Starting phenix.real_space_refine on Wed Feb 12 17:43:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z24_14457/02_2025/7z24_14457.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z24_14457/02_2025/7z24_14457.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7z24_14457/02_2025/7z24_14457.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z24_14457/02_2025/7z24_14457.map" model { file = "/net/cci-nas-00/data/ceres_data/7z24_14457/02_2025/7z24_14457.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z24_14457/02_2025/7z24_14457.cif" } resolution = 3.32 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= 0.024 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 35 5.49 5 S 13 5.16 5 C 5266 2.51 5 N 1378 2.21 5 O 1611 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8303 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4260 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 2, 'PTRANS': 34, 'TRANS': 490} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 3303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3303 Classifications: {'peptide': 402} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 30, 'TRANS': 371} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "E" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 720 Classifications: {'DNA': 34, 'RNA': 2} Modifications used: {'5*END': 1, 'rna3p': 2} Link IDs: {'rna3p': 35} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DA%5*END:plan2': 1, ' DA%5*END:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'NVP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.00, per 1000 atoms: 0.60 Number of scatterers: 8303 At special positions: 0 Unit cell: (97, 109.61, 101.85, 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 13 16.00 P 35 15.00 O 1611 8.00 N 1378 7.00 C 5266 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: 2.40 Conformation dependent library (CDL) restraints added in 832.8 milliseconds 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1750 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 11 sheets defined 39.8% alpha, 15.7% beta 13 base pairs and 26 stacking pairs defined. Time for finding SS restraints: 2.89 Creating SS restraints... Processing helix chain 'A' and resid 27 through 45 removed outlier: 3.931A pdb=" N VAL A 35 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N GLU A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ILE A 37 " --> pdb=" O ALA A 33 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU A 44 " --> pdb=" O GLU A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 84 Processing helix chain 'A' and resid 96 through 100 Processing helix chain 'A' and resid 113 through 117 Processing helix chain 'A' and resid 121 through 127 removed outlier: 4.340A 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 212 removed outlier: 3.580A pdb=" N THR A 200 " --> pdb=" O GLY A 196 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TRP A 212 " --> pdb=" O HIS A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 222 Processing helix chain 'A' and resid 253 through 268 Processing helix chain 'A' and resid 276 through 282 removed outlier: 3.917A pdb=" N LEU A 282 " --> pdb=" O GLN A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 312 removed outlier: 4.529A pdb=" N GLU A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 384 Processing helix chain 'A' and resid 394 through 405 Processing helix chain 'A' and resid 473 through 488 removed outlier: 4.006A pdb=" N ILE A 482 " --> pdb=" O GLU A 478 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR A 483 " --> pdb=" O LEU A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 508 removed outlier: 3.891A pdb=" N ALA A 508 " --> pdb=" O GLY A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 528 removed outlier: 3.602A pdb=" N LYS A 527 " --> pdb=" O GLU A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 546 removed outlier: 3.576A pdb=" N GLU A 546 " --> pdb=" O GLY A 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 44 removed outlier: 3.528A pdb=" N LEU B 34 " --> pdb=" O LYS B 30 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS B 43 " --> pdb=" O