Starting phenix.real_space_refine on Fri Feb 14 17:35:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s9a_24930/02_2025/7s9a_24930.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s9a_24930/02_2025/7s9a_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_24930/02_2025/7s9a_24930.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s9a_24930/02_2025/7s9a_24930.map" model { file = "/net/cci-nas-00/data/ceres_data/7s9a_24930/02_2025/7s9a_24930.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s9a_24930/02_2025/7s9a_24930.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'GLN:plan1': 1, 'GLU:plan': 2} 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: {'GLN:plan1': 1, 'GLU:plan': 2} 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: 6.20, per 1000 atoms: 0.60 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: 2.61 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.01 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: 3.22 Time building geometry restraints manager: 3.02 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: 0.05 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: 0.880 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: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 25.020 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.280 ------------------------------------------------------------------------------- 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= 0.195 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (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 TRP 0.003 0.000 TRP A 472 HIS 0.002 0.000 HIS A 220 PHE 0.027 0.001 PHE B 282 TYR 0.010 0.001 TYR A 545 ARG 0.005 0.000 ARG A 399 *********************** 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 : 1.177 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: 0.1958 time to fit residues: 43.0052 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 : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 3.9990 chunk 101 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 68 optimal weight: 0.4980 chunk 54 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 63 optimal weight: 6.9990 chunk 78 optimal weight: 7.9990 chunk 121 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.3556 r_free = 0.3556 target = 0.129572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.097841 restraints weight = 17054.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.096864 restraints weight = 15729.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.098552 restraints weight = 15435.675| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.0834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10652 Z= 0.186 Angle : 0.583 7.851 14476 Z= 0.290 Chirality : 0.043 0.155 1722 Planarity : 0.005 0.062 1802 Dihedral : 4.123 36.827 1444 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.96 % Favored : 93.74 % Rotamer: Outliers : 1.32 % Allowed : 6.67 % Favored : 92.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.25), residues: 1342 helix: 2.18 (0.19), residues: 862 sheet: 3.72 (0.82), residues: 36 loop : -1.46 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 472 HIS 0.002 0.001 HIS A 220 PHE 0.025 0.001 PHE B 388 TYR 0.011 0.001 TYR A 545 ARG 0.003 0.000 ARG A 399 *********************** 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 148 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 133 time to evaluate : 1.063 Fit side-chains REVERT: A 434 SER cc_start: 0.7814 (m) cc_final: 0.7402 (p) REVERT: A 548 ASN cc_start: 0.7691 (t0) cc_final: 0.7356 (p0) REVERT: B 434 SER cc_start: 0.7749 (m) cc_final: 0.7307 (p) REVERT: B 548 ASN cc_start: 0.7749 (t0) cc_final: 0.7425 (p0) outliers start: 15 outliers final: 13 residues processed: 142 average time/residue: 0.2136 time to fit residues: 45.3581 Evaluate side-chains 136 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 1 optimal weight: 0.5980 chunk 22 optimal weight: 9.9990 chunk 71 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 81 optimal weight: 20.0000 chunk 32 optimal weight: 0.3980 chunk 28 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 87 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.3553 r_free = 0.3553 target = 0.129375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.098335 restraints weight = 17182.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.096647 restraints weight = 15938.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.098128 restraints weight = 16590.466| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10652 Z= 0.165 Angle : 0.537 7.850 14476 Z= 0.272 Chirality : 0.042 0.154 1722 Planarity : 0.004 0.051 1802 Dihedral : 4.111 38.168 1444 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.11 % Favored : 93.59 % Rotamer: Outliers : 1.23 % Allowed : 8.95 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.25), residues: 1342 helix: 2.25 (0.19), residues: 862 sheet: 3.56 (0.79), residues: 36 loop : -1.41 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 472 HIS 0.001 0.000 HIS A 220 PHE 0.027 0.001 PHE B 388 TYR 0.009 0.001 TYR A 123 ARG 0.002 0.000 ARG A 399 *********************** 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 139 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 1.423 Fit side-chains REVERT: B 548 ASN cc_start: 0.7945 (t0) cc_final: 0.7740 (p0) outliers start: 14 outliers final: 14 residues processed: 134 average time/residue: 0.2335 time to fit residues: 46.5196 Evaluate side-chains 131 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 1.112 ------------------------------------------------------------------------------- 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 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 59 optimal weight: 0.6980 chunk 77 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 109 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 chunk 117 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3557 r_free = 0.3557 target = 0.129708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.098323 restraints weight = 17023.