Starting phenix.real_space_refine on Sun Apr 7 07:08:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nv0_12601/04_2024/7nv0_12601_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nv0_12601/04_2024/7nv0_12601.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nv0_12601/04_2024/7nv0_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_2024/7nv0_12601_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nv0_12601/04_2024/7nv0_12601_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nv0_12601/04_2024/7nv0_12601.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nv0_12601/04_2024/7nv0_12601.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nv0_12601/04_2024/7nv0_12601_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nv0_12601/04_2024/7nv0_12601_neut_updated.pdb" } resolution = 3.4 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 ------------------------------------------------------------------------------- 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-dev-5288/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: 6.23, per 1000 atoms: 0.63 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: 4.19 Conformation dependent library (CDL) restraints added in 1.7 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: 4.69 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: 3.53 Time building geometry restraints manager: 4.54 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: 5630 31.27 - 62.54: 450 62.54 - 93.81: 14 93.81 - 125.08: 3 125.08 - 156.35: 1 Dihedral angle restraints: 6098 sinusoidal: 2647 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 6095 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: 0.060 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: 0.000 Extract box with map and model: 0.940 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 33.960 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.050 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.650 ------------------------------------------------------------------------------- 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 : 19.870 156.354 3848 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 % Allowed : 13.45 % Favored : 85.25 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 392 HIS 0.006 0.002 HIS A 524 PHE 0.031 0.003 PHE B 169 TYR 0.028 0.004 TYR C 249 ARG 0.007 0.001 ARG A 97 *********************** 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 : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.6912 (mt) cc_final: 0.6650 (mt) REVERT: A 58 LYS cc_start: 0.7220 (mtpt) cc_final: 0.6814 (mttp) REVERT: A 362 GLU cc_start: 0.7033 (tt0) cc_final: 0.6692 (tt0) REVERT: A 527 ARG cc_start: 0.7148 (ttt180) cc_final: 0.6623 (ttm110) REVERT: B 37 LEU cc_start: 0.7841 (tt) cc_final: 0.7550 (tp) REVERT: B 175 LEU cc_start: 0.4600 (OUTLIER) cc_final: 0.3159 (mt) REVERT: B 184 GLN cc_start: 0.5778 (tt0) cc_final: 0.5111 (tp-100) REVERT: B 199 MET cc_start: 0.6687 (tmm) cc_final: 0.6390 (tmm) REVERT: C 118 LEU cc_start: 0.7329 (mt) cc_final: 0.6959 (mm) REVERT: D 138 LYS cc_start: 0.7837 (tmmt) cc_final: 0.7176 (tttp) outliers start: 12 outliers final: 6 residues processed: 310 average time/residue: 0.2603 time to fit residues: 107.6262 Evaluate side-chains 245 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 238 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain D residue 35 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 6.9990 chunk 90 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 94 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 chunk 57 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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 38 GLN D 49 GLN D 213 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6722 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 10179 Z= 0.242 Angle : 0.655 7.422 13999 Z= 0.352 Chirality : 0.043 0.160 1656 Planarity : 0.004 0.051 1599 Dihedral : 20.327 156.711 1856 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.58 % Allowed : 18.22 % Favored : 78.20 % 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: -3.37 (0.21), residues: 1158 helix: -2.33 (0.25), residues: 285 sheet: -1.42 (0.24), residues: 391 loop : -2.76 (0.24), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 392 HIS 0.002 0.001 HIS D 44 PHE 0.010 0.001 PHE B 214 TYR 0.010 0.001 TYR D 249 ARG 0.006 0.001 ARG A 420 *********************** 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: 33 poor density : 238 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.7315 (mtpt) cc_final: 0.7094 (mttp) REVERT: A 392 TRP cc_start: 0.6924 (p-90) cc_final: 0.6622 (p-90) REVERT: A 398 ILE cc_start: 0.5549 (tt) cc_final: 0.5330 (tt) REVERT: A 420 ARG cc_start: 0.6698 (ttm110) cc_final: 0.6466 (ttm110) REVERT: A 527 ARG cc_start: 0.7108 (ttt180) cc_final: 0.6622 (ttm110) REVERT: B 184 GLN cc_start: 0.5700 (tt0) cc_final: 0.5089 (tp-100) REVERT: C 14 LYS cc_start: 0.7391 (mtpt) cc_final: 0.6884 (mttp) REVERT: C 118 LEU cc_start: 0.7262 (mt) cc_final: 0.6901 (mm) REVERT: D 64 ARG cc_start: 0.7424 (mmm-85) cc_final: 0.6995 (mtm110) REVERT: D 138 LYS cc_start: 0.7947 (tmmt) cc_final: 0.7352 (ttmm) outliers start: 33 outliers final: 22 residues processed: 257 average time/residue: 0.2383 time to fit residues: 83.8856 Evaluate side-chains 242 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 220 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain C residue 24 ASN Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 153 HIS Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 179 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 8.9990 chunk 33 optimal weight: 4.9990 chunk 90 optimal weight: 8.9990 chunk 74 optimal weight: 0.9990 chunk 30 optimal weight: 9.9990 chunk 109 optimal weight: 9.9990 chunk 117 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 chunk 108 optimal weight: 10.0000 chunk 37 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 101 ASN ** 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6796 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 10179 Z= 0.347 Angle : 0.729 8.079 13999 Z= 0.387 Chirality : 0.046 0.159 1656 Planarity : 0.005 0.056 1599 Dihedral : 20.121 140.742 1855 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 5.53 % Allowed : 20.61 % Favored : 73.86 % 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: -2.82 (0.23), residues: 1158 helix: -1.97 (0.27), residues: 289 sheet: -1.00 (0.25), residues: 395 loop : -2.46 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 392 HIS 0.004 0.001 HIS B 44 PHE 0.015 0.002 PHE B 214 TYR 0.014 0.002 TYR D 249 ARG 0.006 0.001 ARG A 144 *********************** 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 283 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 232 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.7264 (mtpt) cc_final: 0.7021 (mttp) REVERT: A 295 LYS cc_start: 0.6879 (mtpt) cc_final: 0.6583 (mtpt) REVERT: A 392 TRP cc_start: 0.7006 (p-90) cc_final: 0.6714 (p-90) REVERT: A 398 ILE cc_start: 0.5778 (tt) cc_final: 0.5576 (tt) REVERT: A 527 ARG cc_start: 0.7259 (ttt180) cc_final: 0.6644 (ttm110) REVERT: B 184 GLN cc_start: 0.5765 (tt0) cc_final: 0.5035 (tp-100) REVERT: B 244 MET cc_start: 0.7441 (mmm) cc_final: 0.7235 (tpp) REVERT: C 14 LYS cc_start: 0.7443 (mtpt) cc_final: 0.6838 (mttt) REVERT: D 64 ARG cc_start: 0.7504 (mmm-85) cc_final: 0.7065 (mtm110) REVERT: D 65 ASN cc_start: 0.7162 (OUTLIER) cc_final: 0.6756 (m-40) REVERT: D 138 LYS cc_start: 0.7977 (tmmt) cc_final: 0.7275 (tttp) outliers start: 51 outliers final: 37 residues processed: 265 average time/residue: 0.2482 time to fit residues: 91.7420 Evaluate side-chains 251 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 213 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 153 HIS Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 179 ASN Chi-restraints excluded: chain D residue 196 THR 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: 2.9990 chunk 56 optimal weight: 9.9990 chunk 12 optimal weight: 0.3980 chunk 52 optimal weight: 5.9990 chunk 73 