Starting phenix.real_space_refine on Thu Jul 2 19:47:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8blw_16114/07_2026/8blw_16114.cif Found real_map, /net/cci-nas-00/data/ceres_data/8blw_16114/07_2026/8blw_16114.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8blw_16114/07_2026/8blw_16114.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8blw_16114/07_2026/8blw_16114.map" model { file = "/net/cci-nas-00/data/ceres_data/8blw_16114/07_2026/8blw_16114.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8blw_16114/07_2026/8blw_16114.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8blw_16114/07_2026/8blw_16114.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8blw_16114/07_2026/8blw_16114.cif" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.001 sd= 0.019 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: 4 Type Number sf(0) Gaussians S 18 5.16 5 C 6239 2.51 5 N 1683 2.21 5 O 1943 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9883 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 624, 4974 Classifications: {'peptide': 624} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 22, 'TRANS': 601} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 1, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 4898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 4898 Classifications: {'peptide': 626} Link IDs: {'PTRANS': 23, 'TRANS': 602} Chain breaks: 1 Chain: "B" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'GAL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.81, per 1000 atoms: 0.18 Number of scatterers: 9883 At special positions: 0 Unit cell: (81.9, 71.89, 141.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 18 16.00 O 1943 8.00 N 1683 7.00 C 6239 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 361.8 milliseconds 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2316 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 20 sheets defined 5.7% alpha, 34.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 62 through 69 Processing helix chain 'A' and resid 74 through 79 removed outlier: 3.708A pdb=" N LYS A 79 " --> pdb=" O SER A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 130 removed outlier: 3.574A pdb=" N ARG A 129 " --> pdb=" O ASP A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 155 Processing helix chain 'A' and resid 457 through 462 Processing helix chain 'A' and resid 620 through 624 removed outlier: 3.594A pdb=" N ARG A 624 " --> pdb=" O SER A 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 87 Processing helix chain 'B' and resid 195 through 199 Processing helix chain 'B' and resid 412 through 416 removed outlier: 3.578A pdb=" N ALA B 416 " --> pdb=" O THR B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 436 Processing helix chain 'B' and resid 613 through 615 No H-bonds generated for 'chain 'B' and resid 613 through 615' Processing sheet with id=AA1, first strand: chain 'A' and resid 58 through 61 removed outlier: 3.567A pdb=" N ARG A 137 " --> pdb=" O GLN A 164 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 85 through 87 Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 177 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 176 through 177 current: chain 'A' and resid 189 through 191 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 189 through 191 current: chain 'A' and resid 204 through 214 removed outlier: 4.443A pdb=" N GLU A 244 " --> pdb=" O SER A 272 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER A 272 " --> pdb=" O GLU A 244 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ALA A 254 " --> pdb=" O TRP A 262 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N TYR A 321 " --> pdb=" O LYS A 293 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 336 through 348 current: chain 'A' and resid 359 through 374 removed outlier: 6.886A pdb=" N SER A 360 " --> pdb=" O LYS A 394 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N LYS A 394 " --> pdb=" O SER A 360 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER A 362 " --> pdb=" O ALA A 392 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LEU A 388 " --> pdb=" O ASP A 366 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ALA A 406 " --> pdb=" O GLY A 393 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU A 442 " --> pdb=" O SER A 486 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 495 through 502 current: chain 'A' and resid 530 through 532 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 530 through 532 current: chain 'A' and resid 553 through 559 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 553 through 559 current: chain 'A' and resid 580 through 581 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 580 through 581 current: chain 'A' and resid 602 through 610 Processing sheet with id=AA4, first strand: chain 'A' and resid 222 through 224 Processing sheet with id=AA5, first strand: chain 'A' and resid 511 through 515 Processing sheet with id=AA6, first strand: chain 'A' and resid 661 through 663 removed outlier: 4.816A pdb=" N VAL A 663 " --> pdb=" O PHE A 666 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 76 through 78 removed outlier: 6.789A pdb=" N GLU B 51 " --> pdb=" O PHE B 373 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N PHE B 373 " --> pdb=" O GLU B 51 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TYR B 53 " --> pdb=" O VAL B 371 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL B 371 " --> pdb=" O TYR B 53 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LEU B 55 " --> pdb=" O ASN B 369 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 94 through 100 removed outlier: 3.697A pdb=" N ILE B 128 " --> pdb=" O VAL B 114 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 140 through 145 removed outlier: 3.819A pdb=" N ALA B 142 " --> pdb=" O CYS B 153 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N THR B 158 " --> pdb=" O SER B 154 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL B 159 " --> pdb=" O ILE B 172 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILE B 172 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ARG B 161 " --> pdb=" O GLU B 170 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 179 through 185 removed outlier: 4.388A pdb=" N ASP B 181 " --> pdb=" O SER B 192 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N THR B 207 " --> pdb=" O ASN B 193 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS B 220 " --> pdb=" O VAL B 210 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ASP B 212 " --> pdb=" O GLU B 218 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLU B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 228 through 233 removed outlier: 5.652A pdb=" N VAL B 242 " --> pdb=" O GLY B 229 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ILE B 231 " --> pdb=" O TYR B 240 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N TYR B 240 " --> pdb=" O ILE B 231 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ALA B 238 " --> pdb=" O PRO B 233 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ASP B 259 " --> pdb=" O VAL B 265 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL B 265 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 275 through 279 removed outlier: 3.610A pdb=" N SER B 275 " --> pdb=" O TYR B 286 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL B 299 " --> pdb=" O ILE B 308 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 322 through 327 removed outlier: 6.856A pdb=" N THR B 337 " --> pdb=" O PHE B 323 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ILE B 325 " --> pdb=" O TYR B 335 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N TYR B 335 " --> pdb=" O ILE B 325 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N GLY B 346 " --> pdb=" O ASN B 362 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N ASN B 362 " --> pdb=" O GLY B 346 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL B 348 " --> pdb=" O ARG B 360 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ARG B 360 " --> pdb=" O VAL B 348 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N CYS B 350 " --> pdb=" O GLN B 358 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 399 through 403 removed outlier: 3.530A pdb=" N GLU B 401 " --> pdb=" O THR B 450 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N VAL B 492 " --> pdb=" O LEU B 511 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 440 through 441 Processing sheet with id=AB7, first strand: chain 'B' and resid 457 through 458 Processing sheet with id=AB8, first strand: chain 'B' and resid 611 through 612 Processing sheet with id=AB9, first strand: chain 'B' and resid 548 through 551 removed outlier: 3.953A pdb=" N ARG B 540 " --> pdb=" O TYR B 530 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ASN B 524 " --> pdb=" O GLY B 576 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLY B 576 " --> pdb=" O ASN B 524 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLU B 526 " --> pdb=" O PHE B 574 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N PHE B 574 " --> pdb=" O GLU B 526 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N THR B 528 " --> pdb=" O ILE B 572 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE B 572 " --> pdb=" O THR B 528 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 583 through 584 removed outlier: 3.868A pdb=" N VAL B 591 " --> pdb=" O ILE B 584 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 642 through 644 removed outlier: 6.030A pdb=" N GLY B 647 " --> pdb=" O VAL B 643 " (cutoff:3.500A) 306 hydrogen bonds defined for protein. 