Starting phenix.real_space_refine on Mon Jul 28 16:53:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s9e_24934/07_2025/7s9e_24934.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s9e_24934/07_2025/7s9e_24934.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7s9e_24934/07_2025/7s9e_24934.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s9e_24934/07_2025/7s9e_24934.map" model { file = "/net/cci-nas-00/data/ceres_data/7s9e_24934/07_2025/7s9e_24934.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s9e_24934/07_2025/7s9e_24934.cif" } resolution = 3.7 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= 0.005 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 48 5.16 5 C 6870 2.51 5 N 1682 2.21 5 O 1876 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10476 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 677, 5228 Classifications: {'peptide': 677} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 33, 'TRANS': 643} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 5228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 677, 5228 Classifications: {'peptide': 677} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 33, 'TRANS': 643} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 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: 7.29, per 1000 atoms: 0.70 Number of scatterers: 10476 At special positions: 0 Unit cell: (117.993, 113.741, 113.741, 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 48 16.00 O 1876 8.00 N 1682 7.00 C 6870 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: 3.24 Conformation dependent library (CDL) restraints added in 1.7 seconds 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2500 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 4 sheets defined 65.9% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 24 through 31 Processing helix chain 'A' and resid 44 through 48 removed outlier: 4.077A pdb=" N LYS A 47 " --> pdb=" O ASP A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 64 Processing helix chain 'A' and resid 66 through 71 removed outlier: 4.123A pdb=" N TRP A 70 " --> pdb=" O PRO A 66 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU A 71 " --> pdb=" O ILE A 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 66 through 71' Processing helix chain 'A' and resid 78 through 104 removed outlier: 3.803A pdb=" N GLY A 82 " --> pdb=" O GLU A 78 " (cutoff:3.500A) Proline residue: A 96 - end of helix Processing helix chain 'A' and resid 109 through 127 removed outlier: 3.951A pdb=" N LEU A 113 " --> pdb=" O PRO A 109 " (cutoff:3.500A) Proline residue: A 119 - end of helix Processing helix chain 'A' and resid 137 through 152 Processing helix chain 'A' and resid 168 through 196 Processing helix chain 'A' and resid 197 through 204 removed outlier: 4.180A pdb=" N PHE A 200 " --> pdb=" O ARG A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 230 removed outlier: 3.579A pdb=" N PHE A 230 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 253 Processing helix chain 'A' and resid 258 through 282 removed outlier: 3.888A pdb=" N GLU A 280 " --> pdb=" O LYS A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 308 removed outlier: 4.088A pdb=" N PHE A 295 " --> pdb=" O PRO A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 314 Processing helix chain 'A' and resid 335 through 338 Processing helix chain 'A' and resid 339 through 365 removed outlier: 3.838A pdb=" N LYS A 364 " --> pdb=" O THR A 360 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N HIS A 365 " --> pdb=" O LEU A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 388 Processing helix chain 'A' and resid 396 through 407 removed outlier: 3.580A pdb=" N SER A 400 " --> pdb=" O SER A 396 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY A 407 " --> pdb=" O GLN A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 427 Processing helix chain 'A' and resid 436 through 448 removed outlier: 3.804A pdb=" N LEU A 440 " --> pdb=" O PRO A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 454 Processing helix chain 'A' and resid 456 through 465 removed outlier: 3.763A pdb=" N PHE A 460 " --> pdb=" O SER A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 481 Processing helix chain 'A' and resid 484 through 502 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: 3.501A 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 removed outlier: 3.826A pdb=" N ASN A 690 " --> pdb=" O ASP A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 701 Processing helix chain 'A' and resid 705 through 721 Processing helix chain 'B' and resid 24 through 31 Processing helix chain 'B' and resid 44 through 48 removed outlier: 4.077A pdb=" N LYS B 47 " --> pdb=" O ASP B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 64 Processing helix chain 'B' and resid 66 through 71 removed outlier: 4.123A pdb=" N TRP B 70 " --> pdb=" O PRO B 66 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU B 71 " --> pdb=" O ILE B 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 66 through 71' Processing helix chain 'B' and resid 78 through 104 removed outlier: 3.804A pdb=" N GLY B 82 " --> pdb=" O