Starting phenix.real_space_refine on Wed Mar 4 03:23:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s9a_24930/03_2026/7s9a_24930.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s9a_24930/03_2026/7s9a_24930.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7s9a_24930/03_2026/7s9a_24930.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s9a_24930/03_2026/7s9a_24930.map" model { file = "/net/cci-nas-00/data/ceres_data/7s9a_24930/03_2026/7s9a_24930.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s9a_24930/03_2026/7s9a_24930.cif" } resolution = 3.8 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= 0.000 sd= 0.004 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 50 5.16 5 C 6832 2.51 5 N 1674 2.21 5 O 1864 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10420 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 675, 5200 Classifications: {'peptide': 675} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 32, 'TRANS': 642} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 5200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 675, 5200 Classifications: {'peptide': 675} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 32, 'TRANS': 642} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'SAL': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'SAL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.53, per 1000 atoms: 0.24 Number of scatterers: 10420 At special positions: 0 Unit cell: (117.993, 109.489, 116.93, 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 50 16.00 O 1864 8.00 N 1674 7.00 C 6832 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: 0.88 Conformation dependent library (CDL) restraints added in 606.7 milliseconds 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2492 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 4 sheets defined 64.9% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 25 through 32 Processing helix chain 'A' and resid 44 through 49 removed outlier: 3.963A pdb=" N GLN A 48 " --> pdb=" O LYS A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 65 Processing helix chain 'A' and resid 65 through 70 removed outlier: 4.266A pdb=" N LYS A 69 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TRP A 70 " --> pdb=" O PRO A 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 65 through 70' Processing helix chain 'A' and resid 78 through 105 Proline residue: A 96 - end of helix removed outlier: 3.615A pdb=" N ALA A 105 " --> pdb=" O PHE A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 126 removed outlier: 3.975A pdb=" N GLY A 112 " --> pdb=" O PRO A 108 " (cutoff:3.500A) Proline residue: A 119 - end of helix removed outlier: 3.803A pdb=" N MET A 122 " --> pdb=" O TYR A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 152 Processing helix chain 'A' and resid 169 through 196 Processing helix chain 'A' and resid 197 through 201 removed outlier: 3.938A pdb=" N PHE A 200 " --> pdb=" O ARG A 197 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL A 201 " --> pdb=" O PHE A 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 197 through 201' Processing helix chain 'A' and resid 206 through 231 removed outlier: 4.243A pdb=" N LYS A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N TYR A 228 " --> pdb=" O SER A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 253 Processing helix chain 'A' and resid 258 through 282 Processing helix chain 'A' and resid 291 through 308 Processing helix chain 'A' and resid 308 through 313 removed outlier: 3.537A pdb=" N TYR A 313 " --> pdb=" O LEU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 363 removed outlier: 3.679A pdb=" N ALA A 343 " --> pdb=" O VAL A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 388 Processing helix chain 'A' and resid 396 through 405 Processing helix chain 'A' and resid 411 through 428 Processing helix chain 'A' and resid 436 through 448 removed outlier: 4.137A pdb=" N LEU A 440 " --> pdb=" O PRO A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 453 Processing helix chain 'A' and resid 456 through 465 removed outlier: 4.121A pdb=" N PHE A 460 " --> pdb=" O SER A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 481 removed outlier: 3.577A pdb=" N LEU A 469 " --> pdb=" O SER A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 505 removed outlier: 4.093A pdb=" N VAL A 499 " --> pdb=" O ALA A 495 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 526 No H-bonds generated for 'chain 'A' and resid 524 through 526' Processing helix chain 'A' and resid 549 through 560 removed outlier: 3.668A pdb=" N THR A 560 " --> pdb=" O LEU A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 579 Processing helix chain 'A' and resid 653 through 671 Processing helix chain 'A' and