819 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.60 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3204 1.34 - 1.46: 2285 1.46 - 1.58: 4584 1.58 - 1.70: 1 1.70 - 1.82: 29 Bond restraints: 10103 Sorted by residual: bond pdb=" CG PRO A 175 " pdb=" CD PRO A 175 " ideal model delta sigma weight residual 1.503 1.363 0.140 3.40e-02 8.65e+02 1.69e+01 bond pdb=" C5 GAL B 701 " pdb=" O5 GAL B 701 " ideal model delta sigma weight residual 1.412 1.481 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" CB PRO A 175 " pdb=" CG PRO A 175 " ideal model delta sigma weight residual 1.492 1.648 -0.156 5.00e-02 4.00e+02 9.75e+00 bond pdb=" N PRO A 175 " pdb=" CD PRO A 175 " ideal model delta sigma weight residual 1.473 1.511 -0.038 1.40e-02 5.10e+03 7.26e+00 bond pdb=" C1 GAL B 701 " pdb=" O5 GAL B 701 " ideal model delta sigma weight residual 1.407 1.451 -0.044 2.00e-02 2.50e+03 4.93e+00 ... (remaining 10098 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.50: 13498 3.50 - 6.99: 194 6.99 - 10.49: 22 10.49 - 13.98: 3 13.98 - 17.48: 2 Bond angle restraints: 13719 Sorted by residual: angle pdb=" CA PRO A 175 " pdb=" N PRO A 175 " pdb=" CD PRO A 175 " ideal model delta sigma weight residual 112.00 94.52 17.48 1.40e+00 5.10e-01 1.56e+02 angle pdb=" N PRO A 175 " pdb=" CD PRO A 175 " pdb=" CG PRO A 175 " ideal model delta sigma weight residual 103.20 92.83 10.37 1.50e+00 4.44e-01 4.78e+01 angle pdb=" C LYS B 147 " pdb=" N ASP B 148 " pdb=" CA ASP B 148 " ideal model delta sigma weight residual 121.54 132.39 -10.85 1.91e+00 2.74e-01 3.22e+01 angle pdb=" C GLN B 62 " pdb=" N ASN B 63 " pdb=" CA ASN B 63 " ideal model delta sigma weight residual 122.46 129.32 -6.86 1.41e+00 5.03e-01 2.36e+01 angle pdb=" N VAL B 44 " pdb=" CA VAL B 44 " pdb=" C VAL B 44 " ideal model delta sigma weight residual 106.21 111.38 -5.17 1.07e+00 8.73e-01 2.33e+01 ... (remaining 13714 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.10: 5387 17.10 - 34.20: 445 34.20 - 51.29: 96 51.29 - 68.39: 15 68.39 - 85.49: 10 Dihedral angle restraints: 5953 sinusoidal: 2320 harmonic: 3633 Sorted by residual: dihedral pdb=" CA GLN B 533 " pdb=" C GLN B 533 " pdb=" N PRO B 534 " pdb=" CA PRO B 534 " ideal model delta harmonic sigma weight residual 180.00 156.06 23.94 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA ARG A 454 " pdb=" C ARG A 454 " pdb=" N LEU A 455 " pdb=" CA LEU A 455 " ideal model delta harmonic sigma weight residual 180.00 157.35 22.65 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA PHE B 550 " pdb=" C PHE B 550 " pdb=" N VAL B 551 " pdb=" CA VAL B 551 " ideal model delta harmonic sigma weight residual 180.00 157.86 22.14 0 5.00e+00 4.00e-02 1.96e+01 ... (remaining 5950 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 1266 0.085 - 0.171: 198 0.171 - 0.256: 24 0.256 - 0.341: 0 0.341 - 0.427: 1 Chirality restraints: 1489 Sorted by residual: chirality pdb=" CB ILE B 403 " pdb=" CA ILE B 403 " pdb=" CG1 ILE B 403 " pdb=" CG2 ILE B 403 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.43 2.00e-01 2.50e+01 4.55e+00 chirality pdb=" CB ILE A 551 " pdb=" CA ILE A 551 " pdb=" CG1 ILE A 551 " pdb=" CG2 ILE A 551 " both_signs ideal model delta sigma weight residual False 2.64 2.90 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CB ILE A 535 " pdb=" CA ILE A 535 " pdb=" CG1 ILE A 535 " pdb=" CG2 ILE A 535 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 1486 not shown) Planarity restraints: 1796 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 174 " -0.127 5.00e-02 4.00e+02 1.75e-01 4.90e+01 pdb=" N PRO A 175 " 0.302 5.00e-02 4.00e+02 pdb=" CA PRO A 175 " -0.091 5.00e-02 4.00e+02 pdb=" CD PRO A 175 " -0.084 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET A 213 " -0.017 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C MET A 213 " 0.058 2.00e-02 2.50e+03 pdb=" O MET A 213 " -0.022 2.00e-02 2.50e+03 pdb=" N SER A 214 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 551 " 0.014 2.00e-02 2.50e+03 2.83e-02 8.03e+00 pdb=" C ILE A 551 " -0.049 2.00e-02 2.50e+03 pdb=" O ILE A 551 " 0.019 2.00e-02 2.50e+03 pdb=" N ASN A 552 " 0.016 2.00e-02 2.50e+03 ... (remaining 1793 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2124 2.79 - 3.31: 8744 3.31 - 3.84: 16923 3.84 - 4.37: 19540 4.37 - 4.90: 34579 Nonbonded interactions: 81910 Sorted by model distance: nonbonded pdb=" O ALA A 82 " pdb=" OG1 THR A 558 " model vdw 2.257 3.040 nonbonded pdb=" OG SER B 324 " pdb=" O ASN B 369 " model vdw 2.291 3.040 nonbonded pdb=" OG1 THR A 598 " pdb=" O LEU A 601 " model vdw 2.296 3.040 nonbonded pdb=" OH TYR B 284 " pdb=" OE1 GLN B 353 " model vdw 2.298 3.040 nonbonded pdb=" OG1 THR B 478 " pdb=" O THR B 480 " model vdw 2.308 3.040 ... (remaining 81905 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: 4.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 9.400 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 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 : 0.005 0.156 10104 Z= 0.257 Angle : 1.048 17.481 13719 Z= 0.577 Chirality : 0.063 0.427 1489 Planarity : 0.008 0.175 1796 Dihedral : 13.627 85.490 3637 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.23), residues: 1238 helix: -2.85 (0.55), residues: 50 sheet: -0.41 (0.23), residues: 536 loop : -1.94 (0.23), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 141 TYR 0.034 0.003 TYR A 395 PHE 0.035 0.003 PHE B 216 TRP 0.036 0.002 TRP B 590 HIS 0.014 0.002 HIS A 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.26 (10103) covalent geometry : angle 1.04846 / 0.58 (13719) hydrogen bonds : bond 0.13204 / 8.49 ( 306) hydrogen