Starting phenix.real_space_refine on Fri Jul 3 04:45:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e6i_47566/07_2026/9e6i_47566.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e6i_47566/07_2026/9e6i_47566.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9e6i_47566/07_2026/9e6i_47566.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e6i_47566/07_2026/9e6i_47566.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9e6i_47566/07_2026/9e6i_47566.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e6i_47566/07_2026/9e6i_47566.map" } resolution = 3.2 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 24 atoms to isotropic. 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 43 5.16 5 C 7986 2.51 5 N 1931 2.21 5 O 2120 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 178 residue(s): 0.02s 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: 12080 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5979 Classifications: {'peptide': 728} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 691} Chain: "B" Number of atoms: 5970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 727, 5970 Classifications: {'peptide': 727} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 690} Chain: "C" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 102 Classifications: {'peptide': 16} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 14} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'NNM': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'NNM:plan-6': 1, 'NNM:plan-7': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 2.72, per 1000 atoms: 0.23 Number of scatterers: 12080 At special positions: 0 Unit cell: (105.984, 109.296, 131.652, 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 43 16.00 O 2120 8.00 N 1931 7.00 C 7986 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: 0.87 Conformation dependent library (CDL) restraints added in 526.0 milliseconds 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2802 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 4 sheets defined 55.3% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 37 through 42 Processing helix chain 'A' and resid 48 through 69 removed outlier: 3.720A pdb=" N TYR A 52 " --> pdb=" O PRO A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 94 removed outlier: 4.017A pdb=" N LYS A 86 " --> pdb=" O VAL A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 116 Processing helix chain 'A' and resid 137 through 163 removed outlier: 3.916A pdb=" N VAL A 153 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Proline residue: A 154 - end of helix Processing helix chain 'A' and resid 166 through 179 removed outlier: 3.802A pdb=" N VAL A 177 " --> pdb=" O ALA A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 189 removed outlier: 3.767A pdb=" N LEU A 189 " --> pdb=" O THR A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 217 Processing helix chain 'A' and resid 220 through 241 Processing helix chain 'A' and resid 244 through 264 Processing helix chain 'A' and resid 265 through 268 Processing helix chain 'A' and resid 270 through 286 Processing helix chain 'A' and resid 286 through 304 removed outlier: 3.604A pdb=" N PHE A 297 " --> pdb=" O TYR A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 314 Processing helix chain 'A' and resid 315 through 320 Processing helix chain 'A' and resid 325 through 331 removed outlier: 3.510A pdb=" N ASP A 330 " --> pdb=" O PRO A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 383 No H-bonds generated for 'chain 'A' and resid 381 through 383' Processing helix chain 'A' and resid 440 through 444 Processing helix chain 'A' and resid 447 through 451 Processing helix chain 'A' and resid 459 through 463 Processing helix chain 'A' and resid 494 through 498 Processing helix chain 'A' and resid 511 through 514 Processing helix chain 'A' and resid 525 through 530 removed outlier: 3.664A pdb=" N VAL A 530 " --> pdb=" O GLU A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 558 Processing helix chain 'A' and resid 568 through 572 Processing helix chain 'A' and resid 596 through 623 Processing helix chain 'A' and resid 629 through 638 Processing helix chain 'A' and resid 638 through 652 Processing helix chain 'A' and resid 653 through 657 Processing helix chain 'A' and resid 662 through 665 Processing helix chain 'A' and resid 666 through 685 removed outlier: 3.549A pdb=" N LEU A 675 " --> pdb=" O LEU A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 739 Proline residue: A 735 - end of helix Processing helix chain 'A' and resid 744 through 750 Processing helix chain 'B' and resid 37 through 42 Processing helix chain 'B' and resid 48 through 69 removed outlier: 3.720A pdb=" N TYR B 52 " --> pdb=" O PRO B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 94 