resid 680 through 690 Processing helix chain 'A' and resid 697 through 700 Processing helix chain 'A' and resid 705 through 720 Processing helix chain 'B' and resid 25 through 32 Processing helix chain 'B' and resid 44 through 49 removed outlier: 3.963A pdb=" N GLN B 48 " --> pdb=" O LYS B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 65 Processing helix chain 'B' and resid 65 through 70 removed outlier: 4.265A pdb=" N LYS B 69 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TRP B 70 " --> pdb=" O PRO B 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 65 through 70' Processing helix chain 'B' and resid 78 through 105 Proline residue: B 96 - end of helix removed outlier: 3.615A pdb=" N ALA B 105 " --> pdb=" O PHE B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 126 removed outlier: 3.975A pdb=" N GLY B 112 " --> pdb=" O PRO B 108 " (cutoff:3.500A) Proline residue: B 119 - end of helix removed outlier: 3.803A pdb=" N MET B 122 " --> pdb=" O TYR B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 152 Processing helix chain 'B' and resid 169 through 196 Processing helix chain 'B' and resid 197 through 201 removed outlier: 3.938A pdb=" N PHE B 200 " --> pdb=" O ARG B 197 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL B 201 " --> pdb=" O PHE B 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 197 through 201' Processing helix chain 'B' and resid 206 through 231 removed outlier: 4.244A pdb=" N LYS B 227 " --> pdb=" O THR B 223 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N TYR B 228 " --> pdb=" O SER B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 253 Processing helix chain 'B' and resid 258 through 282 Processing helix chain 'B' and resid 291 through 308 Processing helix chain 'B' and resid 308 through 313 removed outlier: 3.537A pdb=" N TYR B 313 " --> pdb=" O LEU B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 363 removed outlier: 3.678A pdb=" N ALA B 343 " --> pdb=" O VAL B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 388 Processing helix chain 'B' and resid 396 through 405 Processing helix chain 'B' and resid 411 through 428 Processing helix chain 'B' and resid 436 through 448 removed outlier: 4.137A pdb=" N LEU B 440 " --> pdb=" O PRO B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 453 Processing helix chain 'B' and resid 456 through 465 removed outlier: 4.121A pdb=" N PHE B 460 " --> pdb=" O SER B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 481 removed outlier: 3.577A pdb=" N LEU B 469 " --> pdb=" O SER B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 505 removed outlier: 4.596A pdb=" N VAL B 499 " --> pdb=" O ALA B 495 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 526 No H-bonds generated for 'chain 'B' and resid 524 through 526' Processing helix chain 'B' and resid 549 through 560 removed outlier: 3.667A pdb=" N THR B 560 " --> pdb=" O LEU B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 579 Processing helix chain 'B' and resid 653 through 671 Processing helix chain 'B' and resid 680 through 690 Processing helix chain 'B' and resid 697 through 700 Processing helix chain 'B' and resid 705 through 720 Processing sheet with id=AA1, first strand: chain 'A' and resid 134 through 135 Processing sheet with id=AA2, first strand: chain 'A' and resid 520 through 522 removed outlier: 4.715A pdb=" N ILE A 537 " --> pdb=" O LEU A 511 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N GLN A 513 " --> pdb=" O ILE A 535 " (cutoff:3.500A) removed outlier: 11.952A pdb=" N ILE A 535 " --> pdb=" O GLN A 513 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LYS A 536 " --> pdb=" O ILE A 643 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N ASP A 645 " --> pdb=" O LYS A 536 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N PHE A 538 " --> pdb=" O ASP A 645 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N PHE A 703 " --> pdb=" O VAL A 674 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU A 676 " --> pdb=" O PHE A 703 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 134 through 135 Processing sheet with id=AA4, first strand: chain 'B' and resid 520 through 522 removed outlier: 4.716A pdb=" N ILE B 537 " --> pdb=" O LEU B 511 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N GLN B 513 " --> pdb=" O ILE B 535 " (cutoff:3.500A) removed outlier: 11.952A pdb=" N ILE B 535 " --> pdb=" O GLN B 513 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LYS B 536 " --> pdb=" O ILE B 643 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ASP B 645 " --> pdb=" O LYS B 536 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N PHE B 538 " --> pdb=" O ASP B 645 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N PHE B 703 " --> pdb=" O VAL B 674 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU B 676 " --> pdb=" O PHE B 703 " (cutoff:3.500A) 618 hydrogen bonds defined for protein. 