bonds : angle 7.87148 / 5.33 ( 819) Misc. bond : bond 0.00105 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.343 Fit side-chains REVERT: A 113 ASP cc_start: 0.7168 (t70) cc_final: 0.6868 (t0) REVERT: B 369 ASN cc_start: 0.8108 (t0) cc_final: 0.7907 (t0) REVERT: B 429 HIS cc_start: 0.7729 (m-70) cc_final: 0.7399 (m170) REVERT: B 508 TRP cc_start: 0.7598 (m100) cc_final: 0.6735 (m100) REVERT: B 597 TRP cc_start: 0.8764 (p-90) cc_final: 0.7910 (p-90) REVERT: B 616 TRP cc_start: 0.8423 (m-10) cc_final: 0.8195 (m-10) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.0576 time to fit residues: 9.9091 Evaluate side-chains 71 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 0.0010 chunk 113 optimal weight: 0.4980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.0070 chunk 51 optimal weight: 1.9990 overall best weight: 0.4404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 133 ASN ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 ASN ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 571 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.151394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.115998 restraints weight = 13077.281| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.44 r_work: 0.3582 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3430 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10104 Z= 0.124 Angle : 0.580 6.822 13719 Z= 0.312 Chirality : 0.047 0.209 1489 Planarity : 0.004 0.075 1796 Dihedral : 5.235 20.622 1371 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 1.03 % Allowed : 7.32 % Favored : 91.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.23), residues: 1238 helix: -1.46 (0.69), residues: 50 sheet: -0.55 (0.22), residues: 548 loop : -1.71 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 132 TYR 0.020 0.001 TYR A 269 PHE 0.018 0.001 PHE A 311 TRP 0.013 0.001 TRP A 399 HIS 0.002 0.001 HIS B 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (10103) covalent geometry : angle 0.58038 / 0.31 (13719) hydrogen bonds : bond 0.03530 / 2.30 ( 306) hydrogen bonds : angle 6.65964 / 4.53 ( 819) Misc. bond : bond 0.00006 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 ASP cc_start: 0.7708 (t70) cc_final: 0.7330 (t0) REVERT: A 519 LEU cc_start: 0.8781 (mt) cc_final: 0.8578 (mp) REVERT: B 429 HIS cc_start: 0.8056 (m-70) cc_final: 0.7847 (m170) REVERT: B 508 TRP cc_start: 0.7693 (m100) cc_final: 0.6918 (m100) REVERT: B 597 TRP cc_start: 0.8808 (p-90) cc_final: 0.7923 (p-90) REVERT: B 616 TRP cc_start: 0.8578 (m-10) cc_final: 0.8120 (m-10) outliers start: 11 outliers final: 9 residues processed: 99 average time/residue: 0.0668 time to fit residues: 10.1646 Evaluate side-chains 86 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 169 HIS Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 420 ASN Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 603 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 21 optimal weight: 0.9980 chunk 108 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 12 optimal weight: 0.4980 chunk 76 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 105 optimal weight: 7.9990 chunk 78 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 571 ASN ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.136597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.099839 restraints weight = 14371.376| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.76 r_work: 0.3422 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 10104 Z= 0.211 Angle : 0.618 11.074 13719 Z= 0.326 Chirality : 0.048 0.231 1489 Planarity : 0.004 0.046 1796 Dihedral : 5.096 20.693 1371 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 1.69 % Allowed : 9.76 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.24), residues: 1238 helix: -1.16 (0.69), residues: 56 sheet: -0.79 (0.22), residues: 558 loop : -1.57 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 141 TYR 0.021 0.002 TYR A 269 PHE 0.018 0.002 PHE A 520 TRP 0.012 0.001 TRP A 399 HIS 0.002 0.001 HIS A 580 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.21 (10103) covalent geometry : angle 0.61754 / 0.33 (13719) hydrogen bonds : bond 0.03599 / 2.33 ( 306) hydrogen bonds : angle 6.55372 / 4.47 ( 819) Misc. bond : bond 0.00064 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.329 Fit side-chains REVERT: A 113 ASP cc_start: 0.7961 (t70) cc_final: 0.7646 (t0) REVERT: A 363 LEU cc_start: 0.8602 (tp) cc_final: 0.8198 (tt) REVERT: A 454 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.7270 (ttt-90) REVERT: A 495 TYR cc_start: 0.7718 (t80) cc_final: 0.7410 (t80) REVERT: B 340 TYR cc_start: 0.8470 (m-10) cc_final: 0.8265 (m-10) REVERT: B 476 GLN cc_start: 0.7736 (mm-40) cc_final: 0.6146 (pm20) REVERT: B 508 TRP cc_start: 0.7591 (m100) cc_final: 0.6528 (m100) REVERT: B 597 TRP cc_start: 0.8728 (p-90) cc_final: 0.7812 (p-90) REVERT: B 616 TRP cc_start: 0.8655 (m-10) cc_final: 0.8192 (m-10) outliers start: 18 outliers final: 12 residues processed: 93 average time/residue: 0.0730 time to fit residues: 11.0648 Evaluate side-chains 