removed outlier: 4.016A pdb=" N LYS B 86 " --> pdb=" O VAL B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 116 Processing helix chain 'B' and resid 137 through 163 removed outlier: 3.916A pdb=" N VAL B 153 " --> pdb=" O GLY B 149 " (cutoff:3.500A) Proline residue: B 154 - end of helix Processing helix chain 'B' and resid 166 through 179 removed outlier: 3.801A pdb=" N VAL B 177 " --> pdb=" O ALA B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 189 removed outlier: 3.766A pdb=" N LEU B 189 " --> pdb=" O THR B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 217 Processing helix chain 'B' and resid 220 through 241 Processing helix chain 'B' and resid 244 through 264 Processing helix chain 'B' and resid 265 through 268 Processing helix chain 'B' and resid 270 through 286 Processing helix chain 'B' and resid 286 through 304 removed outlier: 3.606A pdb=" N PHE B 297 " --> pdb=" O TYR B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 314 Processing helix chain 'B' and resid 315 through 320 Processing helix chain 'B' and resid 381 through 383 No H-bonds generated for 'chain 'B' and resid 381 through 383' Processing helix chain 'B' and resid 440 through 444 Processing helix chain 'B' and resid 447 through 451 Processing helix chain 'B' and resid 459 through 463 Processing helix chain 'B' and resid 494 through 498 Processing helix chain 'B' and resid 511 through 514 Processing helix chain 'B' and resid 525 through 530 removed outlier: 3.611A pdb=" N VAL B 530 " --> pdb=" O GLU B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 558 Processing helix chain 'B' and resid 568 through 572 Processing helix chain 'B' and resid 596 through 623 Processing helix chain 'B' and resid 629 through 638 Processing helix chain 'B' and resid 638 through 652 Processing helix chain 'B' and resid 653 through 657 Processing helix chain 'B' and resid 662 through 665 Processing helix chain 'B' and resid 666 through 685 removed outlier: 3.549A pdb=" N LEU B 675 " --> pdb=" O LEU B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 739 Proline residue: B 735 - end of helix Processing helix chain 'B' and resid 744 through 750 Processing sheet with id=AA1, first strand: chain 'A' and resid 339 through 344 removed outlier: 13.271A pdb=" N ILE A 340 " --> pdb=" O SER A 353 " (cutoff:3.500A) removed outlier: 9.966A pdb=" N SER A 353 " --> pdb=" O ILE A 340 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ILE A 342 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N HIS A 354 " --> pdb=" O GLN A 373 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLN A 373 " --> pdb=" O HIS A 354 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 372 through 377 current: chain 'A' and resid 407 through 412 removed outlier: 13.285A pdb=" N ILE A 408 " --> pdb=" O ALA A 421 " (cutoff:3.500A) removed outlier: 10.047A pdb=" N ALA A 421 " --> pdb=" O ILE A 408 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N LEU A 410 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR A 417 " --> pdb=" O HIS A 412 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LEU A 420 " --> pdb=" O VAL A 438 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL A 438 " --> pdb=" O LEU A 420 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N HIS A 422 " --> pdb=" O THR A 436 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N THR A 436 " --> pdb=" O HIS A 422 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N VAL A 424 " --> pdb=" O GLU A 434 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 433 through 439 current: chain 'A' and resid 473 through 478 removed outlier: 13.817A pdb=" N PHE A 474 " --> pdb=" O THR A 487 " (cutoff:3.500A) removed outlier: 10.442A pdb=" N THR A 487 " --> pdb=" O PHE A 474 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N LEU A 476 " --> pdb=" O LEU A 485 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 579 through 584 removed outlier: 6.362A pdb=" N ILE A 591 " --> pdb=" O PHE A 581 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N THR A 583 " --> pdb=" O LYS A 589 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LYS A 589 " --> pdb=" O THR A 583 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 339 through 344 removed outlier: 13.270A pdb=" N ILE B 340 " --> pdb=" O SER B 353 " (cutoff:3.500A) removed outlier: 9.966A pdb=" N SER B 353 " --> pdb=" O ILE B 340 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N ILE B 342 " --> pdb=" O LEU B 351 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N HIS B 354 " --> pdb=" O GLN B 373 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLN B 373 " --> pdb=" O HIS B 354 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 372 through 377 current: chain 'B' and resid 407 through 412 removed outlier: 13.287A pdb=" N ILE B 408 " --> pdb=" O ALA B 421 " (cutoff:3.500A) removed outlier: 10.049A pdb=" N ALA B 421 " --> pdb=" O ILE B 408 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N LEU B 410 " --> pdb=" O LEU B 419 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR B 417 " --> pdb=" O HIS B 412 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N LEU B 420 " --> pdb=" O VAL B 438 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL B 438 " --> pdb=" O LEU B 420 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N HIS B 422 " --> pdb=" O THR B 436 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N THR B 436 " --> pdb=" O HIS B 422 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N VAL B 424 " --> pdb=" O GLU B 434 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 433 through 439 current: chain 'B' and resid 473 through 478 removed outlier: 13.815A pdb=" N PHE B 474 " --> pdb=" O THR B 487 " (cutoff:3.500A) removed outlier: 10.438A pdb=" N THR B 487 " --> pdb=" O PHE B 474 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N LEU B 476 " --> pdb=" O LEU B 485 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 579 through 584 removed outlier: 6.362A pdb=" N ILE B 591 " --> pdb=" O PHE B 581 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N THR B 583 " --> pdb=" O LYS B 589 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LYS B 589 " --> pdb=" O THR B 583 " (cutoff:3.500A) 576 hydrogen bonds defined for protein. 1620 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: 1.47 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2417 1.33 - 1.45: 3316 1.45 - 1.58: 6689 1.58 - 1.70: 0 1.70 - 1.82: 65 Bond restraints: 12487 Sorted by residual: bond pdb=" CE1 HIS A 563 " pdb=" NE2 HIS A 563 " ideal model delta sigma weight residual 1.321 1.361 -0.040 1.00e-02 1.00e+04 1.57e+01 bond pdb=" CZ ARG A 409 " pdb=" NH2 ARG A 409 " ideal model delta sigma weight residual 1.330 1.286 0.044 1.30e-02 5.92e+03 1.15e+01 bond pdb=" CZ ARG A 633 " pdb=" NH1 ARG A 633 " ideal model delta sigma weight residual 1.323 1.278 0.045 1.40e-02 5.10e+03 1.03e+01 bond pdb=" CZ ARG B 409 " pdb=" NH2 ARG B 409 " ideal model delta sigma weight residual 1.330 1.288 0.042 1.30e-02 5.92e+03 1.02e+01 bond pdb=" CZ ARG B 528 " pdb=" NH2 ARG B 528 " ideal model delta sigma weight residual 1.330 1.288 0.042 1.30e-02 5.92e+03 1.02e+01 ... (remaining 12482 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 12707 1.77 - 3.55: 3771 3.55 - 5.32: 504 5.32 - 7.09: 30 7.09 - 8.86: 6 Bond angle restraints: 17018 Sorted by residual: angle pdb=" OD1 ASN B 629 " pdb=" CG ASN B 629 " pdb=" ND2 ASN B 629 " ideal model delta sigma weight residual 122.60 116.58 6.02 1.00e+00 1.00e+00 3.63e+01 angle pdb=" OD1 ASN A 629 " pdb=" CG ASN A 629 " pdb=" ND2 ASN A 629 " ideal model delta sigma weight residual 122.60 116.67 5.93 1.00e+00 1.00e+00 3.52e+01 angle pdb=" OE1 GLN B 373 " pdb=" CD GLN B 373 " pdb=" NE2 GLN B 373 " ideal model delta sigma weight residual 122.60 116.97 5.63 1.00e+00 1.00e+00 3.16e+01 angle pdb=" OE1 GLN A 373 " pdb=" CD GLN A 373 " pdb=" NE2 GLN A 373 " ideal model delta sigma weight residual 122.60 117.00 5.60 1.00e+00 1.00e+00 3.13e+01 angle pdb=" OE1 GLN A 660 " pdb=" CD GLN A 660 " pdb=" NE2 GLN A 660 " ideal model delta sigma weight residual 122.60 117.27 5.33 1.00e+00 1.00e+00 2.85e+01 ... (remaining 17013 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.97: 6882 21.97 - 43.94: 227 43.94 - 65.92: 39 65.92 - 87.89: 9 87.89 - 109.86: 3 Dihedral angle restraints: 7160 sinusoidal: 2814 harmonic: 4346 Sorted by residual: dihedral pdb=" CA PRO B 135 " pdb=" C PRO B 135 " pdb=" N ALA B 136 " pdb=" CA ALA B 136 " ideal model delta harmonic sigma weight residual 180.00 159.28 20.72 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA PRO A 135 " pdb=" C PRO A 135 " pdb=" N ALA A 136 " pdb=" CA ALA A 136 " ideal model delta harmonic sigma weight residual 180.00 159.33 20.67 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA PRO A 102 " pdb=" C PRO A 102 " pdb=" N PRO A 103 " pdb=" CA PRO A 103 " ideal model delta harmonic sigma weight residual -180.00 -159.63 -20.37 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 7157 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1085 0.067 - 0.134: 543 0.134 - 0.201: 161 0.201 - 0.269: 38 0.269 - 0.336: 5 Chirality restraints: 1832 Sorted by residual: chirality pdb=" CA ASN A 164 " pdb=" N ASN A 164 " pdb=" C ASN A 164 " pdb=" CB ASN A 164 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" CA THR B 187 " pdb=" N THR B 187 " pdb=" C THR B 187 " pdb=" CB THR B 187 " both_signs ideal model delta sigma weight residual False 2.53 2.20 0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" CA ASN B 164 " pdb=" N ASN B 164 " pdb=" C ASN B 164 " pdb=" CB ASN B 164 