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.097300 restraints weight = 15551.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.098335 restraints weight = 17676.719| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10652 Z= 0.155 Angle : 0.538 7.880 14476 Z= 0.268 Chirality : 0.042 0.152 1722 Planarity : 0.004 0.045 1802 Dihedral : 4.070 38.561 1444 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.04 % Favored : 93.67 % Rotamer: Outliers : 1.49 % Allowed : 10.53 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.25), residues: 1342 helix: 2.31 (0.19), residues: 862 sheet: 3.48 (0.78), residues: 36 loop : -1.41 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 472 HIS 0.001 0.000 HIS A 220 PHE 0.027 0.001 PHE B 278 TYR 0.008 0.001 TYR B 545 ARG 0.002 0.000 ARG A 399 *********************** 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 139 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 1.125 Fit side-chains REVERT: A 423 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8496 (tp) REVERT: B 423 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8519 (tp) outliers start: 17 outliers final: 12 residues processed: 132 average time/residue: 0.2131 time to fit residues: 41.4701 Evaluate side-chains 132 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 1.157 ------------------------------------------------------------------------------- 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 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 58 optimal weight: 3.9990 chunk 68 optimal weight: 0.3980 chunk 52 optimal weight: 0.8980 chunk 72 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 130 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 97 optimal weight: 7.9990 chunk 33 optimal weight: 0.7980 chunk 67 optimal weight: 0.0030 overall best weight: 0.5990 ------------------------------------------------------------------------------- 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 = 0.3566 r_free = 0.3566 target = 0.130380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.099513 restraints weight = 17031.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.097908 restraints weight = 16570.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.099228 restraints weight = 15811.008| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10652 Z= 0.140 Angle : 0.524 8.232 14476 Z= 0.261 Chirality : 0.041 0.147 1722 Planarity : 0.004 0.040 1802 Dihedral : 4.007 38.288 1444 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.74 % Favored : 93.96 % Rotamer: Outliers : 0.96 % Allowed : 11.49 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.25), residues: 1342 helix: 2.34 (0.19), residues: 864 sheet: 3.45 (0.77), residues: 36 loop : -1.35 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 472 HIS 0.001 0.000 HIS A 220 PHE 0.025 0.001 PHE B 278 TYR 0.011 0.001 TYR A 545 ARG 0.002 0.000 ARG A 399 *********************** 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 138 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 1.085 Fit side-chains REVERT: A 423 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8440 (tp) REVERT: B 387 LEU cc_start: 0.8386 (tt) cc_final: 0.8049 (tp) REVERT: B 423 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8429 (tp) outliers start: 11 outliers final: 9 residues processed: 132 average time/residue: 0.2046 time to fit residues: 39.7478 Evaluate side-chains 130 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 119 time to evaluate : 1.277 ------------------------------------------------------------------------------- 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 244 VAL 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 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 53 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 30 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 chunk 99 optimal weight: 0.3980 chunk 20 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.123996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.093741 restraints weight = 17466.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.092722 restraints weight = 16127.