1824 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: 1.64 Time building geometry restraints manager: 1.20 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: 3206 1.34 - 1.46: 1644 1.46 - 1.58: 5720 1.58 - 1.70: 0 1.70 - 1.81: 82 Bond restraints: 10652 Sorted by residual: bond pdb=" N VAL B 139 " pdb=" CA VAL B 139 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.19e-02 7.06e+03 8.30e+00 bond pdb=" N ILE A 494 " pdb=" CA ILE A 494 " ideal model delta sigma weight residual 1.460 1.494 -0.035 1.21e-02 6.83e+03 8.24e+00 bond pdb=" N VAL A 139 " pdb=" CA VAL A 139 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.19e-02 7.06e+03 8.20e+00 bond pdb=" N ILE B 494 " pdb=" CA ILE B 494 " ideal model delta sigma weight residual 1.460 1.494 -0.035 1.21e-02 6.83e+03 8.16e+00 bond pdb=" N VAL B 499 " pdb=" CA VAL B 499 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.19e-02 7.06e+03 7.39e+00 ... (remaining 10647 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 14145 1.63 - 3.26: 253 3.26 - 4.88: 52 4.88 - 6.51: 20 6.51 - 8.14: 6 Bond angle restraints: 14476 Sorted by residual: angle pdb=" O GLY A 135 " pdb=" C GLY A 135 " pdb=" N PRO A 136 " ideal model delta sigma weight residual 121.77 118.21 3.56 1.00e+00 1.00e+00 1.26e+01 angle pdb=" C GLU A 694 " pdb=" N ASN A 695 " pdb=" CA ASN A 695 " ideal model delta sigma weight residual 122.83 126.60 -3.77 1.08e+00 8.57e-01 1.22e+01 angle pdb=" C GLU B 694 " pdb=" N ASN B 695 " pdb=" CA ASN B 695 " ideal model delta sigma weight residual 122.83 126.56 -3.73 1.08e+00 8.57e-01 1.19e+01 angle pdb=" N GLY B 366 " pdb=" CA GLY B 366 " pdb=" C GLY B 366 " ideal model delta sigma weight residual 113.18 121.32 -8.14 2.37e+00 1.78e-01 1.18e+01 angle pdb=" N GLY A 366 " pdb=" CA GLY A 366 " pdb=" C GLY A 366 " ideal model delta sigma weight residual 113.18 121.32 -8.14 2.37e+00 1.78e-01 1.18e+01 ... (remaining 14471 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.62: 5709 16.62 - 33.24: 487 33.24 - 49.86: 86 49.86 - 66.48: 8 66.48 - 83.10: 6 Dihedral angle restraints: 6296 sinusoidal: 2404 harmonic: 3892 Sorted by residual: dihedral pdb=" CA ASN B 695 " pdb=" C ASN B 695 " pdb=" N PRO B 696 " pdb=" CA PRO B 696 " ideal model delta harmonic sigma weight residual 180.00 155.04 24.96 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA ASN A 695 " pdb=" C ASN A 695 " pdb=" N PRO A 696 " pdb=" CA PRO A 696 " ideal model delta harmonic sigma weight residual 180.00 155.04 24.96 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA GLY B 366 " pdb=" C GLY B 366 " pdb=" N TYR B 367 " pdb=" CA TYR B 367 " ideal model delta harmonic sigma weight residual -180.00 -162.06 -17.94 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 6293 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1138 0.039 - 0.077: 415 0.077 - 0.116: 148 0.116 - 0.154: 18 0.154 - 0.192: 3 Chirality restraints: 1722 Sorted by residual: chirality pdb=" CA ILE A 140 " pdb=" N ILE A 140 " pdb=" C ILE A 140 " pdb=" CB ILE A 140 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.26e-01 chirality pdb=" CA VAL A 139 " pdb=" N VAL A 139 " pdb=" C VAL A 139 " pdb=" CB VAL A 139 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 7.81e-01 chirality pdb=" CA VAL B 139 " pdb=" N VAL B 139 " pdb=" C VAL B 139 " pdb=" CB VAL B 139 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.56e-01 ... (remaining 1719 not shown) Planarity restraints: 1802 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 65 " 0.058 5.00e-02 4.00e+02 8.73e-02 1.22e+01 pdb=" N PRO B 66 " -0.151 5.00e-02 4.00e+02 pdb=" CA PRO B 66 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 66 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 65 " 0.058 5.00e-02 4.00e+02 8.72e-02 1.22e+01 pdb=" N PRO A 66 " -0.151 5.00e-02 4.00e+02 pdb=" CA PRO A 66 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 66 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 290 " -0.040 5.00e-02 4.00e+02 6.05e-02 5.86e+00 pdb=" N PRO A 291 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 291 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 291 " -0.033 5.00e-02 4.00e+02 ... (remaining 1799 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2826 2.81 - 3.33: 10410 3.33 - 3.86: 16489 3.86 - 4.38: 17707 4.38 - 4.90: 31907 Nonbonded interactions: 79339 Sorted by model distance: nonbonded pdb=" O GLY A 239 " pdb=" OG SER A 242 " model vdw 2.290 3.040 nonbonded pdb=" O GLY B 239 " pdb=" OG SER B 242 " model vdw 2.290 3.040 nonbonded pdb=" O SER A 505 " pdb=" OG SER A 505 " model vdw 2.328 3.040 nonbonded pdb=" O SER B 505 " pdb=" OG SER B 505 " model vdw 2.328 3.040 nonbonded pdb=" O ALA A 495 " pdb=" CG2 THR A 498 " model vdw 2.355 3.460 ... (remaining 79334 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.300 Find NCS groups from input model: 0.090 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: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 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 : 0.003 0.052 10652 Z= 0.166 Angle : 0.598 8.139 14476 Z= 0.326 Chirality : 0.044 0.192 1722 Planarity : 0.005 0.087 1802 Dihedral : 12.628 83.104 3804 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.56 % Favored : 93.14 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % 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: 1.38 (0.24), residues: 1342 helix: 1.98 (0.19), residues: 860 sheet: 3.56 (0.78), residues: 36 loop : -1.53 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 399 TYR 0.010 0.001 TYR A 545 PHE 0.027 0.001 PHE B 282 TRP 0.003 0.000 TRP A 472 HIS 0.002 0.000 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00308 (10652) covalent geometry : angle 0.59831 (14476) hydrogen bonds : bond 0.13325 ( 618) hydrogen bonds : angle 4.82288 ( 1824) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.320 Fit side-chains REVERT: B 291 PRO cc_start: 0.8667 (Cg_exo) cc_final: 0.8376 (Cg_endo) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.0929 time to fit residues: 20.5462 Evaluate side-chains 123 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 98 optimal weight: 0.4980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.3980 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.0000 chunk 91 optimal weight: 9.9990 chunk 55 optimal weight: 0.0070 overall best weight: 0.3402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 256 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.131608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.100063 restraints weight = 17072.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.099493 restraints weight = 14864.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.100640 restraints weight = 13014.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.100889 restraints weight = 9842.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.101338 restraints weight = 9568.305| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.0875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10652 Z= 0.118 Angle : 0.571 7.751 14476 Z= 0.283 Chirality : 0.042 0.154 1722 Planarity : 0.005 0.060 1802 Dihedral : 4.067 35.402 1444 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.04 % Favored : 93.67 % Rotamer: Outliers : 1.14 % Allowed : 6.67 % Favored : 92.19 % 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: 1.68 (0.25), residues: 1342 helix: 2.19 (0.19), residues: 862 sheet: 3.70 (0.83), residues: 36 loop : -1.39 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 399 TYR 0.011 0.001 TYR A 545 PHE 0.024 0.001 PHE B 388 TRP 0.004 0.001 TRP A 472 HIS 0.002 0.000 HIS A 707 Details of bonding type rmsd covalent geometry : bond 0.00239 (10652) covalent geometry : angle 0.57077 (14476) hydrogen bonds : bond 0.03888 ( 618) hydrogen bonds : angle 3.74651 ( 1824) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 0.317 Fit side-chains REVERT: A 434 SER cc_start: 0.7798 (m) cc_final: 0.7394 (p) REVERT: B 434 SER cc_start: 0.7803 (m) cc_final: 0.7383 (p) outliers start: 13 outliers final: 9 residues processed: 139 average time/residue: 0.0858 time to fit residues: 17.9484 Evaluate side-chains 128 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 119 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 619 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 90 optimal weight: 0.7980 chunk 3 optimal weight: 7.9990 chunk 56 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 106 optimal weight: 9.9990 chunk 112 optimal weight: 0.0040 chunk 61 optimal weight: 4.9990 chunk 77 optimal weight: 0.2980 overall best weight: 1.2196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.129248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.098134 restraints weight = 17208.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.096376 restraints weight = 15619.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.097529 restraints weight = 16675.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.098234 restraints weight = 11177.