THR B 39 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU B 44 " --> pdb=" O GLU B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 85 Processing helix chain 'B' and resid 85 through 90 Processing helix chain 'B' and resid 98 through 102 removed outlier: 3.650A pdb=" N LYS B 101 " --> pdb=" O ALA B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 117 removed outlier: 3.823A pdb=" N SER B 117 " --> pdb=" O ALA B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 129 removed outlier: 3.853A pdb=" N ALA B 129 " --> pdb=" O LYS B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 138 Processing helix chain 'B' and resid 155 through 160 Processing helix chain 'B' and resid 160 through 173 Proline residue: B 170 - end of helix Processing helix chain 'B' and resid 194 through 212 removed outlier: 3.524A pdb=" N THR B 200 " --> pdb=" O GLY B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 271 removed outlier: 4.251A pdb=" N GLN B 269 " --> pdb=" O ASN B 265 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE B 270 " --> pdb=" O TRP B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 312 removed outlier: 3.765A pdb=" N GLU B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS B 311 " --> pdb=" O ARG B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 384 Processing helix chain 'B' and resid 394 through 402 Processing helix chain 'B' and resid 403 through 405 No H-bonds generated for 'chain 'B' and resid 403 through 405' Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 50 removed outlier: 4.605A pdb=" N ARG A 143 " --> pdb=" O ILE A 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 105 through 110 Processing sheet with id=AA3, first strand: chain 'A' and resid 227 through 229 removed outlier: 3.720A pdb=" N LYS A 238 " --> pdb=" O HIS A 235 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 348 through 354 removed outlier: 6.628A pdb=" N ILE A 341 " --> pdb=" O LEU A 349 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N THR A 351 " --> pdb=" O TYR A 339 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N TYR A 339 " --> pdb=" O THR A 351 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LYS A 353 " --> pdb=" O TRP A 337 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N TRP A 337 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N GLN A 336 " --> pdb=" O GLN A 332 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS A 390 " --> pdb=" O ALA A 327 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE A 329 " --> pdb=" O LYS A 390 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N PHE A 389 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 361 through 362 removed outlier: 3.528A pdb=" N THR A 362 " --> pdb=" O LYS A 512 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS A 512 " --> pdb=" O THR A 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 464 through 470 removed outlier: 3.531A pdb=" N LYS A 465 " --> pdb=" O TYR A 457 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU A 452 " --> pdb=" O ASN A 447 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TYR A 441 " --> pdb=" O VAL A 458 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N GLU A 438 " --> pdb=" O ASN A 494 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N VAL A 496 " --> pdb=" O GLU A 438 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N PHE A 440 " --> pdb=" O VAL A 496 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 60 through 63 Processing sheet with id=AA8, first strand: chain 'B' and resid 179 through 183 Processing sheet with id=AA9, first strand: chain 'B' and resid 130 through 132 Processing sheet with id=AB1, first strand: chain 'B' and resid 252 through 253 removed outlier: 4.239A pdb=" N TRP B 252 " --> pdb=" O ILE B 293 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 347 through 355 removed outlier: 8.868A pdb=" N ASN B 348 " --> pdb=" O GLN B 343 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N GLN B 343 " --> pdb=" O ASN B 348 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N GLN B 336 " --> pdb=" O GLN B 332 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE B 329 " --> pdb=" O LYS B 390 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N PHE B 389 " --> pdb=" O GLU B 415 " (cutoff:3.500A) 310 hydrogen bonds defined for protein. 