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.093629 restraints weight = 17095.668| |-----------------------------------------------------------------------------| r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10652 Z= 0.339 Angle : 0.649 8.358 14476 Z= 0.328 Chirality : 0.045 0.159 1722 Planarity : 0.005 0.044 1802 Dihedral : 4.405 44.479 1444 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.63 % Favored : 93.07 % Rotamer: Outliers : 1.75 % Allowed : 12.81 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.25), residues: 1342 helix: 2.17 (0.19), residues: 860 sheet: 2.55 (0.76), residues: 38 loop : -1.67 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 472 HIS 0.003 0.001 HIS A 220 PHE 0.026 0.002 PHE B 278 TYR 0.013 0.002 TYR A 545 ARG 0.004 0.001 ARG A 211 *********************** 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 141 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 1.135 Fit side-chains REVERT: A 186 THR cc_start: 0.9175 (OUTLIER) cc_final: 0.8940 (p) outliers start: 20 outliers final: 16 residues processed: 132 average time/residue: 0.1992 time to fit residues: 38.9456 Evaluate side-chains 132 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 1.144 ------------------------------------------------------------------------------- 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 186 THR Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 301 THR 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 223 THR 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 48 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 = 0.126538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.096092 restraints weight = 17377.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.094768 restraints weight = 15912.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.095924 restraints weight = 17740.894| |-----------------------------------------------------------------------------| r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10652 Z= 0.178 Angle : 0.559 8.367 14476 Z= 0.280 Chirality : 0.043 0.151 1722 Planarity : 0.004 0.057 1802 Dihedral : 4.293 43.933 1444 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.81 % Favored : 93.89 % Rotamer: Outliers : 1.40 % Allowed : 14.39 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.25), residues: 1342 helix: 2.19 (0.19), residues: 864 sheet: 2.83 (0.78), residues: 36 loop : -1.43 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 472 HIS 0.002 0.001 HIS B 337 PHE 0.030 0.001 PHE A 278 TYR 0.010 0.001 TYR A 545 ARG 0.002 0.000 ARG A 399 *********************** 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 136 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 1.201 Fit side-chains REVERT: A 423 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8522 (tp) REVERT: B 423 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8529 (tp) outliers start: 16 outliers final: 14 residues processed: 130 average time/residue: 0.2063 time to fit residues: 39.5904 Evaluate side-chains 131 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 1.127 ------------------------------------------------------------------------------- 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 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 114 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 118 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3532 r_free = 0.3532 target = 0.127898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.096890 restraints weight = 17205.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.095864 restraints weight = 15116.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.097139 restraints weight = 14079.668| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10652 Z= 0.161 Angle : 0.551 8.924 14476 Z= 0.272 Chirality : 0.042 0.145 1722 Planarity : 0.004 0.054 1802 Dihedral : 4.173 42.457 1444 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.96 % Favored : 93.74 % Rotamer: Outliers : 1.58 % Allowed : 15.00 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.25), residues: 1342 helix: 2.27 (0.19), residues: 864 sheet: 2.64 (0.75), residues: 38 loop : -1.42 (0.32), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 472 HIS 0.001 0.001 HIS B 337 PHE 0.028 0.001 PHE A 278 TYR 0.011 0.001 TYR A 545 ARG 0.002 0.000 ARG A 399 *********************** 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 134 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 1.120 Fit side-chains REVERT: A 110 VAL cc_start: 0.7013 (OUTLIER) cc_final: 0.6750 (p) REVERT: A 225 MET cc_start: 0.7688 (OUTLIER) cc_final: 0.7261 (ttm) REVERT: A 423 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8432 (tp) REVERT: B 303 ILE cc_start: 0.8345 (mm) cc_final: 0.8039 (mt) REVERT: B 423 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8440 (tp) outliers start: 18 outliers final: 14 residues processed: 129 average time/residue: 0.2105 time to fit residues: 39.5244 Evaluate side-chains 133 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 1.233 ------------------------------------------------------------------------------- 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 195 VAL Chi-restraints excluded: chain A residue 225 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 70 optimal weight: 8.9990 chunk 34 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 18 optimal weight: 0.0370 chunk 130 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 11 optimal weight: 0.0980 overall best weight: 0.7460 ------------------------------------------------------------------------------- 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 = 0.3544 r_free = 0.3544 target = 0.128791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.098531 restraints weight = 17374.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.097150 restraints weight = 15801.