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.098502 restraints weight = 10160.010| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.0969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10652 Z= 0.126 Angle : 0.549 7.880 14476 Z= 0.276 Chirality : 0.042 0.154 1722 Planarity : 0.004 0.050 1802 Dihedral : 4.073 37.433 1444 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.81 % Favored : 93.89 % Rotamer: Outliers : 1.49 % Allowed : 8.51 % Favored : 90.00 % 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: 1.76 (0.25), residues: 1342 helix: 2.26 (0.19), residues: 864 sheet: 3.64 (0.79), residues: 36 loop : -1.38 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 399 TYR 0.009 0.001 TYR B 545 PHE 0.028 0.001 PHE B 388 TRP 0.005 0.001 TRP A 472 HIS 0.002 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00290 (10652) covalent geometry : angle 0.54878 (14476) hydrogen bonds : bond 0.03933 ( 618) hydrogen bonds : angle 3.56321 ( 1824) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 0.298 Fit side-chains REVERT: A 548 ASN cc_start: 0.7872 (t0) cc_final: 0.7562 (p0) REVERT: B 548 ASN cc_start: 0.7904 (t0) cc_final: 0.7568 (p0) outliers start: 17 outliers final: 15 residues processed: 138 average time/residue: 0.0822 time to fit residues: 16.9844 Evaluate side-chains 133 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain B residue 103 MET Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 619 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 86 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 35 optimal weight: 7.9990 chunk 90 optimal weight: 0.8980 chunk 26 optimal weight: 7.9990 chunk 70 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.129180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.098049 restraints weight = 17153.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.096198 restraints weight = 16383.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.097521 restraints weight = 15902.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.097991 restraints weight = 10892.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.098393 restraints weight = 10299.329| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10652 Z= 0.118 Angle : 0.544 7.885 14476 Z= 0.272 Chirality : 0.042 0.152 1722 Planarity : 0.004 0.045 1802 Dihedral : 4.087 38.777 1444 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.96 % Favored : 93.74 % Rotamer: Outliers : 1.58 % Allowed : 10.53 % Favored : 87.89 % 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 (0.25), residues: 1342 helix: 2.33 (0.19), residues: 860 sheet: 3.48 (0.78), residues: 36 loop : -1.46 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 571 TYR 0.008 0.001 TYR B 545 PHE 0.026 0.001 PHE B 278 TRP 0.006 0.001 TRP B 472 HIS 0.001 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00269 (10652) covalent geometry : angle 0.54449 (14476) hydrogen bonds : bond 0.03681 ( 618) hydrogen bonds : angle 3.47114 ( 1824) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 0.412 Fit side-chains REVERT: A 548 ASN cc_start: 0.8007 (t0) cc_final: 0.7774 (p0) REVERT: B 423 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8554 (tp) REVERT: B 548 ASN cc_start: 0.8027 (t0) cc_final: 0.7815 (p0) outliers start: 18 outliers final: 14 residues processed: 134 average time/residue: 0.0901 time to fit residues: 18.0041 Evaluate side-chains 135 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain B residue 103 MET Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 619 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 100 optimal weight: 0.7980 chunk 31 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.127565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.096555 restraints weight = 17295.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.095575 restraints weight = 15220.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.096395 restraints weight = 15383.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.096798 restraints weight = 11290.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.097181 restraints weight = 10678.113| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10652 Z= 0.135 Angle : 0.554 8.297 14476 Z= 0.278 Chirality : 0.043 0.152 1722 Planarity : 0.004 0.043 1802 Dihedral : 4.146 40.765 1444 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.18 % Favored : 93.52 % Rotamer: Outliers : 1.40 % Allowed : 11.40 % Favored : 87.19 % 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: 1.75 (0.25), residues: 1342 helix: 2.30 (0.19), residues: 862 sheet: 3.28 (0.78), residues: 36 loop : -1.45 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 211 TYR 0.009 0.001 TYR A 545 PHE 0.023 0.001 PHE B 278 TRP 0.006 0.001 TRP B 472 HIS 0.002 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00318 (10652) covalent geometry : angle 0.55373 (14476) hydrogen bonds : bond 0.03928 ( 618) hydrogen bonds : angle 3.46778 ( 1824) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.407 Fit side-chains REVERT: A 387 LEU cc_start: 0.8426 (tt) cc_final: 0.8062 (tp) REVERT: B 387 LEU