840 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 36 hydrogen bonds 72 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 26 stacking parallelities Total time for adding SS restraints: 2.57 Time building geometry restraints manager: 2.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1472 1.33 - 1.45: 2307 1.45 - 1.57: 4721 1.57 - 1.69: 71 1.69 - 1.81: 23 Bond restraints: 8594 Sorted by residual: bond pdb=" N GLU B 169 " pdb=" CA GLU B 169 " ideal model delta sigma weight residual 1.459 1.500 -0.040 1.04e-02 9.25e+03 1.51e+01 bond pdb=" N VAL B 241 " pdb=" CA VAL B 241 " ideal model delta sigma weight residual 1.457 1.501 -0.045 1.19e-02 7.06e+03 1.40e+01 bond pdb=" N ILE B 293 " pdb=" CA ILE B 293 " ideal model delta sigma weight residual 1.456 1.488 -0.032 8.70e-03 1.32e+04 1.35e+01 bond pdb=" N ILE B 244 " pdb=" CA ILE B 244 " ideal model delta sigma weight residual 1.457 1.501 -0.044 1.22e-02 6.72e+03 1.29e+01 bond pdb=" N GLY B 285 " pdb=" CA GLY B 285 " ideal model delta sigma weight residual 1.444 1.478 -0.035 1.02e-02 9.61e+03 1.15e+01 ... (remaining 8589 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 11443 2.75 - 5.51: 357 5.51 - 8.26: 29 8.26 - 11.02: 3 11.02 - 13.77: 2 Bond angle restraints: 11834 Sorted by residual: angle pdb=" C5' DG E 12 " pdb=" C4' DG E 12 " pdb=" O4' DG E 12 " ideal model delta sigma weight residual 109.40 123.17 -13.77 1.50e+00 4.44e-01 8.43e+01 angle pdb=" C5' DT E 13 " pdb=" C4' DT E 13 " pdb=" O4' DT E 13 " ideal model delta sigma weight residual 109.40 122.69 -13.29 1.50e+00 4.44e-01 7.85e+01 angle pdb=" C5' DG E 19 " pdb=" C4' DG E 19 " pdb=" O4' DG E 19 " ideal model delta sigma weight residual 109.40 120.19 -10.79 1.50e+00 4.44e-01 5.17e+01 angle pdb=" C HIS B 235 " pdb=" CA HIS B 235 " pdb=" CB HIS B 235 " ideal model delta sigma weight residual 110.08 117.91 -7.83 1.15e+00 7.56e-01 4.63e+01 angle pdb=" C3' OMC E 2 " pdb=" C2' OMC E 2 " pdb=" C1' OMC E 2 " ideal model delta sigma weight residual 101.30 106.98 -5.68 1.00e+00 1.00e+00 3.22e+01 ... (remaining 11829 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.40: 4354 19.40 - 38.80: 495 38.80 - 58.20: 137 58.20 - 77.59: 31 77.59 - 96.99: 8 Dihedral angle restraints: 5025 sinusoidal: 2313 harmonic: 2712 Sorted by residual: dihedral pdb=" C PHE B 346 " pdb=" N PHE B 346 " pdb=" CA PHE B 346 " pdb=" CB PHE B 346 " ideal model delta harmonic sigma weight residual -122.60 -133.18 10.58 0 2.50e+00 1.60e-01 1.79e+01 dihedral pdb=" C GLU B 291 " pdb=" N GLU B 291 " pdb=" CA GLU B 291 " pdb=" CB GLU B 291 " ideal model delta harmonic sigma weight residual -122.60 -132.67 10.07 0 2.50e+00 1.60e-01 1.62e+01 dihedral pdb=" CD ARG A 277 " pdb=" NE ARG A 277 " pdb=" CZ ARG A 277 " pdb=" NH1 ARG A 277 " ideal model delta sinusoidal sigma weight residual 0.00 32.46 -32.46 1 1.00e+01 1.00e-02 1.50e+01 ... (remaining 5022 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 1140 0.109 - 0.217: 125 0.217 - 0.326: 23 0.326 - 0.434: 2 0.434 - 0.543: 2 Chirality restraints: 1292 Sorted by residual: chirality pdb=" C4' DG E 12 " pdb=" C5' DG E 12 " pdb=" O4' DG E 12 " pdb=" C3' DG E 12 " both_signs ideal model delta sigma weight residual False -2.53 -1.98 -0.54 2.00e-01 2.50e+01 7.36e+00 chirality pdb=" C4' DT E 13 " pdb=" C5' DT E 13 " pdb=" O4' DT E 13 " pdb=" C3' DT E 13 " both_signs ideal model delta sigma weight residual False -2.53 -2.07 -0.45 2.00e-01 2.50e+01 5.09e+00 chirality pdb=" C4' DC E 20 " pdb=" C5' DC E 20 " pdb=" O4' DC E 20 " pdb=" C3' DC E 20 " both_signs ideal model delta sigma weight residual False -2.53 -2.17 -0.36 2.00e-01 2.50e+01 3.16e+00 ... (remaining 1289 not shown) Planarity restraints: 1367 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 277 " 0.582 9.50e-02 1.11e+02 2.61e-01 4.16e+01 pdb=" NE ARG A 277 " -0.035 2.00e-02 2.50e+03 pdb=" CZ ARG A 277 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 277 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 