Starting phenix.real_space_refine on Thu Mar 13 07:52:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wb2_21585/03_2025/6wb2_21585.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wb2_21585/03_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_21585/03_2025/6wb2_21585.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wb2_21585/03_2025/6wb2_21585.map" model { file = "/net/cci-nas-00/data/ceres_data/6wb2_21585/03_2025/6wb2_21585.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wb2_21585/03_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 5.47, per 1000 atoms: 0.65 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: 2.29 Conformation dependent library (CDL) restraints added in 861.0 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: 2.96 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: 2.96 Time building geometry restraints manager: 2.69 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: 14.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 24.300 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.250 ------------------------------------------------------------------------------- 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 : 0.802 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: 0.2993 time to fit residues: 42.1469 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 : 0.980 ------------------------------------------------------------------------------- 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 = 51)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.051715 restraints weight = 56737.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.053032 restraints weight = 33240.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.053953 restraints weight = 22793.522| |-----------------------------------------------------------------------------| 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 : 0.982 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: 0.9236 (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: 0.8533 (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: 0.2818 time to fit residues: 34.1557 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 : 1.668 ------------------------------------------------------------------------------- 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: 0.0060 chunk 14 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 79 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 20 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 chunk 27 optimal weight: 9.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- 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 = 0.3315 r_free = 0.3315 target = 0.063187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.051285 restraints weight = 58207.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.052600 restraints weight = 33850.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.053516 restraints weight = 22991.402| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1894 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= 0.118 Angle : 0.460 5.614 12407 Z= 0.230 Chirality : 0.038 0.147 1471 Planarity : 0.004 0.043 1302 Dihedral : 17.389 76.549 2139 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.17 % Allowed : 3.06 % Favored : 96.77 % 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: -1.61 (0.27), residues: 932 helix: 0.66 (0.31), residues: 325 sheet: -1.46 (0.47), residues: 107 loop : -2.26 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 402 HIS 0.010 0.001 HIS B 208 PHE 0.004 0.001 PHE B 346 TYR 0.013 0.001 TYR A 188 ARG 0.004 0.000 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 77 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 76 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 ASP cc_start: 0.9126 (t0) cc_final: 0.8853 (t0) REVERT: A 520 GLN cc_start: 0.9462 (pt0) cc_final: 0.9260 (pp30) REVERT: B 149 LEU cc_start: 0.8839 (mm) cc_final: 0.8591 (mm) REVERT: B 153 TRP cc_start: 0.8759 (t60) cc_final: 0.8059 (t60) REVERT: B 373 GLN cc_start: 0.9158 (mt0) cc_final: 0.8547 (tm-30) REVERT: B 378 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8167 (mt-10) outliers start: 1 outliers final: 0 residues processed: 76 average time/residue: 0.1912 time to fit residues: 21.0545 Evaluate side-chains 52 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.922 ------------------------------------------------------------------------------- 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: 1.9990 chunk 75 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 chunk 27 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 chunk 79 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 52 optimal weight: 0.0370 chunk 60 optimal weight: 10.0000 overall best weight: 3.2066 ------------------------------------------------------------------------------- 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 ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 GLN B 269 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.057008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.045234 restraints weight = 59284.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.046396 restraints weight = 34713.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.047211 restraints weight = 23958.938| |-----------------------------------------------------------------------------| r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8789 Z= 0.311 Angle : 0.588 6.566 12407 Z= 0.297 Chirality : 0.040 0.163 1471 Planarity : 0.004 0.051 1302 Dihedral : 17.800 81.307 2139 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % 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: -1.46 (0.27), residues: 932 helix: 0.85 (0.31), residues: 326 sheet: -1.48 (0.47), residues: 109 loop : -2.20 (0.26), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 426 HIS 0.010 0.002 HIS B 208 PHE 0.013 0.002 PHE A 227 TYR 0.013 0.002 TYR B 115 ARG 0.004 0.001 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 51 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 373 GLN cc_start: 0.9282 (mt0) cc_final: 0.8717 (tm-30) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1897 time to fit residues: 14.4121 Evaluate side-chains 34 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.961 ------------------------------------------------------------------------------- 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: 0.0770 chunk 48 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 100 optimal weight: 8.9990 chunk 40 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 91 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 overall best weight: 1.3344 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.058402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.046574 restraints weight = 57650.