cc_start: 0.8429 (tt) cc_final: 0.8075 (tp) REVERT: B 423 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8522 (tp) outliers start: 16 outliers final: 14 residues processed: 133 average time/residue: 0.0865 time to fit residues: 17.1290 Evaluate side-chains 134 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain B residue 103 MET Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 619 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 89 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 115 optimal weight: 0.9980 chunk 121 optimal weight: 0.7980 chunk 102 optimal weight: 7.9990 chunk 52 optimal weight: 0.9990 chunk 80 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.125678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.095188 restraints weight = 17423.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.094286 restraints weight = 15701.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.095351 restraints weight = 13891.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.095777 restraints weight = 10322.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.096113 restraints weight = 10204.118| |-----------------------------------------------------------------------------| r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10652 Z= 0.159 Angle : 0.582 8.131 14476 Z= 0.294 Chirality : 0.043 0.153 1722 Planarity : 0.004 0.042 1802 Dihedral : 4.292 43.642 1444 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.26 % Favored : 93.44 % Rotamer: Outliers : 1.49 % Allowed : 12.98 % Favored : 85.53 % 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: 1.66 (0.25), residues: 1342 helix: 2.24 (0.19), residues: 864 sheet: 3.01 (0.78), residues: 36 loop : -1.49 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 211 TYR 0.010 0.001 TYR A 123 PHE 0.023 0.002 PHE B 269 TRP 0.007 0.001 TRP B 472 HIS 0.002 0.001 HIS A 640 Details of bonding type rmsd covalent geometry : bond 0.00380 (10652) covalent geometry : angle 0.58174 (14476) hydrogen bonds : bond 0.04322 ( 618) hydrogen bonds : angle 3.56286 ( 1824) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.413 Fit side-chains REVERT: A 387 LEU cc_start: 0.8382 (tt) cc_final: 0.8177 (tp) REVERT: B 387 LEU cc_start: 0.8410 (tt) cc_final: 0.8206 (tp) REVERT: B 423 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8543 (tp) outliers start: 17 outliers final: 15 residues processed: 127 average time/residue: 0.0929 time to fit residues: 17.4400 Evaluate side-chains 130 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain B residue 103 MET Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 192 CYS Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 619 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 115 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 120 optimal weight: 0.6980 chunk 116 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 126 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.126795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.096161 restraints weight = 17429.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.094822 restraints weight = 16417.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.095806 restraints weight = 15486.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.096208 restraints weight = 11136.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.096558 restraints weight = 10569.157| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10652 Z= 0.128 Angle : 0.559 7.975 14476 Z= 0.281 Chirality : 0.042 0.149 1722 Planarity : 0.004 0.042 1802 Dihedral : 4.267 43.558 1444 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.18 % Favored : 93.52 % Rotamer: Outliers : 1.58 % Allowed : 13.60 % Favored : 84.82 % 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: 1.67 (0.25), residues: 1342 helix: 2.23 (0.19), residues: 864 sheet: 2.95 (0.78), residues: 36 loop : -1.44 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 399 TYR 0.013 0.001 TYR A 123 PHE 0.030 0.001 PHE A 278 TRP 0.009 0.001 TRP B 472 HIS 0.002 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00296 (10652) covalent geometry : angle 0.55926 (14476) hydrogen bonds : bond 0.03958 ( 618) hydrogen bonds : angle 3.51789 ( 1824) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.385 Fit side-chains REVERT: A 387 LEU cc_start: 0.8430 (tt) cc_final: 0.8181 (tp) REVERT: A 423 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8540 (tp) REVERT: B 387 LEU cc_start: 0.8431 (tt) cc_final: 0.8203 (tp) REVERT: B 423 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8458 (tp) outliers start: 18 outliers final: 15 residues processed: 134 average time/residue: 0.0911 time to fit residues: 17.9940 Evaluate side-chains 134 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain B residue 103 MET Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 619 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 122 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 119 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 117 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 57 optimal weight: 0.7980 chunk 112 optimal weight: 0.0370 chunk 2 optimal weight: 1.9990 overall best weight: 1.3664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.126578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.095967 restraints weight = 17234.