277 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 419 " 0.079 5.00e-02 4.00e+02 1.17e-01 2.20e+01 pdb=" N PRO B 420 " -0.203 5.00e-02 4.00e+02 pdb=" CA PRO B 420 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO B 420 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 246 " -0.057 5.00e-02 4.00e+02 8.69e-02 1.21e+01 pdb=" N PRO A 247 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO A 247 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 247 " -0.047 5.00e-02 4.00e+02 ... (remaining 1364 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 3009 2.89 - 3.39: 7440 3.39 - 3.89: 13877 3.89 - 4.40: 15907 4.40 - 4.90: 26057 Nonbonded interactions: 66290 Sorted by model distance: nonbonded pdb=" O VAL A 276 " pdb=" OG SER A 280 " model vdw 2.387 3.040 nonbonded pdb=" OG1 THR A 286 " pdb=" OE2 GLU A 291 " model vdw 2.390 3.040 nonbonded pdb=" O TYR B 56 " pdb=" NH2 ARG B 143 " model vdw 2.417 3.120 nonbonded pdb=" N THR B 290 " pdb=" OG1 THR B 290 " model vdw 2.459 2.496 nonbonded pdb=" OE1 GLN A 330 " pdb=" NE2 GLN A 340 " model vdw 2.466 3.120 ... (remaining 66285 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.660 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 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 : 0.007 0.087 8594 Z= 0.469 Angle : 1.050 13.772 11834 Z= 0.706 Chirality : 0.076 0.543 1292 Planarity : 0.010 0.261 1367 Dihedral : 18.098 96.992 3275 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.07 % Allowed : 3.04 % Favored : 94.89 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 3.03 % 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: -0.18 (0.28), residues: 917 helix: 1.09 (0.30), residues: 311 sheet: -0.29 (0.40), residues: 177 loop : -0.90 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B 414 HIS 0.006 0.001 HIS A 315 PHE 0.021 0.002 PHE A 124 TYR 0.020 0.002 TYR A 532 ARG 0.004 0.001 ARG B 211 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 0.864 Fit side-chains revert: symmetry clash REVERT: A 498 ASN cc_start: 0.6968 (t0) cc_final: 0.6588 (t0) REVERT: B 280 SER cc_start: 0.7756 (p) cc_final: 0.7080 (t) outliers start: 17 outliers final: 9 residues processed: 134 average time/residue: 0.2063 time to fit residues: 38.0244 Evaluate side-chains 105 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain B residue 101 LYS Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 317 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 80 optimal weight: 10.0000 chunk 72 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 74 optimal weight: 20.0000 chunk 28 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 GLN A 255 ASN A 332 GLN ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.214478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.175040 restraints weight = 8615.360| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 1.97 r_work: 0.3675 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8594 Z= 0.229 Angle : 0.608 7.592 11834 Z= 0.321 Chirality : 0.042 0.144 1292 Planarity : 0.006 0.077 1367 Dihedral : 16.966 81.921 1360 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.07 % Allowed : 9.85 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.13 (0.28), residues: 917 helix: 1.00 (0.29), residues: 331 sheet: -0.17 (0.40), residues: 172 loop : -0.89 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 402 HIS 0.004 0.001 HIS B 235 PHE 0.019 0.002 PHE B 87 TYR 0.012 0.002 TYR A 501 ARG 0.004 0.001 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.892 Fit side-chains REVERT: A 31 ILE cc_start: 0.4789 (mt) cc_final: 0.4541 (mp) REVERT: A 78 ARG cc_start: 0.6128 (mmp80) cc_final: 0.5318 (mmt-90) REVERT: A 147 ASN cc_start: 0.7262 (m110) cc_final: 0.6714 (t0) REVERT: A 375 ILE cc_start: 0.8394 (OUTLIER) cc_final: 0.8132 (mt) REVERT: A 530 LYS cc_start: 0.7031 (mtpt) cc_final: 0.6768 (mtmt) REVERT: B 280 SER cc_start: 0.7773 (p) cc_final: 0.7329 (t) outliers start: 17 outliers final: 12 residues processed: 116 average time/residue: 0.2022 time to fit residues: 32.6790 Evaluate side-chains 108 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain B residue 101 LYS Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 317 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 23 optimal weight: 8.9990 chunk 77 optimal weight: 0.0980 chunk 5 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 64 optimal weight: 9.9990 chunk 79 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 66 optimal weight: 9.9990 chunk 62 optimal weight: 20.0000 chunk 87 optimal weight: 2.