83 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 454 ARG Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 155 TYR Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 603 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 81 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 119 optimal weight: 9.9990 chunk 67 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 91 optimal weight: 0.1980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 ASN ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 GLN A 571 ASN ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.137307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.100995 restraints weight = 14333.556| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.72 r_work: 0.3440 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10104 Z= 0.154 Angle : 0.567 11.100 13719 Z= 0.299 Chirality : 0.047 0.211 1489 Planarity : 0.003 0.039 1796 Dihedral : 4.886 19.674 1371 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 2.06 % Allowed : 11.26 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.24), residues: 1238 helix: -1.07 (0.70), residues: 56 sheet: -0.79 (0.22), residues: 544 loop : -1.49 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 132 TYR 0.020 0.001 TYR A 269 PHE 0.017 0.001 PHE A 296 TRP 0.007 0.001 TRP A 399 HIS 0.003 0.001 HIS B 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (10103) covalent geometry : angle 0.56738 / 0.30 (13719) hydrogen bonds : bond 0.03185 / 2.06 ( 306) hydrogen bonds : angle 6.38957 / 4.36 ( 819) Misc. bond : bond 0.00033 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 ASP cc_start: 0.7952 (t70) cc_final: 0.7599 (t0) REVERT: A 297 ILE cc_start: 0.8795 (OUTLIER) cc_final: 0.8579 (mp) REVERT: A 304 GLU cc_start: 0.7949 (tm-30) cc_final: 0.7453 (tm-30) REVERT: A 460 ASP cc_start: 0.8494 (m-30) cc_final: 0.8078 (m-30) REVERT: A 495 TYR cc_start: 0.7784 (t80) cc_final: 0.7485 (t80) REVERT: B 44 VAL cc_start: 0.8064 (OUTLIER) cc_final: 0.7854 (m) REVERT: B 508 TRP cc_start: 0.7608 (m100) cc_final: 0.6600 (m100) REVERT: B 541 TRP cc_start: 0.8027 (p-90) cc_final: 0.7629 (p-90) outliers start: 22 outliers final: 16 residues processed: 95 average time/residue: 0.0675 time to fit residues: 10.2406 Evaluate side-chains 89 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 219 TYR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 420 ASN Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 155 TYR Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 327 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 6 optimal weight: 0.7980 chunk 99 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 100 optimal weight: 8.9990 chunk 89 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 80 optimal weight: 0.3980 chunk 121 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 51 optimal weight: 0.0370 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 322 GLN A 420 ASN A 571 ASN ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.137709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.100780 restraints weight = 14383.046| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.84 r_work: 0.3436 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10104 Z= 0.141 Angle : 0.554 9.332 13719 Z= 0.293 Chirality : 0.046 0.222 1489 Planarity : 0.003 0.039 1796 Dihedral : 4.742 19.394 1371 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 2.63 % Allowed : 11.82 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.24), residues: 1238 helix: -0.96 (0.72), residues: 56 sheet: -0.81 (0.22), residues: 544 loop : -1.40 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 132 TYR 0.021 0.001 TYR A 269 PHE 0.016 0.001 PHE A 296 TRP 0.007 0.001 TRP B 616 HIS 0.002 0.000 HIS B 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (10103) covalent geometry : angle 0.55414 / 0.29 (13719) hydrogen bonds : bond 0.03063 / 1.98 ( 306) hydrogen bonds : angle 6.26047 / 4.26 ( 819) Misc. bond : bond 0.00025 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 75 time to evaluate : 0.377 Fit side-chains REVERT: A 113 ASP cc_start: 0.7953 (t70) cc_final: 0.7577 (t0) REVERT: A 297 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8516 (mp) REVERT: A 495 TYR cc_start: 0.7763 (t80) cc_final: 0.7443 (t80) REVERT: B 44 VAL cc_start: 0.7935 (OUTLIER) cc_final: 0.7723 (m) REVERT: B 347 ASP cc_start: 0.7981 (m-30) cc_final: 0.7554 (m-30) REVERT: B 508 TRP cc_start: 0.7558 (m100) cc_final: 0.7086 (m100) REVERT: B 541 TRP cc_start: 0.7968 (p-90) cc_final: 0.7569 (p-90) REVERT: B 597 TRP cc_start: 0.8618 (p-90) cc_final: 0.7708 (p-90) outliers start: 28 outliers final: 22 residues processed: 95 average time/residue: 0.0659 time to fit residues: 10.1228 Evaluate side-chains 95 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 71 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 169 HIS Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 219 TYR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 420 ASN Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 155 TYR