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.094438 restraints weight = 15709.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.095676 restraints weight = 17575.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.096191 restraints weight = 10563.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.096582 restraints weight = 9721.001| |-----------------------------------------------------------------------------| r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10652 Z= 0.130 Angle : 0.555 8.000 14476 Z= 0.280 Chirality : 0.043 0.148 1722 Planarity : 0.004 0.042 1802 Dihedral : 4.236 43.554 1444 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.26 % Favored : 93.44 % Rotamer: Outliers : 1.58 % Allowed : 14.65 % Favored : 83.77 % 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: 1.65 (0.25), residues: 1342 helix: 2.21 (0.19), residues: 864 sheet: 2.92 (0.77), residues: 36 loop : -1.44 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 399 TYR 0.011 0.001 TYR A 545 PHE 0.029 0.001 PHE B 278 TRP 0.009 0.001 TRP B 472 HIS 0.002 0.001 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00304 (10652) covalent geometry : angle 0.55521 (14476) hydrogen bonds : bond 0.03934 ( 618) hydrogen bonds : angle 3.48135 ( 1824) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.296 Fit side-chains REVERT: A 387 LEU cc_start: 0.8437 (tt) cc_final: 0.8191 (tp) REVERT: A 423 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8524 (tp) REVERT: B 303 ILE cc_start: 0.8398 (mm) cc_final: 0.8090 (mt) REVERT: B 387 LEU cc_start: 0.8418 (tt) cc_final: 0.8185 (tp) REVERT: B 423 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8470 (tp) outliers start: 18 outliers final: 16 residues processed: 132 average time/residue: 0.0900 time to fit residues: 17.4778 Evaluate side-chains 132 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain B residue 103 MET Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 192 CYS Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 619 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 96 optimal weight: 7.9990 chunk 108 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 chunk 81 optimal weight: 10.0000 chunk 132 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.127587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.097069 restraints weight = 17126.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.095726 restraints weight = 15462.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.096154 restraints weight = 18177.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.098116 restraints weight = 12131.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.097979 restraints weight = 9406.640| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10652 Z= 0.114 Angle : 0.534 7.909 14476 Z= 0.269 Chirality : 0.042 0.147 1722 Planarity : 0.004 0.041 1802 Dihedral : 4.156 42.348 1444 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.96 % Favored : 93.74 % Rotamer: Outliers : 1.75 % Allowed : 14.47 % Favored : 83.77 % 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: 1.70 (0.25), residues: 1342 helix: 2.24 (0.19), residues: 864 sheet: 2.69 (0.75), residues: 38 loop : -1.41 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 399 TYR 0.011 0.001 TYR A 545 PHE 0.028 0.001 PHE B 278 TRP 0.010 0.001 TRP B 472 HIS 0.002 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00259 (10652) covalent geometry : angle 0.53443 (14476) hydrogen bonds : bond 0.03589 ( 618) hydrogen bonds : angle 3.40346 ( 1824) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 0.464 Fit side-chains REVERT: A 110 VAL cc_start: 0.7018 (OUTLIER) cc_final: 0.6753 (p) REVERT: A 387 LEU cc_start: 0.8432 (tt) cc_final: 0.8180 (tp) REVERT: A 422 LEU cc_start: 0.9407 (OUTLIER) cc_final: 0.9194 (tt) REVERT: A 423 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8424 (tp) REVERT: B 110 VAL cc_start: 0.7053 (OUTLIER) cc_final: 0.6757 (p) REVERT: B 143 MET cc_start: 0.8343 (mtp) cc_final: 0.8076 (mtp) REVERT: B 303 ILE cc_start: 0.8335 (mm) cc_final: 0.8038 (mt) REVERT: B 387 LEU cc_start: 0.8435 (tt) cc_final: 0.8205 (tp) REVERT: B 423 