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 GLN A 332 GLN ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 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 = 0.4356 r_free = 0.4356 target = 0.216030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.176907 restraints weight = 8740.480| |-----------------------------------------------------------------------------| r_work (start): 0.3951 rms_B_bonded: 1.90 r_work: 0.3704 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8594 Z= 0.186 Angle : 0.548 8.007 11834 Z= 0.286 Chirality : 0.041 0.139 1292 Planarity : 0.005 0.062 1367 Dihedral : 16.514 81.837 1356 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.43 % Allowed : 12.17 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.10 (0.28), residues: 917 helix: 1.18 (0.30), residues: 331 sheet: 0.08 (0.41), residues: 155 loop : -0.79 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 402 HIS 0.003 0.001 HIS B 235 PHE 0.022 0.001 PHE B 87 TYR 0.014 0.001 TYR A 501 ARG 0.005 0.001 ARG A 83 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.858 Fit side-chains REVERT: A 29 GLU cc_start: 0.5333 (OUTLIER) cc_final: 0.4777 (tp30) REVERT: A 147 ASN cc_start: 0.7285 (m110) cc_final: 0.6734 (t0) REVERT: A 375 ILE cc_start: 0.8382 (OUTLIER) cc_final: 0.8150 (mt) REVERT: A 530 LYS cc_start: 0.6935 (mtpt) cc_final: 0.6693 (mtmt) REVERT: B 233 GLU cc_start: 0.6466 (mp0) cc_final: 0.6256 (pm20) REVERT: B 280 SER cc_start: 0.7770 (p) cc_final: 0.7236 (t) outliers start: 20 outliers final: 12 residues processed: 124 average time/residue: 0.1956 time to fit residues: 34.0675 Evaluate side-chains 118 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 317 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 45 optimal weight: 6.9990 chunk 73 optimal weight: 20.0000 chunk 52 optimal weight: 6.9990 chunk 90 optimal weight: 10.0000 chunk 70 optimal weight: 6.9990 chunk 55 optimal weight: 9.9990 chunk 93 optimal weight: 20.0000 chunk 50 optimal weight: 6.9990 chunk 43 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 78 optimal weight: 40.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 ASN ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 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 = 0.4317 r_free = 0.4317 target = 0.211312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.171841 restraints weight = 8737.910| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 1.83 r_work: 0.3642 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 8594 Z= 0.365 Angle : 0.670 11.622 11834 Z= 0.349 Chirality : 0.045 0.158 1292 Planarity : 0.006 0.058 1367 Dihedral : 16.814 82.243 1351 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.43 % Allowed : 14.84 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.37 (0.27), residues: 917 helix: 0.73 (0.29), residues: 332 sheet: -0.29 (0.41), residues: 159 loop : -0.97 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 402 HIS 0.009 0.002 HIS A 315 PHE 0.025 0.002 PHE A 124 TYR 0.017 0.002 TYR A 501 ARG 0.004 0.001 ARG A 83 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.852 Fit side-chains REVERT: A 91 GLN cc_start: 0.6521 (mm110) cc_final: 0.6317 (tp40) REVERT: A 147 ASN cc_start: 0.7248 (m110) cc_final: 0.6808 (t0) REVERT: A 375 ILE cc_start: 0.8416 (OUTLIER) cc_final: 0.8159 (mt) REVERT: A 530 LYS cc_start: 0.7108 (mtpt) cc_final: 0.6883 (mtmt) REVERT: B 233 GLU cc_start: 0.6590 (mp0) cc_final: 0.6348 (pm20) outliers start: 20 outliers final: 14 residues processed: 112 average time/residue: 0.2005 time to fit residues: 31.6091 Evaluate side-chains 111 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 317 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 50 optimal weight: 10.0000 chunk 32 optimal weight: 0.9980 chunk 84 optimal weight: 6.9990 chunk 78 optimal weight: 20.0000 chunk 79 optimal weight: 30.0000 chunk 37 optimal weight: 20.0000 chunk 11 optimal weight: 20.0000 chunk 81 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 overall best weight: 5.