Chi-restraints excluded: chain B residue 213 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 107 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 102 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 54 optimal weight: 0.0060 chunk 67 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 120 optimal weight: 20.0000 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 ASN A 571 ASN ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 63 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 = 0.3968 r_free = 0.3968 target = 0.137017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.099966 restraints weight = 14380.534| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.85 r_work: 0.3428 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10104 Z= 0.151 Angle : 0.557 8.881 13719 Z= 0.294 Chirality : 0.046 0.235 1489 Planarity : 0.003 0.039 1796 Dihedral : 4.694 19.753 1371 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 3.10 % Allowed : 11.54 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.24), residues: 1238 helix: -0.97 (0.71), residues: 56 sheet: -0.89 (0.22), residues: 555 loop : -1.35 (0.25), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 132 TYR 0.024 0.001 TYR B 340 PHE 0.016 0.001 PHE A 296 TRP 0.009 0.001 TRP B 616 HIS 0.002 0.000 HIS A 580 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (10103) covalent geometry : angle 0.55678 / 0.29 (13719) hydrogen bonds : bond 0.03051 / 1.98 ( 306) hydrogen bonds : angle 6.20527 / 4.22 ( 819) Misc. bond : bond 0.00022 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 73 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: A 113 ASP cc_start: 0.7982 (t70) cc_final: 0.7708 (t70) REVERT: A 297 ILE cc_start: 0.8768 (OUTLIER) cc_final: 0.8537 (mp) REVERT: A 495 TYR cc_start: 0.7784 (t80) cc_final: 0.7460 (t80) REVERT: B 44 VAL cc_start: 0.7939 (OUTLIER) cc_final: 0.7624 (m) REVERT: B 45 PHE cc_start: 0.7271 (m-10) cc_final: 0.7044 (m-10) REVERT: B 476 GLN cc_start: 0.7907 (mm-40) cc_final: 0.6268 (pm20) REVERT: B 508 TRP cc_start: 0.7565 (m100) cc_final: 0.7077 (m100) REVERT: B 541 TRP cc_start: 0.7995 (p-90) cc_final: 0.7633 (p-90) REVERT: B 597 TRP cc_start: 0.8616 (p-90) cc_final: 0.7803 (p-90) REVERT: B 616 TRP cc_start: 0.8673 (m-10) cc_final: 0.8336 (m-10) outliers start: 33 outliers final: 23 residues processed: 96 average time/residue: 0.0622 time to fit residues: 10.0490 Evaluate side-chains 97 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 72 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 219 TYR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 420 ASN Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 155 TYR Chi-restraints excluded: chain B residue 213 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 116 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 105 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 ASN A 571 ASN ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 63 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 = 0.3733 r_free = 0.3733 target = 0.125941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.087873 restraints weight = 14691.628| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 3.07 r_work: 0.3133 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 10104 Z= 0.218 Angle : 0.606 10.255 13719 Z= 0.318 Chirality : 0.048 0.230 1489 Planarity : 0.004 0.038 1796 Dihedral : 4.854 20.214 1371 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 3.19 % Allowed : 12.20 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.24), residues: 1238 helix: -0.87 (0.72), residues: 55 sheet: -1.06 (0.22), residues: 556 loop : -1.35 (0.25), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 69 TYR 0.021 0.002 TYR A 269 PHE 0.020 0.001 PHE A 311 TRP 0.008 0.001 TRP A 187 HIS 0.003 0.001 HIS A 580 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.22 (10103) covalent geometry : angle 0.60632 / 0.32 (13719) hydrogen bonds : bond 0.03272 / 2.10 ( 306) hydrogen bonds : angle 6.36175 / 4.33 ( 819) Misc. bond : bond 0.00032 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 76 time to evaluate : 0.415 Fit side-chains REVERT: A 113 ASP cc_start: 0.8053 (t70) cc_final: 0.7763 (t70) REVERT: A 297 ILE cc_start: 0.8555 (OUTLIER) cc_final: 0.8328 (mp) REVERT: A 495 TYR cc_start: 0.7671 (t80) cc_final: 0.7333 (t80) REVERT: B 44 VAL cc_start: 0.7801 (OUTLIER) cc_final: 0.7511 (m) REVERT: B 45 PHE cc_start: 0.7184 (m-10) cc_final: 0.6952 (m-10) REVERT: B 309 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.8008 (mtm110) REVERT: B 340 TYR cc_start: 0.8468 (m-10) cc_final: 0.7978 (m-10) REVERT: B 347 ASP cc_start: 0.7860 (m-30) cc_final: 0.7331 (m-30) REVERT: B 419 ASP cc_start: 0.9066 (m-30) cc_final: 0.8818 (p0) REVERT: B 476 GLN cc_start: 0.8013 (mm-40) cc_final: 0.6396 (pm20) REVERT: B 508 TRP cc_start: 0.7192 (m100) cc_final: 0.6170 (m100) REVERT: B 541 TRP cc_start: 0.7793 (p-90) cc_final: 0.7397 (p-90) REVERT: B 597 TRP cc_start: 0.8476 (p-90) cc_final: 0.7568 (p-90) REVERT: B 616 TRP cc_start: 0.8594 (m-10) cc_final: 