Starting phenix.real_space_refine on Thu Feb 13 05:58:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wb2_21585/02_2025/6wb2_21585.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wb2_21585/02_2025/6wb2_21585.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6wb2_21585/02_2025/6wb2_21585.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wb2_21585/02_2025/6wb2_21585.map" model { file = "/net/cci-nas-00/data/ceres_data/6wb2_21585/02_2025/6wb2_21585.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wb2_21585/02_2025/6wb2_21585.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 72 5.49 5 S 9 5.16 5 C 5150 2.51 5 N 1465 2.21 5 O 1711 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8407 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 705 Classifications: {'RNA': 33} Modifications used: {'5*END': 1, 'rna3p_pur': 19, 'rna3p_pyr': 13} Link IDs: {'rna3p': 32} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 880 Inner-chain residues flagged as termini: ['pdbres=" G D 46 "'] Classifications: {'DNA': 4, 'RNA': 38} Modifications used: {'5*END': 2, 'rna3p_pur': 15, 'rna3p_pyr': 21} Link IDs: {'rna3p': 41} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 3854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 3854 Classifications: {'peptide': 540} Incomplete info: {'truncation_to_alanine': 154} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 504} Chain breaks: 3 Unresolved non-hydrogen bonds: 543 Unresolved non-hydrogen angles: 669 Unresolved non-hydrogen dihedrals: 429 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 8, 'ASP:plan': 10, 'PHE:plan': 2, 'GLU:plan': 33, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 287 Chain: "B" Number of atoms: 2968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 2968 Classifications: {'peptide': 406} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'PTRANS': 30, 'TRANS': 375} Chain breaks: 2 Unresolved non-hydrogen bonds: 389 Unresolved non-hydrogen angles: 471 Unresolved non-hydrogen dihedrals: 313 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 12, 'GLU:plan': 29, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 210 Time building chain proxies: 5.55, per 1000 atoms: 0.66 Number of scatterers: 8407 At special positions: 0 Unit cell: (100.7, 97.52, 119.78, 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 9 16.00 P 72 15.00 O 1711 8.00 N 1465 7.00 C 5150 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.54 Conformation dependent library (CDL) restraints added in 880.2 milliseconds 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1780 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 13 sheets defined 38.7% alpha, 11.4% beta 37 base pairs and 45 stacking pairs defined. Time for finding SS restraints: 3.28 Creating SS restraints... Processing helix chain 'A' and resid 30 through 45 removed outlier: 3.787A pdb=" N LEU A 34 " --> pdb=" O LYS A 30 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU A 44 " --> pdb=" O GLU A 40 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY A 45 " --> pdb=" O MET A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 84 removed outlier: 3.684A pdb=" N ARG A 83 " --> pdb=" O GLU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 100 removed outlier: 3.643A pdb=" N LEU A 100 " --> pdb=" O PRO A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 118 removed outlier: 3.666A pdb=" N PHE A 116 " --> pdb=" O ASP A 113 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL A 118 " --> pdb=" O TYR A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 127 removed outlier: 3.749A pdb=" N LYS A 126 " --> pdb=" O ASP A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 175 Proline residue: A 170 - end of helix Processing helix chain 'A' and resid 194 through 211 Processing helix chain 'A' and resid 253 through 269 removed outlier: 3.533A pdb=" N GLN A 269 " --> pdb=" O ASN A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 283 Processing helix chain 'A' and resid 297 through 311 Processing helix chain 'A' and resid 363 through 383 Processing helix chain 'A' and resid 394 through 404 Processing helix chain 'A' and resid 473 through 488 removed