optimal weight: 10.0000 chunk 109 optimal weight: 9.9990 chunk 115 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- 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 ** 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: 0.6752 moved from start: 0.3107 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= 0.233 Angle : 0.620 7.189 13999 Z= 0.332 Chirality : 0.043 0.193 1656 Planarity : 0.004 0.051 1599 Dihedral : 20.004 144.153 1855 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 5.10 % Allowed : 22.45 % Favored : 72.45 % 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: -2.28 (0.23), residues: 1158 helix: -1.49 (0.28), residues: 290 sheet: -0.68 (0.25), residues: 400 loop : -2.17 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 392 HIS 0.003 0.001 HIS A 397 PHE 0.018 0.001 PHE A 49 TYR 0.011 0.001 TYR D 239 ARG 0.004 0.001 ARG D 53 *********************** 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 276 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 229 time to evaluate : 1.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.7290 (mtpt) cc_final: 0.7044 (mttp) REVERT: A 291 GLN cc_start: 0.6218 (tp-100) cc_final: 0.5887 (tp-100) REVERT: A 392 TRP cc_start: 0.7040 (p-90) cc_final: 0.6785 (p-90) REVERT: A 398 ILE cc_start: 0.5674 (tt) cc_final: 0.5470 (tt) REVERT: A 444 GLN cc_start: 0.5958 (tp-100) cc_final: 0.5652 (tp40) REVERT: A 489 LYS cc_start: 0.6670 (ttpt) cc_final: 0.6324 (tttm) REVERT: A 527 ARG cc_start: 0.7304 (ttt180) cc_final: 0.6648 (ttm110) REVERT: B 40 MET cc_start: 0.7499 (tpp) cc_final: 0.7031 (tpp) REVERT: B 184 GLN cc_start: 0.5770 (tt0) cc_final: 0.5096 (tp-100) REVERT: B 224 THR cc_start: 0.7626 (t) cc_final: 0.7184 (m) REVERT: C 12 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7532 (mp) REVERT: C 14 LYS cc_start: 0.7470 (mtpt) cc_final: 0.6887 (mttt) REVERT: C 91 ARG cc_start: 0.6687 (ttm110) cc_final: 0.6243 (ttm-80) REVERT: D 64 ARG cc_start: 0.7561 (mmm-85) cc_final: 0.7085 (mtm110) REVERT: D 138 LYS cc_start: 0.7876 (tmmt) cc_final: 0.7192 (tttp) outliers start: 47 outliers final: 36 residues processed: 262 average time/residue: 0.2386 time to fit residues: 85.7965 Evaluate side-chains 258 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 221 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 81 CYS Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 153 HIS Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 162 CYS Chi-restraints excluded: chain D residue 179 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 1 optimal weight: 4.9990 chunk 86 optimal weight: 9.9990 chunk 47 optimal weight: 6.9990 chunk 98 optimal weight: 0.4980 chunk 80 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 104 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- 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** C 36 ASN ** 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: 0.6771 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10179 Z= 0.275 Angle : 0.652 9.836 13999 Z= 0.343 Chirality : 0.044 0.153 1656 Planarity : 0.004 0.039 1599 Dihedral : 19.956 141.276 1855 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 5.53 % Allowed : 23.32 % Favored : 71.15 % 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: -2.11 (0.24), residues: 1158 helix: -1.24 (0.29), residues: 292 sheet: -0.58 (0.25), residues: 400 loop : -2.15 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 392 HIS 0.002 0.001 HIS A 393 PHE 0.015 0.002 PHE A 111 TYR 0.012 0.002 TYR D 239 ARG 0.007 0.001 ARG C 146 *********************** 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 269 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 218 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.7286 (mtpt) cc_final: 0.7053 (mttp) REVERT: A 291 GLN cc_start: 0.6043 (tp-100) cc_final: 0.5662 (tp-100) REVERT: A 392 TRP cc_start: 0.7014 (p-90) cc_final: 0.6771 (p-90) REVERT: A 444 GLN cc_start: 0.5785 (tp-100) cc_final: 0.5523 (tp40) REVERT: A 489 LYS cc_start: 0.6631 (ttpt) cc_final: 0.6265 (tttm) REVERT: A 527 ARG cc_start: 0.7371 (ttt180) cc_final: 0.6710 (ttm110) REVERT: B 40 MET cc_start: 0.7555 (tpp) cc_final: 0.7116 (tpp) REVERT: B 184 GLN cc_start: 0.5786 (tt0) cc_final: 0.5118 (tp-100) REVERT: B 209 LEU cc_start: 0.7336 (mp) cc_final: 0.7109 (mt) REVERT: B 224 THR cc_start: 0.7717 (t) cc_final: 0.7299 (m) REVERT: C 12 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7532 (mp) REVERT: C 14 LYS cc_start: 0.7462 (mtpt) cc_final: 0.6862 (mttp) REVERT: C 91 ARG cc_start: 0.6677 (ttm110) cc_final: 0.6214 (ttm-80) REVERT: D 64 ARG cc_start: 0.7551 (mmm-85) cc_final: 0.7125 (mtm110) REVERT: D 65 ASN cc_start: 0.7192 (OUTLIER) cc_final: 0.6733 (m-40) REVERT: D 138 LYS cc_start: 0.7914 (tmmt) cc_final: 0.7157 (tttp) outliers start: 51 outliers final: 39 residues processed: 252 average time/residue: 0.2414 time to fit residues: 83.7446 Evaluate side-chains 261 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 220 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 81 CYS Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 153 HIS Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain D residue 24 ASN Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 162 CYS Chi-restraints excluded: chain D residue 179 ASN Chi-restraints excluded: chain D residue 196 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 0.0970 chunk 104 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 116 optimal weight: 20.0000 chunk 96 optimal weight: 0.0970 chunk 53 optimal weight: 9.9990 chunk 9 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 60 optimal weight: 0.3980 overall best weight: 1.3180 ------------------------------------------------------------------------------- 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** ** 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: 0.6694 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10179 Z= 0.177 Angle : 0.569 8.309 13999 Z= 0.302 Chirality : 0.041 0.143 1656 Planarity : 0.003 0.041 1599 Dihedral : 19.716 144.739 1854 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.25 % Allowed : 25.49 % Favored : 71.26 % 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: -1.66 (0.24), residues: 1158 helix: -0.76 (0.30), residues: 291 sheet: -0.27 (0.26), residues: 400 loop : -1.99 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 392 HIS 0.002 0.000 HIS B 246 PHE 0.011 0.001 PHE A 111 TYR 0.009 0.001 TYR D 239 ARG 0.006 0.001 ARG C 146 *********************** 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 263 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 233 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.6621 (tpt) cc_final: 0.6336 (tpt) REVERT: A 118 ARG cc_start: 0.6930 (ptt180) cc_final: 0.6441 (ptm160) REVERT: A 305 THR cc_start: 0.6956 (p) cc_final: 0.6046 (t) REVERT: A 343 MET cc_start: 0.6626 (mmm) cc_final: 0.6406 (mmp) REVERT: A 392 TRP cc_start: 0.7135 (p-90) cc_final: 0.6925 (p-90) REVERT: A 444 GLN cc_start: 0.5727 (tp-100) cc_final: 0.5456 (tp40) REVERT: A 527 ARG cc_start: 0.7328 (ttt180) cc_final: 0.6747 (ttm110) REVERT: B 40 MET cc_start: 0.7526 (tpp) cc_final: 0.7090 (tpp) REVERT: B 184 GLN cc_start: 0.5775 (tt0) cc_final: 0.4875 (tp-100) REVERT: B 224 THR cc_start: 0.7605 (t) cc_final: 0.7210 (m) REVERT: B 229 MET cc_start: 0.5209 (ttm) cc_final: 0.5001 (ttm) REVERT: B 244 MET cc_start: 0.7421 (tpp) cc_final: 0.7131 (tpp) REVERT: B 250 TYR cc_start: 0.7312 (m-80) cc_final: 0.7099 (m-80) REVERT: C 14 LYS cc_start: 0.7257 (mtpt) cc_final: 0.6679 (mmtm) REVERT: C 91 ARG cc_start: 0.6525 (ttm110) cc_final: 0.6244 (ttm-80) REVERT: C 181 LYS cc_start: 0.7721 (tptp) cc_final: 0.7419 (tppt) REVERT: D 64 ARG cc_start: 0.7537 (mmm-85) cc_final: 0.7137 (mtm110) REVERT: D 138 LYS cc_start: 0.7783 (tmmt) cc_final: 0.7199 (tttp) outliers start: 30 outliers final: 25 residues processed: 253 average time/residue: 0.2508 time to fit residues: 86.3732 Evaluate side-chains 246 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 221 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 