0.8233 (m-10) outliers start: 34 outliers final: 23 residues processed: 98 average time/residue: 0.0662 time to fit residues: 10.4287 Evaluate side-chains 98 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 72 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 219 TYR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 420 ASN Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 155 TYR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 309 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 12 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 110 optimal weight: 10.0000 chunk 11 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 113 optimal weight: 9.9990 chunk 68 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 72 optimal weight: 0.9980 chunk 70 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 ASN A 571 ASN ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 63 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 = 0.3752 r_free = 0.3752 target = 0.127367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.089621 restraints weight = 14524.784| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 3.06 r_work: 0.3164 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10104 Z= 0.152 Angle : 0.578 9.467 13719 Z= 0.302 Chirality : 0.047 0.221 1489 Planarity : 0.003 0.036 1796 Dihedral : 4.742 20.072 1371 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 2.91 % Allowed : 12.85 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.24), residues: 1238 helix: -1.07 (0.71), residues: 55 sheet: -1.04 (0.22), residues: 558 loop : -1.28 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 141 TYR 0.022 0.002 TYR A 636 PHE 0.019 0.001 PHE A 311 TRP 0.007 0.001 TRP B 590 HIS 0.006 0.001 HIS A 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (10103) covalent geometry : angle 0.57836 / 0.30 (13719) hydrogen bonds : bond 0.03059 / 1.96 ( 306) hydrogen bonds : angle 6.20708 / 4.24 ( 819) Misc. bond : bond 0.00023 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 73 time to evaluate : 0.371 Fit side-chains REVERT: A 113 ASP cc_start: 0.8048 (t70) cc_final: 0.7715 (t70) REVERT: A 297 ILE cc_start: 0.8557 (OUTLIER) cc_final: 0.8321 (mp) REVERT: A 495 TYR cc_start: 0.7597 (t80) cc_final: 0.7237 (t80) REVERT: A 636 TYR cc_start: 0.6940 (t80) cc_final: 0.6678 (t80) REVERT: B 44 VAL cc_start: 0.7722 (OUTLIER) cc_final: 0.7416 (m) REVERT: B 45 PHE cc_start: 0.7164 (m-10) cc_final: 0.6932 (m-10) REVERT: B 340 TYR cc_start: 0.8410 (m-10) cc_final: 0.7843 (m-10) REVERT: B 374 SER cc_start: 0.8478 (t) cc_final: 0.8245 (p) REVERT: B 476 GLN cc_start: 0.7986 (mm-40) cc_final: 0.6359 (pm20) REVERT: B 508 TRP cc_start: 0.7146 (m100) cc_final: 0.6063 (m100) REVERT: B 597 TRP cc_start: 0.8457 (p-90) cc_final: 0.7535 (p-90) REVERT: B 616 TRP cc_start: 0.8547 (m-10) cc_final: 0.8222 (m-10) outliers start: 31 outliers final: 25 residues processed: 96 average time/residue: 0.0664 time to fit residues: 10.1349 Evaluate side-chains 98 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 71 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 169 HIS Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 219 TYR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 420 ASN Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 155 TYR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 274 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 44 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 73 optimal weight: 0.0980 chunk 76 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 105 optimal weight: 8.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 ASN A 571 ASN ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 63 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 = 0.3734 r_free = 0.3734 target = 0.125951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.088067 restraints weight = 14560.790| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 3.07 r_work: 0.3118 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10104 Z= 0.191 Angle : 0.593 9.597 13719 Z= 0.310 Chirality : 0.047 0.216 1489 Planarity : 0.003 0.037 1796 Dihedral : 4.780 20.850 1371 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 3.10 % Allowed : 13.04 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.92 (0.24), residues: 1238 helix: -1.05 (0.71), residues: 55 sheet: -1.18 (0.22), residues: 551 loop : -1.28 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 132 TYR 0.020 0.002 TYR A 269 PHE 0.018 0.001 PHE A 311 TRP 0.007 0.001 TRP B 590 HIS 0.004 0.001 HIS A 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.19 (10103) covalent geometry : angle 0.59324 / 0.31 (13719) hydrogen bonds : bond 0.03170 / 2.03 ( 306) hydrogen bonds : angle 6.27966 / 4.28 ( 819) Misc. bond : bond 0.00028 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 73 time to evaluate : 0.396 Fit side-chains revert: symmetry clash REVERT: A 113 ASP cc_start: 0.8070 (t70) cc_final: 0.7744 (t70) REVERT: A 297 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.8320 (mp) REVERT: A 495 TYR