outlier: 3.534A pdb=" N ASP A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 509 removed outlier: 3.582A pdb=" N LEU A 503 " --> pdb=" O SER A 499 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN A 509 " --> pdb=" O ILE A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 527 removed outlier: 3.763A pdb=" N ASN A 519 " --> pdb=" O SER A 515 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LYS A 527 " --> pdb=" O GLU A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 553 Processing helix chain 'B' and resid 27 through 44 removed outlier: 3.695A pdb=" N ALA B 33 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLU B 40 " --> pdb=" O GLU B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 91 removed outlier: 6.140A pdb=" N ASP B 86 " --> pdb=" O LYS B 82 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N PHE B 87 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N TRP B 88 " --> pdb=" O THR B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 103 removed outlier: 3.557A pdb=" N LYS B 103 " --> pdb=" O LEU B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 116 Processing helix chain 'B' and resid 121 through 128 removed outlier: 4.657A pdb=" N LYS B 126 " --> pdb=" O ASP B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 138 removed outlier: 3.775A pdb=" N ASN B 137 " --> pdb=" O SER B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 173 removed outlier: 3.720A pdb=" N ALA B 158 " --> pdb=" O LYS B 154 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N SER B 162 " --> pdb=" O ALA B 158 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N SER B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) Proline residue: B 170 - end of helix Processing helix chain 'B' and resid 194 through 211 Processing helix chain 'B' and resid 253 through 268 Processing helix chain 'B' and resid 278 through 283 removed outlier: 4.001A pdb=" N LEU B 282 " --> pdb=" O GLN B 278 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU B 283 " --> pdb=" O LEU B 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 278 through 283' Processing helix chain 'B' and resid 296 through 311 Processing helix chain 'B' and resid 364 through 383 removed outlier: 3.979A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 402 removed outlier: 3.513A pdb=" N TRP B 398 " --> pdb=" O GLN B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 426 Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 48 Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 63 removed outlier: 3.620A pdb=" N ARG A 72 " --> pdb=" O ILE A 63 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 105 through 107 Processing sheet with id=AA4, first strand: chain 'A' and resid 227 through 229 Processing sheet with id=AA5, first strand: chain 'A' and resid 347 through 351 removed outlier: 7.312A pdb=" N LYS A 347 " --> pdb=" O GLN A 343 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLN A 343 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ILE A 341 " --> pdb=" O LEU A 349 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N THR A 351 " --> pdb=" O TYR A 339 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N TYR A 339 " --> pdb=" O THR A 351 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N GLN A 336 " --> pdb=" O GLN A 332 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE A 329 " --> pdb=" O LYS A 390 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 361 through 362 removed outlier: 3.556A pdb=" N THR A 362 " --> pdb=" O LYS A 512 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS A 512 " --> pdb=" O THR A 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 454 through 455 Processing sheet with id=AA8, first strand: chain 'A' and resid 492 through 497 removed outlier: 4.133A pdb=" N VAL A 493 " --> pdb=" O LYS A 530 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR A 532 " --> pdb=" O VAL A 493 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N THR A 497 " --> pdb=" O ALA A 534 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 47 through 48 Processing sheet with id=AB1, first strand: chain 'B' and resid 60 through 62 removed outlier: 3.710A pdb=" N PHE B 