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 GLN ** A 494 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 = 0.4319 r_free = 0.4319 target = 0.211505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.172100 restraints weight = 8593.162| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 1.76 r_work: 0.3686 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8594 Z= 0.322 Angle : 0.650 11.977 11834 Z= 0.338 Chirality : 0.045 0.197 1292 Planarity : 0.006 0.054 1367 Dihedral : 16.966 82.078 1351 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.92 % Allowed : 14.84 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.45 (0.28), residues: 917 helix: 0.66 (0.29), residues: 332 sheet: -0.29 (0.41), residues: 159 loop : -1.01 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 402 HIS 0.006 0.001 HIS A 315 PHE 0.026 0.002 PHE B 87 TYR 0.016 0.002 TYR A 501 ARG 0.003 0.001 ARG A 284 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 0.802 Fit side-chains REVERT: A 91 GLN cc_start: 0.6559 (mm110) cc_final: 0.6314 (tp40) REVERT: A 375 ILE cc_start: 0.8419 (OUTLIER) cc_final: 0.8146 (mt) REVERT: A 530 LYS cc_start: 0.7244 (mtpt) cc_final: 0.6984 (mtmt) REVERT: B 233 GLU cc_start: 0.6605 (mp0) cc_final: 0.6376 (pm20) REVERT: B 280 SER cc_start: 0.8026 (p) cc_final: 0.7493 (t) outliers start: 24 outliers final: 17 residues processed: 121 average time/residue: 0.2061 time to fit residues: 34.9921 Evaluate side-chains 116 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 239 TRP Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 317 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 11 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 94 optimal weight: 20.0000 chunk 40 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 5 optimal weight: 20.0000 chunk 76 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 545 ASN B 373 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.213267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.173518 restraints weight = 8683.963| |-----------------------------------------------------------------------------| r_work (start): 0.3953 rms_B_bonded: 1.79 r_work: 0.3705 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8594 Z= 0.242 Angle : 0.593 11.389 11834 Z= 0.308 Chirality : 0.043 0.190 1292 Planarity : 0.005 0.049 1367 Dihedral : 16.965 82.037 1351 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.68 % Allowed : 16.42 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.32 (0.28), residues: 917 helix: 0.86 (0.29), residues: 333 sheet: -0.43 (0.39), residues: 169 loop : -0.94 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 402 HIS 0.004 0.001 HIS A 315 PHE 0.024 0.002 PHE B 87 TYR 0.015 0.002 TYR A 501 ARG 0.005 0.000 ARG A 83 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.896 Fit side-chains REVERT: A 29 GLU cc_start: 0.5552 (OUTLIER) cc_final: 0.4783 (tp30) REVERT: A 91 GLN cc_start: 0.6527 (mm110) cc_final: 0.6269 (tp40) REVERT: A 375 ILE cc_start: 0.8392 (OUTLIER) cc_final: 0.8104 (mt) REVERT: A 530 LYS cc_start: 0.7171 (mtpt) cc_final: 0.6898 (mtmm) REVERT: B 206 ARG cc_start: 0.7092 (ttp80) cc_final: 0.6552 (ttp-170) REVERT: B 233 GLU cc_start: 0.6696 (mp0) cc_final: 0.6454 (pm20) REVERT: B 280 SER cc_start: 0.8026 (p) cc_final: 0.7453 (t) outliers start: 22 outliers final: 19 residues processed: 116 average time/residue: 0.1981 time to fit residues: 32.3245 Evaluate side-chains 120 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 239 TRP Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 410 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 32 optimal weight: 4.9990 chunk 73 optimal weight: 20.0000 chunk 41 optimal weight: 7.9990 chunk 48 optimal weight: 20.0000 chunk 87 optimal weight: 10.0000 chunk 75 optimal weight: 9.9990 chunk 