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.60e+00 ... (remaining 1829 not shown) Planarity restraints: 2124 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 242 " 0.081 2.00e-02 2.50e+03 5.41e-02 5.86e+01 pdb=" CG TYR B 242 " -0.002 2.00e-02 2.50e+03 pdb=" CD1 TYR B 242 " -0.046 2.00e-02 2.50e+03 pdb=" CD2 TYR B 242 " -0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR B 242 " -0.035 2.00e-02 2.50e+03 pdb=" CE2 TYR B 242 " -0.048 2.00e-02 2.50e+03 pdb=" CZ TYR B 242 " -0.024 2.00e-02 2.50e+03 pdb=" OH TYR B 242 " 0.100 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 242 " -0.081 2.00e-02 2.50e+03 5.40e-02 5.84e+01 pdb=" CG TYR A 242 " 0.003 2.00e-02 2.50e+03 pdb=" CD1 TYR A 242 " 0.045 2.00e-02 2.50e+03 pdb=" CD2 TYR A 242 " 0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR A 242 " 0.036 2.00e-02 2.50e+03 pdb=" CE2 TYR A 242 " 0.048 2.00e-02 2.50e+03 pdb=" CZ TYR A 242 " 0.024 2.00e-02 2.50e+03 pdb=" OH TYR A 242 " -0.100 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 40 " -0.070 2.00e-02 2.50e+03 4.39e-02 4.82e+01 pdb=" CG TRP A 40 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP A 40 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP A 40 " 0.063 2.00e-02 2.50e+03 pdb=" NE1 TRP A 40 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 TRP A 40 " 0.034 2.00e-02 2.50e+03 pdb=" CE3 TRP A 40 " 0.056 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 40 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 40 " -0.026 2.00e-02 2.50e+03 pdb=" CH2 TRP A 40 " -0.063 2.00e-02 2.50e+03 ... (remaining 2121 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.37: 3 2.37 - 3.00: 5949 3.00 - 3.63: 18511 3.63 - 4.27: 29639 4.27 - 4.90: 49814 Nonbonded interactions: 103916 Sorted by model distance: nonbonded pdb=" CD2 LEU A 656 " pdb=" CD2 LEU B 656 " model vdw 1.734 3.880 nonbonded pdb=" O SER C 8 " pdb=" OG SER C 9 " model vdw 2.237 3.040 nonbonded pdb=" CD1 LEU B 404 " pdb=" OD2 ASP B 462 " model vdw 2.246 3.460 nonbonded pdb=" OD1 ASN A 759 " pdb=" OG1 THR C 7 " model vdw 2.386 3.040 nonbonded pdb=" O LEU C 16 " pdb=" C LYS C 17 " model vdw 2.413 3.270 ... (remaining 103911 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 36 through 762) selection = chain 'B' } 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: 0.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 10.640 Find NCS groups from input model: 0.180 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: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 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 : 0.013 0.045 12487 Z= 0.743 Angle : 1.607 8.863 17018 Z= 1.088 Chirality : 0.085 0.336 1832 Planarity : 0.014 0.145 2124 Dihedral : 12.010 109.858 4358 Min Nonbonded Distance : 1.734 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.14 % Favored : 96.66 % Rotamer: Outliers : 0.15 % Allowed : 1.07 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: 0.29 (0.20), residues: 1465 helix: 0.39 (0.18), residues: 717 sheet: -1.06 (0.53), residues: 84 loop : 0.37 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.002 ARG A 409 TYR 0.100 0.016 TYR B 242 PHE 0.052 0.011 PHE A 455 TRP 0.081 0.017 TRP A 486 HIS 0.019 0.007 HIS A 478 Details of bonding type rmsd/Z covalent geometry : bond 0.01310 / 0.74 (12487) covalent geometry : angle 1.60731 / 1.09 (17018) hydrogen bonds : bond 0.15652 / 9.94 ( 576) hydrogen bonds : angle 6.35198 / 4.56 ( 1620) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 135 time to evaluate : 0.461 Fit side-chains revert: symmetry clash REVERT: A 69 TYR cc_start: 0.8075 (t80) cc_final: 0.7841 (t80) REVERT: A 156 MET cc_start: 0.7659 (mmm) cc_final: 0.7177 (mmm) REVERT: A 204 MET cc_start: 0.8265 (mmt) cc_final: 0.7993 (mmt) REVERT: A 248 TYR cc_start: 0.7793 (m-80) cc_final: 0.6671 (m-80) REVERT: A 716 THR cc_start: 0.8572 (m) cc_final: 0.8307 (p) REVERT: B 188 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7883 (ptm160) REVERT: B 204 MET cc_start: 0.8522 (mmt) cc_final: 0.8072 (mmt) REVERT: B 275 MET cc_start: 0.8441 (mmm) cc_final: 0.8233 (mmm) REVERT: B 459 LYS cc_start: 0.7106 (mmtt) cc_final: 0.6863 (mmmt) outliers start: 2 outliers final: 1 residues processed: 137 average time/residue: 0.0821 time to fit residues: 17.4481 Evaluate side-chains 77 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 75 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain C residue 11 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 345 GLN A 354 HIS B 456 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.120379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.103588 restraints weight = 22325.517| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.45 r_work: 0.3325 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12487 Z= 0.151 Angle : 0.528 5.952 17018 Z= 0.281 Chirality : 0.044 0.191 1832 Planarity : 0.004 0.032 2124 Dihedral : 6.066 85.016 1619 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.54 % Allowed : 3.75 % Favored : 95.