61 " --> pdb=" O LEU B 74 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B 74 " --> pdb=" O PHE B 61 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 179 through 181 removed outlier: 3.586A pdb=" N VAL B 189 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N THR B 107 " --> pdb=" O VAL B 189 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 131 through 132 removed outlier: 3.797A pdb=" N ILE B 132 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE B 142 " --> pdb=" O ILE B 132 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 347 through 354 removed outlier: 7.378A pdb=" N LYS B 347 " --> pdb=" O GLN B 343 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLN B 343 " --> pdb=" O LYS B 347 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE B 341 " --> pdb=" O LEU B 349 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N THR B 351 " --> pdb=" O TYR B 339 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N TYR B 339 " --> pdb=" O THR B 351 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N LYS B 353 " --> pdb=" O TRP B 337 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N TRP B 337 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS B 390 " --> pdb=" O ALA B 327 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE B 329 " --> pdb=" O LYS B 390 " (cutoff:3.500A) 277 hydrogen bonds defined for protein. 762 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 97 hydrogen bonds 186 hydrogen bond angles 0 basepair planarities 37 basepair parallelities 45 stacking parallelities Total time for adding SS restraints: 3.09 Time building geometry restraints manager: 2.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2109 1.33 - 1.45: 2037 1.45 - 1.57: 4484 1.57 - 1.69: 143 1.69 - 1.80: 16 Bond restraints: 8789 Sorted by residual: bond pdb=" CA VAL A 536 " pdb=" CB VAL A 536 " ideal model delta sigma weight residual 1.537 1.549 -0.012 1.29e-02 6.01e+03 8.63e-01 bond pdb=" CA VAL A 536 " pdb=" C VAL A 536 " ideal model delta sigma weight residual 1.524 1.516 0.008 1.05e-02 9.07e+03 5.93e-01 bond pdb=" C GLU A 432 " pdb=" N PRO A 433 " ideal model delta sigma weight residual 1.331 1.339 -0.008 1.21e-02 6.83e+03 3.88e-01 bond pdb=" CA GLU B 169 " pdb=" C GLU B 169 " ideal model delta sigma weight residual 1.520 1.528 -0.007 1.23e-02 6.61e+03 3.44e-01 bond pdb=" CA THR A 386 " pdb=" CB THR A 386 " ideal model delta sigma weight residual 1.524 1.533 -0.009 1.55e-02 4.16e+03 3.41e-01 ... (remaining 8784 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 12252 1.62 - 3.25: 142 3.25 - 4.87: 9 4.87 - 6.49: 3 6.49 - 8.12: 1 Bond angle restraints: 12407 Sorted by residual: angle pdb=" CA LEU A 525 " pdb=" CB LEU A 525 " pdb=" CG LEU A 525 " ideal model delta sigma weight residual 116.30 124.42 -8.12 3.50e+00 8.16e-02 5.38e+00 angle pdb=" CA VAL B 35 " pdb=" CB VAL B 35 " pdb=" CG2 VAL B 35 " ideal model delta sigma weight residual 110.40 113.21 -2.81 1.70e+00 3.46e-01 2.72e+00 angle pdb=" C ILE A 37 " pdb=" N CYS A 38 " pdb=" CA CYS A 38 " ideal model delta sigma weight residual 120.31 117.97 2.34 1.52e+00 4.33e-01 2.36e+00 angle pdb=" CA LEU A 260 " pdb=" CB LEU A 260 " pdb=" CG LEU A 260 " ideal model delta sigma weight residual 116.30 121.67 -5.37 3.50e+00 8.16e-02 2.35e+00 angle pdb=" N PRO A 4 " pdb=" CA PRO A 4 " pdb=" C PRO A 4 " ideal model delta sigma weight residual 114.68 113.09 1.59 1.04e+00 9.25e-01 2.32e+00 ... (remaining 12402 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.57: 4701 16.57 - 33.13: 297 33.13 - 49.70: 103 49.70 - 66.26: 102 66.26 - 82.83: 27 Dihedral angle restraints: 5230 sinusoidal: 2476 harmonic: 2754 Sorted by residual: dihedral pdb=" O5' C D 68 " pdb=" C5' C D 68 " pdb=" C4' C D 68 " pdb=" C3' C D 68 " ideal model delta sinusoidal sigma weight residual 175.00 117.96 57.04 3 1.50e+01 4.44e-03 9.42e+00 dihedral pdb=" O5' C D 61 " pdb=" C5' C D 61 " pdb=" C4' C D 61 " pdb=" C3' C D 61 " ideal model delta sinusoidal sigma weight residual 55.00 111.70 -56.70 3 1.50e+01 4.44e-03 9.41e+00 dihedral pdb=" CB LYS B 70 " pdb=" CG LYS B 70 " pdb=" CD LYS B 70 " pdb=" CE LYS B 70 " ideal model delta sinusoidal sigma weight