16 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 545 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.213009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.173718 restraints weight = 8645.102| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 1.87 r_work: 0.3691 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8594 Z= 0.251 Angle : 0.594 11.756 11834 Z= 0.308 Chirality : 0.043 0.178 1292 Planarity : 0.005 0.049 1367 Dihedral : 16.965 81.976 1351 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.53 % Allowed : 15.69 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.22 (0.28), residues: 917 helix: 0.95 (0.29), residues: 331 sheet: -0.27 (0.40), residues: 159 loop : -0.93 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 402 HIS 0.004 0.001 HIS A 315 PHE 0.026 0.002 PHE B 87 TYR 0.015 0.002 TYR A 501 ARG 0.005 0.000 ARG A 83 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 99 time to evaluate : 0.892 Fit side-chains REVERT: A 29 GLU cc_start: 0.5501 (OUTLIER) cc_final: 0.4711 (tp30) REVERT: A 91 GLN cc_start: 0.6509 (mm110) cc_final: 0.6248 (tp40) REVERT: A 375 ILE cc_start: 0.8412 (OUTLIER) cc_final: 0.8130 (mt) REVERT: A 530 LYS cc_start: 0.7150 (mtpt) cc_final: 0.6878 (mtmt) REVERT: B 206 ARG cc_start: 0.7162 (ttp80) cc_final: 0.6600 (ttp-170) REVERT: B 233 GLU cc_start: 0.6678 (mp0) cc_final: 0.6468 (pm20) REVERT: B 280 SER cc_start: 0.8012 (p) cc_final: 0.7440 (t) REVERT: B 405 TYR cc_start: 0.8124 (OUTLIER) cc_final: 0.7289 (m-80) outliers start: 29 outliers final: 20 residues processed: 123 average time/residue: 0.2018 time to fit residues: 34.8820 Evaluate side-chains 121 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 98 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 239 TRP Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 410 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 43 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 15 optimal weight: 30.0000 chunk 5 optimal weight: 0.5980 chunk 86 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 chunk 40 optimal weight: 7.9990 chunk 84 optimal weight: 1.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 545 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.214923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.175290 restraints weight = 8654.532| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 1.84 r_work: 0.3703 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3554 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8594 Z= 0.193 Angle : 0.559 10.937 11834 Z= 0.290 Chirality : 0.042 0.184 1292 Planarity : 0.005 0.046 1367 Dihedral : 16.842 81.895 1351 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.80 % Allowed : 16.55 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.05 (0.28), residues: 917 helix: 1.17 (0.29), residues: 330 sheet: -0.48 (0.38), residues: 180 loop : -0.75 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 402 HIS 0.003 0.001 HIS B 235 PHE 0.025 0.001 PHE B 87 TYR 0.014 0.001 TYR A 501 ARG 0.003 0.000 ARG A 83 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 0.907 Fit side-chains REVERT: A 29 GLU cc_start: 0.5043 (OUTLIER) cc_final: 0.4614 (tp30) REVERT: A 34 LEU cc_start: 0.4313 (OUTLIER) cc_final: 0.4065 (tt) REVERT: A 83 ARG cc_start: 0.7159 (mmp80) cc_final: 0.6532 (mmp80) REVERT: A 375 ILE cc_start: 0.8406 (OUTLIER) cc_final: 0.8170 (mt) REVERT: A 530 LYS cc_start: 0.7203 (mtpt) cc_final: 0.6981 (mtpt) REVERT: B 206 ARG cc_start: 0.7062 (ttp80) cc_final: 0.6537 (ttp-170) REVERT: B 233 GLU cc_start: 0.6749 (mp0) cc_final: 0.6476 (pm20) REVERT: B 280 SER cc_start: 0.7946 (p) cc_final: 0.7383 (t) outliers start: 23 outliers final: 17 residues processed: 122 average time/residue: 0.1946 time to fit residues: 33.3844 Evaluate side-chains 121 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 317 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 91 optimal weight: 4.9990 chunk 5 optimal weight: 0.2980 chunk 50 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 52 optimal weight: 0.3980 chunk 74 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 chunk 16 optimal weight: 9.