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: 1.58 (0.22), residues: 1465 helix: 1.84 (0.19), residues: 721 sheet: -0.95 (0.52), residues: 98 loop : 0.62 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 188 TYR 0.018 0.002 TYR B 118 PHE 0.012 0.002 PHE A 642 TRP 0.018 0.001 TRP B 223 HIS 0.007 0.001 HIS B 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (12487) covalent geometry : angle 0.52846 / 0.28 (17018) hydrogen bonds : bond 0.05154 / 3.24 ( 576) hydrogen bonds : angle 4.41036 / 3.15 ( 1620) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: A 248 TYR cc_start: 0.8547 (m-80) cc_final: 0.7787 (m-80) REVERT: A 552 MET cc_start: 0.8773 (mtt) cc_final: 0.8551 (mtt) REVERT: A 716 THR cc_start: 0.9048 (m) cc_final: 0.8810 (p) REVERT: B 275 MET cc_start: 0.8853 (mmm) cc_final: 0.8504 (mmm) REVERT: B 459 LYS cc_start: 0.7393 (mmtt) cc_final: 0.7130 (mmmt) outliers start: 7 outliers final: 3 residues processed: 88 average time/residue: 0.0719 time to fit residues: 10.1956 Evaluate side-chains 70 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 67 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 422 HIS Chi-restraints excluded: chain A residue 431 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 56 optimal weight: 0.9990 chunk 17 optimal weight: 7.9990 chunk 25 optimal weight: 8.9990 chunk 69 optimal weight: 8.9990 chunk 4 optimal weight: 0.7980 chunk 101 optimal weight: 10.0000 chunk 74 optimal weight: 0.9990 chunk 95 optimal weight: 8.9990 chunk 103 optimal weight: 20.0000 chunk 47 optimal weight: 10.0000 chunk 92 optimal weight: 0.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 664 HIS A 759 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.117293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.100400 restraints weight = 22541.410| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.48 r_work: 0.3275 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12487 Z= 0.142 Angle : 0.490 5.606 17018 Z= 0.258 Chirality : 0.043 0.259 1832 Planarity : 0.004 0.034 2124 Dihedral : 5.181 61.123 1614 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.61 % Allowed : 4.43 % Favored : 94.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: 1.56 (0.22), residues: 1465 helix: 1.83 (0.19), residues: 727 sheet: -0.98 (0.56), residues: 87 loop : 0.54 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 67 TYR 0.014 0.001 TYR A 207 PHE 0.013 0.001 PHE A 642 TRP 0.024 0.001 TRP B 223 HIS 0.006 0.001 HIS B 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 (12487) covalent geometry : angle 0.48995 / 0.26 (17018) hydrogen bonds : bond 0.04877 / 3.07 ( 576) hydrogen bonds : angle 4.19696 / 2.97 ( 1620) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: A 248 TYR cc_start: 0.8577 (m-80) cc_final: 0.7713 (m-80) REVERT: A 339 ILE cc_start: 0.7907 (mt) cc_final: 0.7631 (mm) REVERT: A 449 PRO cc_start: 0.7502 (Cg_exo) cc_final: 0.7296 (Cg_endo) REVERT: A 716 THR cc_start: 0.9163 (m) cc_final: 0.8900 (p) REVERT: B 459 LYS cc_start: 0.7471 (mmtt) cc_final: 0.7166 (mmmt) outliers start: 8 outliers final: 5 residues processed: 82 average time/residue: 0.0804 time to fit residues: 10.7333 Evaluate side-chains 68 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 422 HIS Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 329 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 124 optimal weight: 20.0000 chunk 41 optimal weight: 10.0000 chunk 89 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 120 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 134 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 81 optimal weight: 10.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.115395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.098653 restraints weight = 22450.360| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.46 r_work: 0.3248 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12487 Z= 0.155 Angle : 0.490 8.607 17018 Z= 0.255 Chirality : 0.043 0.215 1832 Planarity : 0.004 0.035 2124 Dihedral : 5.098 53.281 1614 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.69 % Allowed : 4.89 % Favored : 94.