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.047799 restraints weight = 33240.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.048666 restraints weight = 22725.595| |-----------------------------------------------------------------------------| r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8789 Z= 0.148 Angle : 0.471 5.558 12407 Z= 0.235 Chirality : 0.038 0.147 1471 Planarity : 0.004 0.042 1302 Dihedral : 17.671 80.544 2139 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % 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: 1.14 (0.31), residues: 328 sheet: -1.25 (0.47), residues: 109 loop : -2.03 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 414 HIS 0.009 0.001 HIS B 198 PHE 0.006 0.001 PHE B 77 TYR 0.011 0.001 TYR B 115 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 65 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 MET cc_start: 0.9453 (mmm) cc_final: 0.9242 (tpp) REVERT: A 399 GLU cc_start: 0.9004 (tm-30) cc_final: 0.8604 (tm-30) REVERT: B 40 GLU cc_start: 0.9099 (mp0) cc_final: 0.8848 (mp0) REVERT: B 89 GLU cc_start: 0.9158 (mm-30) cc_final: 0.8781 (mm-30) REVERT: B 153 TRP cc_start: 0.9027 (t60) cc_final: 0.8013 (t60) REVERT: B 171 PHE cc_start: 0.8436 (p90) cc_final: 0.8166 (p90) REVERT: B 208 HIS cc_start: 0.8742 (m90) cc_final: 0.8346 (m-70) REVERT: B 373 GLN cc_start: 0.9296 (mt0) cc_final: 0.8692 (tm-30) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.1873 time to fit residues: 17.7388 Evaluate side-chains 52 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.801 ------------------------------------------------------------------------------- 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: 7.9990 chunk 83 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 92 optimal weight: 7.9990 chunk 60 optimal weight: 9.9990 chunk 63 optimal weight: 1.9990 chunk 88 optimal weight: 7.9990 chunk 78 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 chunk 77 optimal weight: 0.0970 chunk 9 optimal weight: 0.8980 overall best weight: 2.9984 ------------------------------------------------------------------------------- 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 198 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.055206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.043759 restraints weight = 58491.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.044911 restraints weight = 33850.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.045729 restraints weight = 23199.529| |-----------------------------------------------------------------------------| r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8789 Z= 0.288 Angle : 0.575 5.899 12407 Z= 0.291 Chirality : 0.040 0.149 1471 Planarity : 0.004 0.051 1302 Dihedral : 17.903 85.049 2139 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % 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: -1.22 (0.28), residues: 932 helix: 0.80 (0.30), residues: 336 sheet: -1.35 (0.47), residues: 111 loop : -1.92 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 426 HIS 0.006 0.001 HIS B 208 PHE 0.011 0.002 PHE B 171 TYR 0.016 0.002 TYR A 183 ARG 0.004 0.001 ARG A 143 *********************** 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 49 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 MET cc_start: 0.9484 (mmm) cc_final: 0.9182 (tpp) REVERT: B 40 GLU cc_start: 0.9159 (mp0) cc_final: 0.8894 (mp0) REVERT: B 373 GLN cc_start: 0.9279 (mt0) cc_final: 0.8707 (tm-30) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.2012 time to fit residues: 14.6887 Evaluate side-chains 41 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.877 ------------------------------------------------------------------------------- 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: 0.9990 chunk 10 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 1 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 49 optimal weight: 8.9990 chunk 24 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 198 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.055819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.044229 restraints weight = 59278.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.045391 restraints weight = 34389.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.046208 restraints weight = 23710.533| |-----------------------------------------------------------------------------| r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8789 Z= 0.221 Angle : 0.525 5.506 12407 Z= 0.264 Chirality : 0.039 0.171 1471 Planarity : 0.004 0.044 1302 Dihedral : 17.891 85.094 2139 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % 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: -1.06 (0.28), residues: 932 helix: 0.93 (0.31), residues: 336 sheet: -0.92 (0.50), residues: 104 loop : -1.90 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 414 HIS 0.008 0.001 HIS B 208 PHE 0.011 0.001 PHE A 440 TYR 0.018 0.001 TYR A 183 ARG 0.002 0.000 ARG B 206 *********************** 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 57 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 GLU cc_start: 0.9091 (tm-30) cc_final: 0.8653 (tm-30) REVERT: B 40 GLU cc_start: 0.9172 (mp0) cc_final: 0.8900 (mp0) REVERT: B 373 GLN cc_start: 0.9117 (tt0) cc_final: 0.8655 (tm-30) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.1975 time to fit residues: 16.4929 Evaluate side-chains 41 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.901 ------------------------------------------------------------------------------- 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: 0.9980 chunk 61 optimal weight: 7.9990 chunk 74 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 9 optimal weight: 0.2980 chunk 49 optimal weight: 8.9990 chunk 52 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 overall best weight: 1.4582 ------------------------------------------------------------------------------- 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 198 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.056276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.044680 restraints weight = 58604.