81 CYS Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 153 HIS Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain D residue 24 ASN Chi-restraints excluded: chain D residue 162 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 84 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 97 optimal weight: 8.9990 chunk 64 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN B 71 ASN ** 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: 0.6783 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 10179 Z= 0.339 Angle : 0.689 11.388 13999 Z= 0.359 Chirality : 0.046 0.190 1656 Planarity : 0.004 0.041 1599 Dihedral : 19.853 139.024 1854 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 5.53 % Allowed : 24.19 % Favored : 70.28 % 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: -1.84 (0.24), residues: 1158 helix: -1.03 (0.29), residues: 300 sheet: -0.38 (0.25), residues: 400 loop : -2.02 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 392 HIS 0.003 0.001 HIS C 153 PHE 0.026 0.002 PHE A 49 TYR 0.012 0.002 TYR A 50 ARG 0.006 0.001 ARG C 146 *********************** 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 275 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 224 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 MET cc_start: 0.6712 (mmm) cc_final: 0.6480 (mmp) REVERT: A 362 GLU cc_start: 0.7015 (OUTLIER) cc_final: 0.6790 (tt0) REVERT: A 392 TRP cc_start: 0.7288 (p-90) cc_final: 0.7057 (p-90) REVERT: A 524 HIS cc_start: 0.7326 (OUTLIER) cc_final: 0.7081 (m90) REVERT: A 527 ARG cc_start: 0.7438 (ttt180) cc_final: 0.6838 (ttm110) REVERT: B 40 MET cc_start: 0.7571 (tpp) cc_final: 0.7105 (tpp) REVERT: B 184 GLN cc_start: 0.5776 (tt0) cc_final: 0.5017 (tp-100) REVERT: C 12 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.7668 (mp) REVERT: C 14 LYS cc_start: 0.7422 (mtpt) cc_final: 0.6816 (mmtm) REVERT: C 91 ARG cc_start: 0.6748 (ttm110) cc_final: 0.6305 (ttm-80) REVERT: D 65 ASN cc_start: 0.7156 (OUTLIER) cc_final: 0.6687 (m-40) REVERT: D 138 LYS cc_start: 0.8014 (tmmt) cc_final: 0.7343 (tttp) outliers start: 51 outliers final: 37 residues processed: 260 average time/residue: 0.2421 time to fit residues: 85.8772 Evaluate side-chains 258 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 217 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 524 HIS Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 81 CYS Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 153 HIS Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain D residue 24 ASN Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 95 ASN Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 162 CYS Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 226 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 7.9990 chunk 46 optimal weight: 7.9990 chunk 69 optimal weight: 6.9990 chunk 34 optimal weight: 8.9990 chunk 22 optimal weight: 10.0000 chunk 73 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 10 optimal weight: 0.4980 chunk 90 optimal weight: 8.9990 chunk 105 optimal weight: 0.0980 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 379 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: 0.6764 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 10179 Z= 0.280 Angle : 0.649 11.506 13999 Z= 0.340 Chirality : 0.044 0.190 1656 Planarity : 0.004 0.037 1599 Dihedral : 19.852 139.937 1854 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 5.21 % Allowed : 24.51 % Favored : 70.28 % 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: -1.75 (0.24), residues: 1158 helix: -0.94 (0.29), residues: 300 sheet: -0.32 (0.25), residues: 402 loop : -1.99 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 392 HIS 0.002 0.001 HIS A 393 PHE 0.021 0.002 PHE A 49 TYR 0.012 0.002 TYR A 50 ARG 0.007 0.001 ARG C 146 *********************** 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 264 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 216 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 362 GLU cc_start: 0.7070 (OUTLIER) cc_final: 0.6846 (tt0) REVERT: A 524 HIS cc_start: 0.7325 (OUTLIER) cc_final: 0.7070 (m90) REVERT: A 527 ARG cc_start: 0.7418 (ttt180) cc_final: 0.6913 (ttm110) REVERT: B 40 MET cc_start: 0.7578 (tpp) cc_final: 0.7121 (tpp) REVERT: B 184 GLN cc_start: 0.5783 (tt0) cc_final: 0.5071 (tp-100) REVERT: B 229 MET cc_start: 0.5559 (ttm) cc_final: 0.5334 (ttm) REVERT: B 250 TYR cc_start: 0.7235 (m-80) cc_final: 0.7015 (m-80) REVERT: C 12 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.7698 (mp) REVERT: C 14 LYS cc_start: 0.7379 (mtpt) cc_final: 0.6783 (mmtm) REVERT: C 91 ARG cc_start: 0.6779 (ttm110) cc_final: 0.6256 (ttm-80) REVERT: D 37 LEU cc_start: 0.7012 (OUTLIER) cc_final: 0.6604 (tt) REVERT: D 65 ASN cc_start: 0.7212 (OUTLIER) cc_final: 0.6754 (m-40) REVERT: D 138 LYS cc_start: 0.7966 (tmmt) cc_final: 0.7311 (tttp) outliers start: 48 outliers final: 36 residues processed: 249 average time/residue: 0.2357 time to fit residues: 81.0464 Evaluate side-chains 254 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 213 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 524 HIS Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 81 CYS Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 153 HIS Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 24 ASN Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 162 CYS Chi-restraints excluded: chain D residue 226 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 10.0000 chunk 101 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 chunk 33 optimal weight: 8.9990 chunk 97 optimal weight: 5.9990 chunk 70 optimal weight: 7.9990 chunk 113 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6735 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10179 Z= 0.226 Angle : 0.618 10.549 13999 Z= 0.326 Chirality : 0.043 0.195 1656 Planarity : 0.003 0.037 1599 Dihedral : 19.734 140.915 1853 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 4.77 % Allowed : 25.05 % Favored : 70.17 % 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: -0.71 (0.29), residues: 300 sheet: -0.17 (0.25), residues: 400 loop : -1.98 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 392 HIS 0.002 0.000 HIS A 393 PHE 0.018 0.001 PHE A 49 TYR 0.010 0.001 TYR D 239 ARG 0.014 0.001 ARG A 175 *********************** 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 261 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 217 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 524 HIS cc_start: 0.7200 (OUTLIER) cc_final: 0.6956 (m90) REVERT: A 527 ARG cc_start: 0.7377 (ttt180) cc_final: 0.6851 (ttm110) REVERT: B 40 MET cc_start: 0.7573 (tpp) cc_final: 0.7189 (tpp) REVERT: B 184 GLN cc_start: 0.5813 (tt0) cc_final: 0.5059 (tp-100) REVERT: B 229 MET cc_start: 0.5602 (ttm) cc_final: 0.5382 (ttm) REVERT: B 250 TYR cc_start: 0.7289 (m-80) cc_final: 0.7082 (m-80) REVERT: C 12 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.7663 (mp) REVERT: C 14 LYS cc_start: 0.7338 (mtpt) cc_final: 0.6762 (mmtm) REVERT: C 91 ARG cc_start: 0.6653 (ttm110) cc_final: 0.6206 (ttm-80) REVERT: D 30 ILE cc_start: 0.7143 (OUTLIER) cc_final: 0.6908 (mm) REVERT: D 37 LEU cc_start: 0.6934 (OUTLIER) cc_final: 0.6479 (tt) REVERT: D 138 LYS cc_start: 0.7879 (tmmt) cc_final: 0.7307 (tttp) outliers start: 44 outliers final: 34 residues processed: 247 average time/residue: 0.2408 time to fit residues: 82.8870 Evaluate side-chains 251 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 213 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 524 HIS Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 81 CYS Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 153 HIS Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain D residue 24 ASN Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 95 ASN Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 162 CYS Chi-restraints excluded: chain D residue 179 ASN Chi-restraints excluded: chain D residue 226 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 8.9990 chunk 79 optimal weight: 9.9990 chunk 119 optimal weight: 10.0000 chunk 110 optimal weight: 0.0000 chunk 95 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 chunk 101 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 overall best weight: 4.