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: 1.38 (0.22), residues: 1465 helix: 1.73 (0.19), residues: 729 sheet: -1.15 (0.51), residues: 98 loop : 0.44 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 67 TYR 0.013 0.001 TYR A 207 PHE 0.019 0.001 PHE A 172 TRP 0.019 0.001 TRP B 223 HIS 0.006 0.001 HIS B 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.15 (12487) covalent geometry : angle 0.49025 / 0.26 (17018) hydrogen bonds : bond 0.04758 / 3.00 ( 576) hydrogen bonds : angle 4.15919 / 2.93 ( 1620) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.459 Fit side-chains revert: symmetry clash REVERT: A 203 THR cc_start: 0.9222 (m) cc_final: 0.8970 (m) REVERT: A 248 TYR cc_start: 0.8649 (m-80) cc_final: 0.7735 (m-80) REVERT: A 339 ILE cc_start: 0.7883 (mt) cc_final: 0.7608 (mm) REVERT: A 467 LEU cc_start: 0.8122 (tp) cc_final: 0.7906 (tp) REVERT: A 613 ILE cc_start: 0.8757 (OUTLIER) cc_final: 0.8500 (mp) REVERT: A 716 THR cc_start: 0.9264 (m) cc_final: 0.8978 (p) REVERT: B 459 LYS cc_start: 0.7543 (mmtt) cc_final: 0.7214 (mmmt) outliers start: 9 outliers final: 7 residues processed: 81 average time/residue: 0.0723 time to fit residues: 9.8811 Evaluate side-chains 72 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 422 HIS Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 530 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 88 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 79 optimal weight: 10.0000 chunk 81 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 22 optimal weight: 0.5980 chunk 125 optimal weight: 10.0000 chunk 133 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 89 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.117727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.101086 restraints weight = 22566.273| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.49 r_work: 0.3279 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12487 Z= 0.106 Angle : 0.439 6.094 17018 Z= 0.228 Chirality : 0.041 0.158 1832 Planarity : 0.004 0.035 2124 Dihedral : 4.835 59.422 1614 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.46 % Allowed : 5.96 % Favored : 93.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: 1.58 (0.22), residues: 1465 helix: 1.96 (0.19), residues: 728 sheet: -1.18 (0.50), residues: 98 loop : 0.46 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 188 TYR 0.012 0.001 TYR A 207 PHE 0.009 0.001 PHE A 124 TRP 0.017 0.001 TRP B 223 HIS 0.005 0.001 HIS B 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (12487) covalent geometry : angle 0.43865 / 0.23 (17018) hydrogen bonds : bond 0.04198 / 2.65 ( 576) hydrogen bonds : angle 3.97426 / 2.80 ( 1620) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: A 248 TYR cc_start: 0.8587 (m-80) cc_final: 0.7712 (m-80) REVERT: A 339 ILE cc_start: 0.7876 (mt) cc_final: 0.7610 (mm) REVERT: A 467 LEU cc_start: 0.8086 (tp) cc_final: 0.7873 (tp) REVERT: A 613 ILE cc_start: 0.8708 (OUTLIER) cc_final: 0.8436 (mp) REVERT: A 716 THR cc_start: 0.9260 (m) cc_final: 0.8987 (p) REVERT: B 156 MET cc_start: 0.8296 (mmm) cc_final: 0.7749 (mtm) REVERT: B 459 LYS cc_start: 0.7488 (mmtt) cc_final: 0.7192 (mmmt) outliers start: 6 outliers final: 4 residues processed: 82 average time/residue: 0.0731 time to fit residues: 9.6977 Evaluate side-chains 74 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 HIS Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 530 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 24 optimal weight: 3.9990 chunk 111 optimal weight: 0.3980 chunk 38 optimal weight: 20.0000 chunk 127 optimal weight: 9.9990 chunk 37 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 chunk 112 optimal weight: 0.1980 chunk 50 optimal weight: 2.9990 chunk 33 optimal weight: 20.0000 chunk 118 optimal weight: 5.9990 chunk 67 optimal weight: 0.0020 overall best weight: 1.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.117754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.101156 restraints weight = 22483.408| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.47 r_work: 0.3282 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12487 Z= 0.107 Angle : 0.437 5.796 17018 Z= 0.228 Chirality : 0.040 0.179 1832 Planarity : 0.004 0.035 2124 Dihedral : 4.707 55.054 1614 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.61 % Allowed : 5.66 % Favored : 93.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: 1.57 (0.22), residues: 1465 helix: 1.95 (0.19), residues: 729 sheet: -1.15 (0.50), residues: 98 loop : 0.47 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 188 TYR 0.013 0.001 TYR A 207 PHE 0.009 0.001 PHE A 124 TRP 0.016 0.001 TRP B 223 HIS 0.005 0.001 HIS B 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (12487) covalent geometry : angle 0.43668 / 0.23 (17018) hydrogen bonds : bond 0.04159 / 2.61 ( 576) hydrogen bonds : angle 3.95751 / 2.80 ( 1620) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: A 248 TYR cc_start: 0.8566 (m-80) cc_final: 0.7690 (m-80) REVERT: A 339 ILE cc_start: 0.7894 (mt) cc_final: 0.7641 (mm) REVERT: A 613 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8425 (mp) REVERT: A 716 THR cc_start: 0.9275 (m) cc_final: 0.8990 (p) REVERT: B 156 MET cc_start: 0.8286 (mmm) cc_final: 0.7750 (mtm) REVERT: B 459 LYS cc_start: 0.7496 (mmtt) cc_final: 0.7205 (mmmt) outliers start: 8 outliers final: 6 residues processed: 79 average time/residue: 0.0698 time to fit residues: 9.1904 Evaluate side-chains 78 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 422 HIS Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 530 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 73 optimal weight: 0.2980 chunk 34 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 80 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 126 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.117217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.100607 restraints weight = 22544.179| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.48 r_work: 0.3274 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12487 Z= 0.117 Angle : 0.441 6.280 17018 Z= 0.229 Chirality : 0.041 0.210 1832 Planarity : 0.004 0.036 2124 Dihedral : 4.654 46.939 1614 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.76 % Allowed : 5.81 % Favored : 93.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: 1.55 (0.22), residues: 1465 helix: 1.93 (0.19), residues: 729 sheet: -1.09 (0.50), residues: 98 loop : 0.45 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 188 TYR 0.013 0.001 TYR A 207 PHE 0.010 0.001 PHE B 54 TRP 0.014 0.001 TRP B 223 HIS 0.005 0.001 HIS B 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (12487) covalent geometry : angle 0.44120 / 0.23 (17018) hydrogen bonds : bond 0.04223 / 2.67 ( 576) hydrogen bonds : angle 3.96426 / 2.80 ( 1620) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: A 248 TYR cc_start: 0.8617 (m-80) cc_final: 0.7703 (m-80) REVERT: A 339 ILE cc_start: 0.7895 (mt) cc_final: 0.7636 (mm) REVERT: A 613 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8419 (mp) REVERT: A 716 THR cc_start: 0.9271 (m) cc_final: 0.8987 (p) REVERT: B 156 MET cc_start: 0.8377 (mmm) cc_final: 0.7753 (mtm) REVERT: B 459 LYS cc_start: 0.7509 (mmtt) cc_final: 0.7192 (mmmt) outliers start: 10 outliers final: 7 residues processed: 80 average time/residue: 0.0736 time to fit residues: 9.4866 Evaluate side-chains 80 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 422 HIS Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 530 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 107 optimal weight: 9.9990 chunk 90 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 36 optimal weight: 9.9990 chunk 52 optimal weight: 8.9990 chunk 10 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.113211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.096488 restraints weight = 22602.114| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.46 r_work: 0.3211 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 12487 Z= 0.224 Angle : 0.524 5.714 17018 Z= 0.273 Chirality : 0.044 0.241 1832 Planarity : 0.004 0.038 2124 Dihedral : 5.018 45.045 1614 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.76 % Allowed : 5.73 % Favored : 93.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: 1.13 (0.21), residues: 1465 helix: 1.59 (0.19), residues: 729 sheet: -1.17 (0.49), residues: 98 loop : 0.20 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 67 TYR 0.017 0.002 TYR B 207 PHE 0.020 0.002 PHE B 54 TRP 0.014 0.001 TRP A 681 HIS 0.007 0.001 HIS B 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00558 / 0.22 (12487) covalent geometry : angle 0.52439 / 0.27 (17018) hydrogen bonds : bond 0.05169 / 3.27 ( 576) hydrogen bonds : angle 4.24925 / 2.98 ( 1620) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: A 339 ILE cc_start: 0.7941 (mt) cc_final: 0.7669 (mm) REVERT: A 613 ILE cc_start: 0.8686 (OUTLIER) cc_final: 0.8451 (mp) REVERT: A 716 THR cc_start: 0.9312 (m) cc_final: 0.9025 (p) REVERT: B 156 MET cc_start: 0.8475 (mmm) cc_final: 0.7862 (mtm) REVERT: B 459 LYS cc_start: 0.7667 (mmtt) cc_final: 0.7276 (mmmt) outliers start: 10 outliers final: 8 residues processed: 77 average time/residue: 0.0877 time to fit residues: 10.9795 Evaluate side-chains 70 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 422 HIS Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 530 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 131 optimal weight: 6.9990 chunk 114 optimal weight: 0.4980 chunk 129 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 660 GLN B 664 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.116819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.100232 restraints weight = 22400.819| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.47 r_work: 0.3267 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12487 Z= 0.105 Angle : 0.439 5.938 17018 Z= 0.229 Chirality : 0.041 0.195 1832 Planarity : 0.004 0.037 2124 Dihedral : 4.721 46.554 1614 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.61 % Allowed : 6.12 % Favored : 93.