residual 60.00 112.90 -52.90 3 1.50e+01 4.44e-03 9.16e+00 ... (remaining 5227 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1011 0.028 - 0.056: 282 0.056 - 0.084: 88 0.084 - 0.112: 69 0.112 - 0.141: 21 Chirality restraints: 1471 Sorted by residual: chirality pdb=" CA VAL A 536 " pdb=" N VAL A 536 " pdb=" C VAL A 536 " pdb=" CB VAL A 536 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.94e-01 chirality pdb=" CA ILE A 63 " pdb=" N ILE A 63 " pdb=" C ILE A 63 " pdb=" CB ILE A 63 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.92e-01 chirality pdb=" CA ILE A 50 " pdb=" N ILE A 50 " pdb=" C ILE A 50 " pdb=" CB ILE A 50 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.30e-01 ... (remaining 1468 not shown) Planarity restraints: 1302 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 278 " -0.011 2.00e-02 2.50e+03 2.19e-02 4.80e+00 pdb=" C GLN A 278 " 0.038 2.00e-02 2.50e+03 pdb=" O GLN A 278 " -0.014 2.00e-02 2.50e+03 pdb=" N LEU A 279 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 51 " -0.024 5.00e-02 4.00e+02 3.69e-02 2.18e+00 pdb=" N PRO A 52 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 52 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 52 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 94 " -0.022 5.00e-02 4.00e+02 3.42e-02 1.87e+00 pdb=" N PRO A 95 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 95 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 95 " -0.019 5.00e-02 4.00e+02 ... (remaining 1299 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2438 2.81 - 3.34: 7343 3.34 - 3.86: 14475 3.86 - 4.38: 15217 4.38 - 4.90: 24135 Nonbonded interactions: 63608 Sorted by model distance: nonbonded pdb=" OG1 THR A 58 " pdb=" O ALA A 129 " model vdw 2.293 3.040 nonbonded pdb=" OG1 THR A 240 " pdb=" O VAL A 314 " model vdw 2.306 3.040 nonbonded pdb=" O GLY A 543 " pdb=" NE2 GLN A 547 " model vdw 2.324 3.120 nonbonded pdb=" OD2 ASP A 320 " pdb=" OG SER A 322 " model vdw 2.326 3.040 nonbonded pdb=" OD1 ASN A 460 " pdb=" N LYS A 461 " model vdw 2.366 3.120 ... (remaining 63603 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.080 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.200 Find NCS groups from input model: 0.090 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 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 : 0.002 0.022 8789 Z= 0.104 Angle : 0.443 8.118 12407 Z= 0.224 Chirality : 0.037 0.141 1471 Planarity : 0.004 0.037 1302 Dihedral : 16.508 82.830 3450 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.17 % Allowed : 4.59 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -3.59 (0.23), residues: 932 helix: -1.60 (0.25), residues: 325 sheet: -2.38 (0.46), residues: 104 loop : -3.00 (0.23), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.000 TRP A 402 HIS 0.001 0.000 HIS B 208 PHE 0.005 0.000 PHE A 77 TYR 0.003 0.000 TYR B 115 ARG 0.001 0.000 ARG B 199 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 105 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 370 GLU cc_start: 0.9004 (mm-30) cc_final: 0.8526 (tp30) REVERT: A 399 GLU cc_start: 0.8630 (pp20) cc_final: 0.8363 (tm-30) REVERT: B 24 TRP cc_start: 0.6859 (p90) cc_final: 0.6536 (p90) REVERT: B 31 ILE cc_start: 0.9566 (mt) cc_final: 0.9311 (tp) REVERT: B 116 PHE cc_start: 0.8193 (m-10) cc_final: 0.7976 (m-10) REVERT: B 149 LEU cc_start: 0.8714 (mm) cc_final: 0.8326 (mt) REVERT: B 153 TRP cc_start: 0.8522 (t60) cc_final: 0.8155 (t60) REVERT: B 373 GLN cc_start: 0.9130 (mt0) cc_final: 0.8616 (tm-30) REVERT: B 378 GLU cc_start: 0.8379 (mt-10) cc_final: 0.8132 (mt-10) outliers start: 1 outliers final: 1 residues processed: 106 average time/residue: 0.2641 time to fit residues: 36.5034 Evaluate side-chains 66 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 65 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 51 optimal weight: 0.1980 chunk 40 optimal weight: 0.7980 chunk 79 optimal weight: 10.0000 chunk 30 optimal weight: 0.9980 chunk 48 optimal weight: 0.0060 chunk 58 optimal weight: 0.9990 chunk 91 optimal weight: 8.