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.045871 restraints weight = 33870.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.046712 restraints weight = 23238.795| |-----------------------------------------------------------------------------| r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8789 Z= 0.161 Angle : 0.498 5.481 12407 Z= 0.248 Chirality : 0.039 0.176 1471 Planarity : 0.004 0.043 1302 Dihedral : 17.828 83.241 2139 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % 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: -0.87 (0.29), residues: 932 helix: 1.13 (0.31), residues: 334 sheet: -1.08 (0.48), residues: 112 loop : -1.75 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 88 HIS 0.003 0.001 HIS A 361 PHE 0.009 0.001 PHE B 61 TYR 0.016 0.001 TYR A 183 ARG 0.002 0.000 ARG B 206 *********************** 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 54 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 40 GLU cc_start: 0.9152 (mp0) cc_final: 0.8918 (mp0) REVERT: B 171 PHE cc_start: 0.8597 (p90) cc_final: 0.8316 (p90) REVERT: B 208 HIS cc_start: 0.8884 (m90) cc_final: 0.8573 (m170) REVERT: B 373 GLN cc_start: 0.9110 (tt0) cc_final: 0.8608 (tm-30) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1993 time to fit residues: 15.6990 Evaluate side-chains 41 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.871 ------------------------------------------------------------------------------- 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: 9.9990 chunk 64 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 100 optimal weight: 7.9990 chunk 14 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 8 optimal weight: 0.0030 overall best weight: 1.3394 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.056592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.044904 restraints weight = 59551.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.046108 restraints weight = 34441.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.046944 restraints weight = 23566.778| |-----------------------------------------------------------------------------| r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8789 Z= 0.155 Angle : 0.501 6.200 12407 Z= 0.251 Chirality : 0.039 0.166 1471 Planarity : 0.004 0.039 1302 Dihedral : 17.778 82.526 2139 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % 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: -0.69 (0.29), residues: 932 helix: 1.18 (0.31), residues: 334 sheet: -0.93 (0.49), residues: 112 loop : -1.58 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 88 HIS 0.003 0.001 HIS B 208 PHE 0.007 0.001 PHE B 61 TYR 0.017 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 56 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 GLU cc_start: 0.9077 (tm-30) cc_final: 0.8651 (tm-30) REVERT: B 40 GLU cc_start: 0.9171 (mp0) cc_final: 0.8969 (mp0) REVERT: B 373 GLN cc_start: 0.9166 (tt0) cc_final: 0.8578 (tm-30) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.2126 time to fit residues: 16.9722 Evaluate side-chains 38 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.863 ------------------------------------------------------------------------------- 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: 6.9990 chunk 17 optimal weight: 0.4980 chunk 20 optimal weight: 0.6980 chunk 54 optimal weight: 9.9990 chunk 68 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 208 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.057315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.045522 restraints weight = 58008.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.046739 restraints weight = 33869.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.047584 restraints weight = 23292.442| |-----------------------------------------------------------------------------| r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8789 Z= 0.133 Angle : 0.490 6.510 12407 Z= 0.243 Chirality : 0.038 0.160 1471 Planarity : 0.004 0.038 1302 Dihedral : 17.689 81.072 2139 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % 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: 327 sheet: -0.45 (0.51), residues: 103 loop : -1.45 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 88 HIS 0.003 0.001 HIS B 198 PHE 0.007 0.001 PHE B 61 TYR 0.017 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 54 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.9079 (mtm) cc_final: 0.8410 (mpp) REVERT: B 40 GLU cc_start: 0.9203 (mp0) cc_final: 0.9000 (mp0) REVERT: B 373 GLN cc_start: 0.9159 (tt0) cc_final: 0.8589 (tm-30) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1938 time to fit residues: 15.4374 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 : 0.868 ------------------------------------------------------------------------------- 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: 0.9980 chunk 62 optimal weight: 0.2980 chunk 5 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 4 optimal weight: 20.0000 chunk 19 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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** A 460 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.056920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.045123 restraints weight = 59468.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.046349 restraints weight = 34134.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.047220 restraints weight = 23306.559| |-----------------------------------------------------------------------------| r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8789 Z= 0.151 Angle : 0.493 5.661 12407 Z= 0.246 Chirality : 0.038 0.161 1471 Planarity : 0.004 0.039 1302 Dihedral : 17.692 81.405 2139 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % 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: -0.36 (0.29), residues: 932 helix: 1.46 (0.31), residues: 328 sheet: -0.31 (0.50), residues: 103 loop : -1.44 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 88 HIS 0.009 0.001 HIS B 208 PHE 0.015 0.001 PHE B 171 TYR 0.017 0.001 TYR A 183 ARG 0.003 0.000 ARG B 206 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2328.09 seconds wall clock time: 42 minutes 19.42 seconds (2539.42 seconds total)