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8433 (tp) outliers start: 20 outliers final: 15 residues processed: 136 average time/residue: 0.0961 time to fit residues: 19.2627 Evaluate side-chains 137 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain B residue 103 MET Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 192 CYS Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 619 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 66 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 chunk 74 optimal weight: 9.9990 chunk 53 optimal weight: 0.0770 chunk 57 optimal weight: 0.6980 chunk 93 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 overall best weight: 1.1340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.127281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.096764 restraints weight = 17127.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.095319 restraints weight = 16769.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.096092 restraints weight = 15818.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.096864 restraints weight = 11471.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.097154 restraints weight = 10531.601| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10652 Z= 0.119 Angle : 0.540 7.949 14476 Z= 0.272 Chirality : 0.042 0.146 1722 Planarity : 0.004 0.041 1802 Dihedral : 4.128 42.147 1444 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.96 % Favored : 93.74 % Rotamer: Outliers : 1.93 % Allowed : 14.30 % Favored : 83.77 % 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: 1.73 (0.25), residues: 1342 helix: 2.26 (0.19), residues: 864 sheet: 2.64 (0.75), residues: 38 loop : -1.38 (0.32), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 211 TYR 0.011 0.001 TYR A 545 PHE 0.028 0.001 PHE B 278 TRP 0.009 0.001 TRP B 472 HIS 0.002 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00275 (10652) covalent geometry : angle 0.54011 (14476) hydrogen bonds : bond 0.03689 ( 618) hydrogen bonds : angle 3.40394 ( 1824) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 0.340 Fit side-chains REVERT: A 110 VAL cc_start: 0.7022 (OUTLIER) cc_final: 0.6693 (p) REVERT: A 387 LEU cc_start: 0.8438 (tt) cc_final: 0.8195 (tp) REVERT: A 422 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.9162 (tt) REVERT: A 423 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8392 (tp) REVERT: B 110 VAL cc_start: 0.7063 (OUTLIER) cc_final: 0.6764 (p) REVERT: B 143 MET cc_start: 0.8334 (mtp) cc_final: 0.8059 (mtp) REVERT: B 303 ILE cc_start: 0.8326 (mm) cc_final: 0.8042 (mt) REVERT: B 387 LEU cc_start: 0.8442 (tt) cc_final: 0.8219 (tp) REVERT: B 423 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8407 (tp) outliers start: 22 outliers final: 17 residues processed: 133 average time/residue: 0.0909 time to fit residues: 17.8497 Evaluate side-chains 140 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain B residue 103 MET Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 192 CYS Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 619 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 36 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 chunk 58 optimal weight: 0.0010 chunk 124 optimal weight: 5.9990 chunk 68 optimal weight: 0.4980 chunk 11 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.129037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.098761 restraints weight = 17232.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.097838 restraints weight = 15647.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.098363 restraints weight = 18063.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.099142 restraints weight = 10895.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.099385 restraints weight = 9514.493| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10652 Z= 0.103 Angle : 0.523 7.891 14476 Z= 0.261 Chirality : 0.042 0.146 1722 Planarity : 0.004 0.040 1802 Dihedral : 4.026 40.429 1444 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.26 % Favored : 93.44 % Rotamer: Outliers : 1.75 % Allowed : 14.47 % Favored : 83.77 % 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: 1.89 (0.25), residues: 1342 helix: 2.44 (0.19), residues: 850 sheet: 2.74 (0.75), residues: 38 loop : -1.30 (0.31), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 571 TYR 0.010 0.001 TYR A 545 PHE 0.028 0.001 PHE B 278 TRP 0.011 0.001 TRP B 472 HIS 0.002 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00227 (10652) covalent geometry : angle 0.52289 (14476) hydrogen bonds : bond 0.03248 ( 618) hydrogen bonds : angle 3.31840 ( 1824) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1375.59 seconds wall clock time: 24 minutes 33.95 seconds (1473.95 seconds total)