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 HIS A 151 GLN A 174 GLN A 487 GLN A 494 ASN A 547 GLN B 57 ASN B 367 GLN B 373 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.063637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.051717 restraints weight = 56738.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.053030 restraints weight = 33224.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.053952 restraints weight = 22794.808| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8789 Z= 0.141 Angle : 0.473 5.698 12407 Z= 0.235 Chirality : 0.038 0.154 1471 Planarity : 0.005 0.077 1302 Dihedral : 17.424 75.629 2139 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.17 % Allowed : 4.08 % Favored : 95.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -2.17 (0.27), residues: 932 helix: 0.02 (0.29), residues: 325 sheet: -1.71 (0.46), residues: 107 loop : -2.48 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 402 HIS 0.015 0.001 HIS B 208 PHE 0.023 0.002 PHE B 171 TYR 0.022 0.001 TYR A 441 ARG 0.005 0.001 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 83 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 370 GLU cc_start: 0.9269 (mm-30) cc_final: 0.8932 (tp30) REVERT: A 396 GLU cc_start: 0.9235 (pm20) cc_final: 0.8573 (pm20) REVERT: B 149 LEU cc_start: 0.8905 (mm) cc_final: 0.8470 (mt) REVERT: B 153 TRP cc_start: 0.8767 (t60) cc_final: 0.8195 (t60) REVERT: B 373 GLN cc_start: 0.9059 (mt0) cc_final: 0.8534 (tm-30) REVERT: B 378 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8173 (mt-10) outliers start: 1 outliers final: 0 residues processed: 84 average time/residue: 0.2191 time to fit residues: 25.5146 Evaluate side-chains 55 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 37 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 68 optimal weight: 0.0570 chunk 20 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 overall best weight: 1.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN A 367 GLN ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.060523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.048620 restraints weight = 56500.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.049861 restraints weight = 33136.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.050730 restraints weight = 22724.350| |-----------------------------------------------------------------------------| r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8789 Z= 0.176 Angle : 0.495 5.610 12407 Z= 0.250 Chirality : 0.039 0.152 1471 Planarity : 0.004 0.047 1302 Dihedral : 17.495 77.507 2139 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.17 % Allowed : 4.25 % Favored : 95.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -1.51 (0.27), residues: 932 helix: 0.80 (0.31), residues: 323 sheet: -1.41 (0.47), residues: 107 loop : -2.23 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 88 HIS 0.009 0.001 HIS B 208 PHE 0.007 0.001 PHE A 227 TYR 0.012 0.001 TYR B 354 ARG 0.004 0.001 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 69 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 ASP cc_start: 0.9221 (t0) cc_final: 0.8992 (t0) REVERT: B 149 LEU cc_start: 0.8927 (mm) cc_final: 0.8678 (mm) REVERT: B 153 TRP cc_start: 0.8899 (t60) cc_final: 0.8187 (t60) REVERT: B 367 GLN cc_start: 0.8950 (pt0) cc_final: 0.8566 (pm20) REVERT: B 373 GLN cc_start: 0.9237 (mt0) cc_final: 0.8582 (tm-30) REVERT: B 378 GLU cc_start: 0.8778 (mt-10) cc_final: 0.8304 (mt-10) REVERT: B 401 TRP cc_start: 0.8736 (m100) cc_final: 0.8292 (m100) outliers start: 1 outliers final: 0 residues processed: 69 average time/residue: 0.2173 time to fit residues: 21.6915 Evaluate side-chains 50 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 57 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 27 optimal weight: 10.0000 chunk 32 optimal weight: 0.8980 chunk 79 optimal weight: 8.9990 chunk 21 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 52 optimal weight: 0.1980 chunk 60 optimal weight: 8.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.060942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.049199 restraints weight = 55458.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.050437 restraints weight = 32530.