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 545 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.215025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.175416 restraints weight = 8726.005| |-----------------------------------------------------------------------------| r_work (start): 0.3970 rms_B_bonded: 1.98 r_work: 0.3712 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8594 Z= 0.196 Angle : 0.552 11.068 11834 Z= 0.284 Chirality : 0.042 0.178 1292 Planarity : 0.005 0.045 1367 Dihedral : 16.808 81.651 1351 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.92 % Allowed : 16.42 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.00 (0.28), residues: 917 helix: 1.19 (0.29), residues: 328 sheet: -0.41 (0.38), residues: 180 loop : -0.72 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 402 HIS 0.003 0.001 HIS B 235 PHE 0.026 0.001 PHE B 87 TYR 0.014 0.001 TYR A 501 ARG 0.002 0.000 ARG B 125 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 0.865 Fit side-chains REVERT: A 29 GLU cc_start: 0.4974 (OUTLIER) cc_final: 0.4594 (tp30) REVERT: A 34 LEU cc_start: 0.4320 (OUTLIER) cc_final: 0.4067 (tt) REVERT: A 83 ARG cc_start: 0.7139 (mmp80) cc_final: 0.6557 (mmp80) REVERT: A 375 ILE cc_start: 0.8377 (OUTLIER) cc_final: 0.8146 (mt) REVERT: A 530 LYS cc_start: 0.7104 (mtpt) cc_final: 0.6882 (mtpt) REVERT: B 206 ARG cc_start: 0.7077 (ttp80) cc_final: 0.6536 (ttp-170) REVERT: B 233 GLU cc_start: 0.6670 (mp0) cc_final: 0.6415 (pm20) REVERT: B 280 SER cc_start: 0.7976 (p) cc_final: 0.7391 (t) outliers start: 24 outliers final: 20 residues processed: 117 average time/residue: 0.2004 time to fit residues: 33.0189 Evaluate side-chains 121 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 98 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 402 TRP Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 410 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 65.8852 > 50: distance: 38 - 40: 28.968 distance: 40 - 41: 22.876 distance: 40 - 46: 31.095 distance: 41 - 42: 59.676 distance: 41 - 44: 41.230 distance: 42 - 43: 53.199 distance: 42 - 47: 31.154 distance: 44 - 45: 14.287 distance: 45 - 46: 6.572 distance: 47 - 48: 20.358 distance: 48 - 49: 18.008 distance: 48 - 51: 14.378 distance: 49 - 50: 40.070 distance: 49 - 56: 15.018 distance: 51 - 52: 20.859 distance: 52 - 53: 43.160 distance: 53 - 54: 35.454 distance: 53 - 55: 31.214 distance: 56 - 57: 23.105 distance: 57 - 58: 31.913 distance: 57 - 60: 26.961 distance: 58 - 59: 44.461 distance: 58 - 64: 17.495 distance: 60 - 61: 41.380 distance: 61 - 62: 5.612 distance: 64 - 65: 33.539 distance: 64 - 70: 21.031 distance: 65 - 66: 21.338 distance: 65 - 68: 35.874 distance: 66 - 67: 36.492 distance: 66 - 71: 17.997 distance: 68 - 69: 35.219 distance: 69 - 70: 27.232 distance: 71 - 72: 34.922 distance: 72 - 73: 11.821 distance: 72 - 75: 42.551 distance: 73 - 74: 51.512 distance: 73 - 83: 49.461 distance: 75 - 76: 60.416 distance: 76 - 77: 41.704 distance: 76 - 78: 43.922 distance: 77 - 79: 17.387 distance: 78 - 80: 12.275 distance: 79 - 81: 31.809 distance: 80 - 81: 30.142 distance: 81 - 82: 17.800 distance: 83 - 84: 41.150 distance: 84 - 85: 40.866 distance: 84 - 87: 16.028 distance: 85 - 86: 40.235 distance: 85 - 88: 28.449 distance: 88 - 89: 44.779 distance: 89 - 90: 32.505 distance: 89 - 92: 46.268 distance: 90 - 91: 45.193 distance: 90 - 95: 48.545 distance: 92 - 93: 4.620 distance: 92 - 94: 59.963 distance: 95 - 96: 18.377 distance: 95 - 101: 20.643 distance: 96 - 97: 31.182 distance: 96 - 99: 28.845 distance: 97 - 98: 11.638 distance: 97 - 102: 36.919 distance: 99 - 100: 17.907 distance: 100 - 101: 18.130 distance: 102 - 103: 14.294 distance: 103 - 104: 44.308 distance: 103 - 106: 17.316 distance: 104 - 105: 35.300 distance: 104 - 109: 27.805 distance: 109 - 110: 28.731 distance: 110 - 111: 41.049 distance: 110 - 113: 25.209 distance: 111 - 112: 33.042 distance: 111 - 120: 31.743 distance: 113 - 114: 17.307 distance: 114 - 115: 7.120 distance: 114 - 116: 37.808 distance: 115 - 117: 40.855 distance: 116 - 118: 15.024 distance: 117 - 119: 44.394 distance: 118 - 119: 41.217