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6778 moved from start: 0.3950 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= 0.317 Angle : 0.701 12.448 13999 Z= 0.363 Chirality : 0.045 0.197 1656 Planarity : 0.004 0.052 1599 Dihedral : 19.795 138.107 1853 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 5.21 % Allowed : 24.62 % Favored : 70.17 % 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: -1.67 (0.24), residues: 1158 helix: -0.82 (0.29), residues: 300 sheet: -0.28 (0.25), residues: 406 loop : -1.98 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 392 HIS 0.002 0.001 HIS C 153 PHE 0.019 0.002 PHE A 111 TYR 0.012 0.002 TYR D 239 ARG 0.007 0.001 ARG C 146 ********************** 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 256 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 208 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 362 GLU cc_start: 0.6901 (OUTLIER) cc_final: 0.6651 (tt0) REVERT: A 524 HIS cc_start: 0.7298 (OUTLIER) cc_final: 0.7027 (m90) REVERT: A 527 ARG cc_start: 0.7448 (ttt180) cc_final: 0.6953 (ttm110) REVERT: B 40 MET cc_start: 0.7606 (tpp) cc_final: 0.7195 (tpp) REVERT: B 184 GLN cc_start: 0.5845 (tt0) cc_final: 0.5066 (tp-100) REVERT: B 229 MET cc_start: 0.5505 (ttm) cc_final: 0.5277 (ttm) REVERT: C 12 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.7660 (mp) REVERT: C 14 LYS cc_start: 0.7422 (mtpt) cc_final: 0.6792 (mmtm) REVERT: C 91 ARG cc_start: 0.6768 (ttm110) cc_final: 0.6285 (ttm-80) REVERT: D 37 LEU cc_start: 0.7071 (OUTLIER) cc_final: 0.6646 (tt) REVERT: D 65 ASN cc_start: 0.7215 (OUTLIER) cc_final: 0.6782 (m-40) REVERT: D 138 LYS cc_start: 0.7923 (tmmt) cc_final: 0.7328 (tttp) outliers start: 48 outliers final: 37 residues processed: 241 average time/residue: 0.2336 time to fit residues: 78.0807 Evaluate side-chains 250 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 208 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 524 HIS Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 81 CYS Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 153 HIS Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain D residue 24 ASN Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 95 ASN Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 162 CYS Chi-restraints excluded: chain D residue 226 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 6.9990 chunk 14 optimal weight: 0.2980 chunk 26 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 12 optimal weight: 0.1980 chunk 17 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 5 optimal weight: 0.0270 chunk 68 optimal weight: 0.9980 overall best weight: 0.5038 ------------------------------------------------------------------------------- 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** D 179 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.194911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.155965 restraints weight = 12023.188| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 2.13 r_work: 0.3672 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6768 moved from start: 0.4247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10179 Z= 0.168 Angle : 0.576 8.735 13999 Z= 0.306 Chirality : 0.042 0.196 1656 Planarity : 0.003 0.037 1599 Dihedral : 19.469 143.618 1853 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.25 % Allowed : 26.79 % Favored : 69.96 % 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: -0.21 (0.31), residues: 295 sheet: 0.09 (0.26), residues: 401 loop : -1.73 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 392 HIS 0.002 0.001 HIS B 246 PHE 0.019 0.001 PHE A 299 TYR 0.010 0.001 TYR A 174 ARG 0.008 0.001 ARG A 175 =============================================================================== Job complete usr+sys time: 2486.22 seconds wall clock time: 46 minutes 6.35 seconds (2766.35 seconds total)