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.051322 restraints weight = 22329.429| |-----------------------------------------------------------------------------| r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8789 Z= 0.122 Angle : 0.454 5.558 12407 Z= 0.225 Chirality : 0.038 0.159 1471 Planarity : 0.004 0.043 1302 Dihedral : 17.509 78.551 2139 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -1.12 (0.28), residues: 932 helix: 1.09 (0.31), residues: 329 sheet: -1.09 (0.48), residues: 107 loop : -2.04 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 88 HIS 0.011 0.001 HIS B 208 PHE 0.004 0.001 PHE B 171 TYR 0.013 0.001 TYR A 188 ARG 0.003 0.000 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 ASP cc_start: 0.9230 (t0) cc_final: 0.8965 (t0) REVERT: A 399 GLU cc_start: 0.8870 (tm-30) cc_final: 0.8599 (tm-30) REVERT: B 149 LEU cc_start: 0.8917 (mm) cc_final: 0.8595 (mm) REVERT: B 153 TRP cc_start: 0.8824 (t60) cc_final: 0.8107 (t60) REVERT: B 367 GLN cc_start: 0.8910 (pt0) cc_final: 0.8559 (pm20) REVERT: B 373 GLN cc_start: 0.9244 (mt0) cc_final: 0.8576 (tm-30) REVERT: B 378 GLU cc_start: 0.8819 (mt-10) cc_final: 0.8277 (mt-10) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1987 time to fit residues: 20.6801 Evaluate side-chains 57 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 51 optimal weight: 0.0670 chunk 48 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 chunk 100 optimal weight: 0.0970 chunk 40 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN A 447 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.061291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.049423 restraints weight = 56905.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.050688 restraints weight = 33072.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.051582 restraints weight = 22579.585| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8789 Z= 0.111 Angle : 0.450 5.548 12407 Z= 0.223 Chirality : 0.038 0.140 1471 Planarity : 0.004 0.042 1302 Dihedral : 17.510 78.862 2139 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.28), residues: 932 helix: 1.30 (0.31), residues: 329 sheet: -0.99 (0.48), residues: 109 loop : -1.81 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 402 HIS 0.011 0.001 HIS B 208 PHE 0.007 0.001 PHE A 130 TYR 0.012 0.001 TYR A 188 ARG 0.003 0.000 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 ASP cc_start: 0.9210 (t0) cc_final: 0.8949 (t0) REVERT: A 399 GLU cc_start: 0.8849 (tm-30) cc_final: 0.8565 (tm-30) REVERT: B 149 LEU cc_start: 0.8897 (mm) cc_final: 0.8555 (mm) REVERT: B 153 TRP cc_start: 0.8817 (t60) cc_final: 0.8040 (t60) REVERT: B 367 GLN cc_start: 0.8875 (pt0) cc_final: 0.8536 (pm20) REVERT: B 373 GLN cc_start: 0.9248 (mt0) cc_final: 0.8553 (tm-30) REVERT: B 378 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8199 (mt-10) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.2056 time to fit residues: 21.2850 Evaluate side-chains 56 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 20 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 22 optimal weight: 0.7980 chunk 92 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 88 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.057898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.046288 restraints weight = 56873.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.047493 restraints weight = 32803.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.048324 restraints weight = 22360.775| |-----------------------------------------------------------------------------| r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8789 Z= 0.226 Angle : 0.518 6.673 12407 Z= 0.259 Chirality : 0.038 0.151 1471 Planarity : 0.004 0.046 1302 Dihedral : 17.696 81.201 2139 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -0.77 (0.28), residues: 932 helix: 1.34 (0.31), residues: 329 sheet: -1.04 (0.48), residues: 109 loop : -1.75 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 414 HIS 0.011 0.001 HIS B 208 PHE 0.009 0.001 PHE A 160 TYR 0.021 0.001 TYR A 183 ARG 0.003 0.001 ARG A 358 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 GLU cc_start: 0.9039 (tm-30) cc_final: 0.8752 (tm-30) REVERT: B 153 TRP cc_start: 0.8960 (t60) cc_final: 0.7964 (t60) REVERT: B 367 GLN cc_start: 0.9092 (pt0) cc_final: 0.8626 (pm20) REVERT: B 373 GLN cc_start: 0.9289 (mt0) cc_final: 0.8659 (tm-30) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.2084 time to fit residues: 18.6142 Evaluate side-chains 40 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 1.9990 chunk 90 optimal weight: 8.9990 chunk 93 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 21 optimal weight: 8.