time: 42 minutes 4.58 seconds (2524.58 seconds total)