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.097931 restraints weight = 18701.846| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10652 Z= 0.148 Angle : 0.536 8.831 14476 Z= 0.265 Chirality : 0.042 0.148 1722 Planarity : 0.004 0.051 1802 Dihedral : 4.059 40.722 1444 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.89 % Favored : 93.82 % Rotamer: Outliers : 1.75 % Allowed : 14.82 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.25), residues: 1342 helix: 2.34 (0.19), residues: 864 sheet: 2.71 (0.74), residues: 38 loop : -1.33 (0.32), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 472 HIS 0.002 0.000 HIS B 220 PHE 0.027 0.001 PHE A 278 TYR 0.010 0.001 TYR A 545 ARG 0.002 0.000 ARG A 571 *********************** 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 139 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 1.118 Fit side-chains REVERT: A 110 VAL cc_start: 0.6804 (OUTLIER) cc_final: 0.6541 (p) REVERT: A 225 MET cc_start: 0.7697 (OUTLIER) cc_final: 0.7252 (ttm) REVERT: A 423 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8388 (tp) REVERT: B 110 VAL cc_start: 0.6939 (OUTLIER) cc_final: 0.6620 (p) REVERT: B 303 ILE cc_start: 0.8315 (mm) cc_final: 0.8027 (mt) REVERT: B 423 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8321 (tp) outliers start: 20 outliers final: 14 residues processed: 132 average time/residue: 0.2270 time to fit residues: 43.8148 Evaluate side-chains 136 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 1.158 ------------------------------------------------------------------------------- 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 195 VAL Chi-restraints excluded: chain A residue 225 MET 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 110 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 13 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 chunk 94 optimal weight: 6.9990 chunk 44 optimal weight: 0.0870 chunk 25 optimal weight: 2.9990 chunk 65 optimal weight: 0.3980 chunk 89 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 overall best weight: 0.6962 ------------------------------------------------------------------------------- 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 = 0.3548 r_free = 0.3548 target = 0.129038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.098612 restraints weight = 17370.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.097990 restraints weight = 15604.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.098497 restraints weight = 17978.350| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10652 Z= 0.146 Angle : 0.540 9.060 14476 Z= 0.264 Chirality : 0.042 0.145 1722 Planarity : 0.004 0.051 1802 Dihedral : 4.015 39.999 1444 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.74 % Favored : 93.96 % Rotamer: Outliers : 1.75 % Allowed : 14.65 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.25), residues: 1342 helix: 2.47 (0.19), residues: 852 sheet: 2.76 (0.74), residues: 38 loop : -1.27 (0.32), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 472 HIS 0.002 0.000 HIS B 220 PHE 0.027 0.001 PHE A 278 TYR 0.011 0.001 TYR A 545 ARG 0.001 0.000 ARG A 399 ********************** 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 138 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 1.138 Fit side-chains REVERT: A 110 VAL cc_start: 0.6818 (OUTLIER) cc_final: 0.6530 (p) REVERT: A 225 MET cc_start: 0.7687 (OUTLIER) cc_final: 0.7242 (ttm) REVERT: A 423 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8258 (tp) REVERT: B 110 VAL cc_start: 0.6904 (OUTLIER) cc_final: 0.6564 (p) REVERT: B 225 MET cc_start: 0.7651 (OUTLIER) cc_final: 0.7298 (ttm) REVERT: B 303 ILE cc_start: 0.8327 (mm) cc_final: 0.8045 (mt) REVERT: B 423 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8320 (tp) outliers start: 20 outliers final: 14 residues processed: 131 average time/residue: 0.2152 time to fit residues: 40.5475 Evaluate side-chains 136 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 1.072 ------------------------------------------------------------------------------- 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 195 VAL Chi-restraints excluded: chain A residue 225 MET 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 110 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 225 MET 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 111 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 80 optimal weight: 7.9990 chunk 88 optimal weight: 0.0570 chunk 86 optimal weight: 0.0170 chunk 37 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 129 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 overall best weight: 0.9340 ------------------------------------------------------------------------------- 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 = 0.3543 r_free = 0.3543 target = 0.128751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.098339 restraints weight = 17059.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.097695 restraints weight = 15536.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.098121 restraints weight = 18333.131| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10652 Z= 0.159 Angle : 0.551 9.170 14476 Z= 0.268 Chirality : 0.042 0.145 1722 Planarity : 0.004 0.050 1802 Dihedral : 4.008 40.098 1444 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.89 % Favored : 93.82 % Rotamer: Outliers : 1.93 % Allowed : 14.56 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.25), residues: 1342 helix: 2.49 (0.19), residues: 850 sheet: 2.76 (0.74), residues: 38 loop : -1.33 (0.31), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 472 HIS 0.002 0.000 HIS B 220 PHE 0.030 0.001 PHE B 278 TYR 0.011 0.001 TYR A 545 ARG 0.002 0.000 ARG A 399 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2561.47 seconds wall clock time: 47 minutes 5.55 seconds (2825.55 seconds total)