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 85 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.057199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.045680 restraints weight = 58135.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.046883 restraints weight = 33204.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.047733 restraints weight = 22535.485| |-----------------------------------------------------------------------------| r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8789 Z= 0.210 Angle : 0.512 6.097 12407 Z= 0.258 Chirality : 0.039 0.178 1471 Planarity : 0.004 0.044 1302 Dihedral : 17.762 82.902 2139 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -0.77 (0.28), residues: 932 helix: 1.12 (0.31), residues: 330 sheet: -0.93 (0.48), residues: 109 loop : -1.61 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 426 HIS 0.010 0.001 HIS B 208 PHE 0.007 0.001 PHE A 87 TYR 0.017 0.001 TYR A 183 ARG 0.002 0.000 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 153 TRP cc_start: 0.9022 (t60) cc_final: 0.7919 (t60) REVERT: B 171 PHE cc_start: 0.8494 (p90) cc_final: 0.8267 (p90) REVERT: B 367 GLN cc_start: 0.9128 (pt0) cc_final: 0.8639 (pm20) REVERT: B 373 GLN cc_start: 0.9158 (tt0) cc_final: 0.8543 (tm-30) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.2057 time to fit residues: 16.4755 Evaluate side-chains 45 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 6 optimal weight: 9.9990 chunk 98 optimal weight: 0.6980 chunk 61 optimal weight: 5.9990 chunk 74 optimal weight: 9.9990 chunk 59 optimal weight: 0.9980 chunk 14 optimal weight: 0.1980 chunk 9 optimal weight: 8.9990 chunk 49 optimal weight: 8.9990 chunk 52 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.056989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.045489 restraints weight = 59036.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.046686 restraints weight = 34350.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.047521 restraints weight = 23604.089| |-----------------------------------------------------------------------------| r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8789 Z= 0.182 Angle : 0.500 5.499 12407 Z= 0.252 Chirality : 0.039 0.166 1471 Planarity : 0.004 0.043 1302 Dihedral : 17.736 82.786 2139 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -0.76 (0.29), residues: 932 helix: 1.13 (0.31), residues: 332 sheet: -1.13 (0.46), residues: 118 loop : -1.57 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 426 HIS 0.009 0.001 HIS B 208 PHE 0.006 0.001 PHE A 77 TYR 0.016 0.001 TYR A 183 ARG 0.002 0.000 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 MET cc_start: 0.9457 (mmm) cc_final: 0.9226 (tpp) REVERT: A 399 GLU cc_start: 0.8948 (tm-30) cc_final: 0.8664 (tm-30) REVERT: B 367 GLN cc_start: 0.9129 (pt0) cc_final: 0.8541 (pm20) REVERT: B 373 GLN cc_start: 0.9162 (tt0) cc_final: 0.8569 (tm-30) REVERT: B 404 GLU cc_start: 0.8475 (pt0) cc_final: 0.8244 (pt0) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.1779 time to fit residues: 14.9081 Evaluate side-chains 40 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 13 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 20 optimal weight: 0.0470 chunk 59 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 100 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 8 optimal weight: 0.0770 overall best weight: 0.5836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.058408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.046727 restraints weight = 58094.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.047982 restraints weight = 33628.