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: 1.45 (0.22), residues: 1465 helix: 1.89 (0.19), residues: 729 sheet: -1.15 (0.50), residues: 98 loop : 0.34 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 188 TYR 0.011 0.001 TYR A 207 PHE 0.010 0.001 PHE B 455 TRP 0.016 0.001 TRP B 223 HIS 0.004 0.001 HIS B 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.10 (12487) covalent geometry : angle 0.43883 / 0.23 (17018) hydrogen bonds : bond 0.04247 / 2.67 ( 576) hydrogen bonds : angle 3.98638 / 2.81 ( 1620) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.486 Fit side-chains revert: symmetry clash REVERT: A 156 MET cc_start: 0.8830 (OUTLIER) cc_final: 0.8129 (mtm) REVERT: A 339 ILE cc_start: 0.7859 (mt) cc_final: 0.7589 (mm) REVERT: A 613 ILE cc_start: 0.8675 (OUTLIER) cc_final: 0.8396 (mp) REVERT: A 716 THR cc_start: 0.9285 (m) cc_final: 0.8989 (p) REVERT: B 156 MET cc_start: 0.8395 (mmm) cc_final: 0.7720 (mtm) REVERT: B 459 LYS cc_start: 0.7555 (mmtt) cc_final: 0.7211 (mmmt) outliers start: 8 outliers final: 5 residues processed: 76 average time/residue: 0.0783 time to fit residues: 9.6474 Evaluate side-chains 77 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 422 HIS Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 530 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 44 optimal weight: 9.9990 chunk 116 optimal weight: 10.0000 chunk 49 optimal weight: 0.0570 chunk 46 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 chunk 74 optimal weight: 7.9990 chunk 134 optimal weight: 5.9990 chunk 140 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 overall best weight: 2.7704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.115253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.098589 restraints weight = 22487.872| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.46 r_work: 0.3242 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12487 Z= 0.150 Angle : 0.468 6.154 17018 Z= 0.243 Chirality : 0.042 0.188 1832 Planarity : 0.004 0.038 2124 Dihedral : 4.770 48.327 1614 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.46 % Allowed : 6.35 % Favored : 93.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: 1.32 (0.22), residues: 1465 helix: 1.78 (0.19), residues: 729 sheet: -1.16 (0.50), residues: 98 loop : 0.27 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 281 TYR 0.014 0.001 TYR A 207 PHE 0.015 0.001 PHE A 172 TRP 0.013 0.001 TRP B 223 HIS 0.005 0.001 HIS B 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.15 (12487) covalent geometry : angle 0.46772 / 0.24 (17018) hydrogen bonds : bond 0.04577 / 2.90 ( 576) hydrogen bonds : angle 4.07304 / 2.87 ( 1620) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.570 Fit side-chains revert: symmetry clash REVERT: A 339 ILE cc_start: 0.7899 (mt) cc_final: 0.7625 (mm) REVERT: A 716 THR cc_start: 0.9286 (m) cc_final: 0.8992 (p) REVERT: B 156 MET cc_start: 0.8429 (mmm) cc_final: 0.7790 (mtm) REVERT: B 459 LYS cc_start: 0.7618 (mmtt) cc_final: 0.7229 (mmmt) outliers start: 6 outliers final: 5 residues processed: 72 average time/residue: 0.0759 time to fit residues: 8.8162 Evaluate side-chains 70 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 422 HIS Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 530 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 33 optimal weight: 10.0000 chunk 112 optimal weight: 0.0470 chunk 93 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 95 optimal weight: 6.9990 chunk 110 optimal weight: 8.9990 chunk 127 optimal weight: 5.9990 chunk 70 optimal weight: 9.9990 chunk 108 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 overall best weight: 3.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.114483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.097814 restraints weight = 22627.540| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.47 r_work: 0.3233 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12487 Z= 0.166 Angle : 0.477 6.104 17018 Z= 0.249 Chirality : 0.042 0.185 1832 Planarity : 0.004 0.038 2124 Dihedral : 4.891 58.787 1614 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.38 % Allowed : 6.57 % Favored : 93.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: 1.24 (0.21), residues: 1465 helix: 1.72 (0.19), residues: 729 sheet: -1.14 (0.50), residues: 98 loop : 0.20 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 67 TYR 0.014 0.001 TYR A 207 PHE 0.015 0.001 PHE B 54 TRP 0.014 0.001 TRP B 223 HIS 0.005 0.001 HIS B 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 (12487) covalent geometry : angle 0.47709 / 0.25 (17018) hydrogen bonds : bond 0.04707 / 2.98 ( 576) hydrogen bonds : angle 4.11875 / 2.90 ( 1620) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2402.79 seconds wall clock time: 42 minutes 5.34 seconds (2525.34 seconds total)