cc_start: 0.7685 (t80) cc_final: 0.7341 (t80) REVERT: A 636 TYR cc_start: 0.7082 (t80) cc_final: 0.6848 (t80) REVERT: B 44 VAL cc_start: 0.7713 (OUTLIER) cc_final: 0.7409 (m) REVERT: B 45 PHE cc_start: 0.7187 (m-10) cc_final: 0.6963 (m-10) REVERT: B 340 TYR cc_start: 0.8424 (m-10) cc_final: 0.7778 (m-10) REVERT: B 374 SER cc_start: 0.8507 (t) cc_final: 0.8258 (p) REVERT: B 508 TRP cc_start: 0.7175 (m100) cc_final: 0.6155 (m100) REVERT: B 597 TRP cc_start: 0.8487 (p-90) cc_final: 0.7558 (p-90) REVERT: B 616 TRP cc_start: 0.8574 (m-10) cc_final: 0.8239 (m-10) outliers start: 33 outliers final: 23 residues processed: 95 average time/residue: 0.0686 time to fit residues: 10.6608 Evaluate side-chains 96 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 71 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 219 TYR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 155 TYR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 274 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 28 optimal weight: 4.9990 chunk 62 optimal weight: 0.3980 chunk 94 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 88 optimal weight: 0.9990 chunk 71 optimal weight: 0.1980 chunk 66 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 118 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 ASN A 571 ASN ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 63 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 = 0.3766 r_free = 0.3766 target = 0.128606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.091070 restraints weight = 14367.366| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 3.05 r_work: 0.3181 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10104 Z= 0.126 Angle : 0.564 9.866 13719 Z= 0.294 Chirality : 0.047 0.216 1489 Planarity : 0.003 0.037 1796 Dihedral : 4.628 21.875 1371 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 2.44 % Allowed : 13.88 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.24), residues: 1238 helix: -1.07 (0.71), residues: 56 sheet: -1.08 (0.22), residues: 554 loop : -1.19 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 454 TYR 0.021 0.001 TYR A 269 PHE 0.018 0.001 PHE A 311 TRP 0.008 0.001 TRP B 590 HIS 0.003 0.001 HIS A 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (10103) covalent geometry : angle 0.56412 / 0.29 (13719) hydrogen bonds : bond 0.02916 / 1.88 ( 306) hydrogen bonds : angle 6.06741 / 4.13 ( 819) Misc. bond : bond 0.00015 / 0.01 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 78 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: A 113 ASP cc_start: 0.8058 (t70) cc_final: 0.7692 (t70) REVERT: A 297 ILE cc_start: 0.8505 (OUTLIER) cc_final: 0.8257 (mp) REVERT: A 495 TYR cc_start: 0.7564 (t80) cc_final: 0.7181 (t80) REVERT: A 636 TYR cc_start: 0.7041 (t80) cc_final: 0.6801 (t80) REVERT: B 45 PHE cc_start: 0.7162 (m-10) cc_final: 0.6928 (m-10) REVERT: B 326 GLN cc_start: 0.7771 (mm110) cc_final: 0.7228 (mm-40) REVERT: B 340 TYR cc_start: 0.8336 (m-10) cc_final: 0.7783 (m-10) REVERT: B 508 TRP cc_start: 0.7123 (m100) cc_final: 0.6040 (m100) REVERT: B 597 TRP cc_start: 0.8476 (p-90) cc_final: 0.7548 (p-90) REVERT: B 616 TRP cc_start: 0.8616 (m-10) cc_final: 0.8232 (m-10) outliers start: 26 outliers final: 22 residues processed: 97 average time/residue: 0.0639 time to fit residues: 10.1373 Evaluate side-chains 94 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 71 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 219 TYR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 155 TYR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 274 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 88 optimal weight: 0.3980 chunk 71 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 96 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 ASN A 571 ASN ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 63 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 = 0.3758 r_free = 0.3758 target = 0.127783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.090004 restraints weight = 14575.701| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 3.07 r_work: 0.3164 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10104 Z= 0.147 Angle : 0.573 9.597 13719 Z= 0.300 Chirality : 0.047 0.211 1489 Planarity : 0.003 0.037 1796 Dihedral : 4.630 23.533 1371 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 2.53 % Allowed : 14.17 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.24), residues: 1238 helix: -0.49 (0.78), residues: 49 sheet: -1.13 (0.22), residues: 559 loop : -1.19 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 132 TYR 0.021 0.001 TYR A 269 PHE 0.021 0.001 PHE A 311 TRP 0.008 0.001 TRP B 590 HIS 0.002 0.001 HIS A 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 (10103) covalent geometry : angle 0.57307 / 0.30 (13719) hydrogen bonds : bond 0.02984 / 1.91 ( 306) hydrogen bonds : angle 6.06840 / 4.13 ( 819) Misc. bond : bond 0.00016 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2015.00 seconds wall clock time: 35 minutes 29.71 seconds (2129.71 seconds total)