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.048853 restraints weight = 23022.202| |-----------------------------------------------------------------------------| r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8789 Z= 0.119 Angle : 0.485 5.518 12407 Z= 0.240 Chirality : 0.038 0.167 1471 Planarity : 0.004 0.039 1302 Dihedral : 17.600 80.386 2139 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -0.40 (0.29), residues: 932 helix: 1.40 (0.32), residues: 324 sheet: -0.53 (0.49), residues: 105 loop : -1.39 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 88 HIS 0.004 0.001 HIS B 208 PHE 0.022 0.001 PHE B 171 TYR 0.016 0.001 TYR A 183 ARG 0.002 0.000 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 153 TRP cc_start: 0.9047 (t60) cc_final: 0.7947 (t60) REVERT: B 367 GLN cc_start: 0.9065 (pt0) cc_final: 0.8452 (pm20) REVERT: B 373 GLN cc_start: 0.9157 (tt0) cc_final: 0.8552 (tm-30) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.2074 time to fit residues: 17.8020 Evaluate side-chains 47 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 94 optimal weight: 6.9990 chunk 90 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 20 optimal weight: 0.0670 chunk 54 optimal weight: 0.5980 chunk 68 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 7 optimal weight: 9.9990 chunk 88 optimal weight: 0.0040 chunk 29 optimal weight: 2.9990 overall best weight: 0.4732 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN A 460 ASN B 208 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.058957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.047234 restraints weight = 57313.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.048484 restraints weight = 33546.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.049344 restraints weight = 23085.677| |-----------------------------------------------------------------------------| r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8789 Z= 0.116 Angle : 0.475 5.550 12407 Z= 0.235 Chirality : 0.038 0.157 1471 Planarity : 0.004 0.038 1302 Dihedral : 17.534 79.288 2139 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -0.26 (0.29), residues: 932 helix: 1.52 (0.32), residues: 325 sheet: -0.56 (0.47), residues: 112 loop : -1.28 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 88 HIS 0.004 0.001 HIS B 208 PHE 0.006 0.001 PHE A 130 TYR 0.014 0.001 TYR A 183 ARG 0.002 0.000 ARG B 78 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 GLU cc_start: 0.8875 (tm-30) cc_final: 0.8616 (tm-30) REVERT: B 367 GLN cc_start: 0.9020 (pt0) cc_final: 0.8291 (pm20) REVERT: B 373 GLN cc_start: 0.9176 (tt0) cc_final: 0.8648 (tm-30) REVERT: B 401 TRP cc_start: 0.8774 (m100) cc_final: 0.8227 (m100) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.1901 time to fit residues: 16.7709 Evaluate side-chains 44 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 37 optimal weight: 0.0470 chunk 62 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 4 optimal weight: 20.0000 chunk 19 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 66 optimal weight: 0.2980 chunk 55 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 overall best weight: 2.2684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.056302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.044576 restraints weight = 59590.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.045794 restraints weight = 34503.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.046633 restraints weight = 23584.714| |-----------------------------------------------------------------------------| r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8789 Z= 0.217 Angle : 0.531 6.310 12407 Z= 0.265 Chirality : 0.039 0.150 1471 Planarity : 0.004 0.039 1302 Dihedral : 17.737 83.754 2139 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -0.39 (0.29), residues: 932 helix: 1.46 (0.31), residues: 325 sheet: -0.85 (0.46), residues: 120 loop : -1.33 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 212 HIS 0.006 0.001 HIS B 208 PHE 0.008 0.001 PHE A 440 TYR 0.019 0.001 TYR A 183 ARG 0.003 0.001 ARG B 78 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2213.89 seconds wall clock time: 40 minutes 34.03 seconds (2434.03 seconds total)