GLU B 78 " (cutoff:3.500A) Proline residue: B 96 - end of helix Processing helix chain 'B' and resid 109 through 127 removed outlier: 3.951A pdb=" N LEU B 113 " --> pdb=" O PRO B 109 " (cutoff:3.500A) Proline residue: B 119 - end of helix Processing helix chain 'B' and resid 137 through 152 Processing helix chain 'B' and resid 168 through 196 Processing helix chain 'B' and resid 197 through 204 removed outlier: 4.180A pdb=" N PHE B 200 " --> pdb=" O ARG B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 230 removed outlier: 3.578A pdb=" N PHE B 230 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 253 Processing helix chain 'B' and resid 258 through 282 removed outlier: 3.890A pdb=" N GLU B 280 " --> pdb=" O LYS B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 308 removed outlier: 4.088A pdb=" N PHE B 295 " --> pdb=" O PRO B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 314 Processing helix chain 'B' and resid 335 through 338 Processing helix chain 'B' and resid 339 through 365 removed outlier: 3.837A pdb=" N LYS B 364 " --> pdb=" O THR B 360 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N HIS B 365 " --> pdb=" O LEU B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 388 Processing helix chain 'B' and resid 396 through 407 removed outlier: 3.580A pdb=" N SER B 400 " --> pdb=" O SER B 396 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY B 407 " --> pdb=" O GLN B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 427 Processing helix chain 'B' and resid 436 through 448 removed outlier: 3.805A pdb=" N LEU B 440 " --> pdb=" O PRO B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 454 Processing helix chain 'B' and resid 456 through 465 removed outlier: 3.763A pdb=" N PHE B 460 " --> pdb=" O SER B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 481 Processing helix chain 'B' and resid 484 through 502 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: 3.501A 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 removed outlier: 3.827A pdb=" N ASN B 690 " --> pdb=" O ASP B 686 " (cutoff:3.500A) Processing helix chain 'B' and resid 697 through 701 Processing helix chain 'B' and resid 705 through 721 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: 4.475A pdb=" N ILE A 537 " --> pdb=" O LEU A 511 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N GLN A 513 " --> pdb=" O ILE A 535 " (cutoff:3.500A) removed outlier: 11.934A pdb=" N ILE A 535 " --> pdb=" O GLN A 513 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LYS A 536 " --> pdb=" O ILE A 643 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N ASP A 645 " --> pdb=" O LYS A 536 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N PHE A 538 " --> pdb=" O ASP A 645 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ILE A 642 " --> pdb=" O TYR A 675 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ALA A 677 " --> pdb=" O ILE A 642 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU A 644 " --> pdb=" O ALA A 677 " (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: 4.475A pdb=" N ILE B 537 " --> pdb=" O LEU B 511 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N GLN B 513 " --> pdb=" O ILE B 535 " (cutoff:3.500A) removed outlier: 11.934A pdb=" N ILE B 535 " --> pdb=" O GLN B 513 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LYS B 536 " --> pdb=" O ILE B 643 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N ASP B 645 " --> pdb=" O LYS B 536 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N PHE B 538 " --> pdb=" O ASP B 645 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE B 642 " --> pdb=" O TYR B 675 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ALA B 677 " --> pdb=" O ILE B 642 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU B 644 " --> pdb=" O ALA B 677 " (cutoff:3.500A) 622 hydrogen bonds defined for protein. 1806 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: 2.95 Time building geometry restraints manager: 3.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3176 1.34 - 1.46: 2107 1.46 - 1.58: 5351 1.58 - 1.70: 0 1.70 - 1.83: 78 Bond restraints: 10712 Sorted by residual: bond pdb=" N VAL B 27 " pdb=" CA VAL B 27 " ideal model delta sigma weight residual 1.461 1.497 -0.036 1.20e-02 6.94e+03 9.18e+00 bond pdb=" N ILE B 22 " pdb=" CA ILE B 22 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.29e-02 6.01e+03 8.87e+00 bond pdb=" N ILE A 494 " pdb=" CA ILE A 494 " ideal model delta sigma weight residual 1.460 1.495 -0.036 1.21e-02 6.83e+03 8.70e+00 bond pdb=" N ILE A 22 " pdb=" CA ILE A 22 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.29e-02 6.01e+03 8.54e+00 bond pdb=" N ILE B 494 " pdb=" CA ILE B 494 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.21e-02 6.83e+03 8.38e+00 ... (remaining 10707 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 14117 1.85 - 3.69: 363 3.69 - 5.54: 66 5.54 - 7.38: 12 7.38 - 9.23: 2 Bond angle restraints: 14560 Sorted by residual: angle pdb=" C GLU B 694 " pdb=" N ASN B 695 " pdb=" CA ASN B 695 " ideal model delta sigma weight residual 122.83 127.56 -4.73 1.08e+00 8.57e-01 1.92e+01 angle pdb=" C GLU A 694 " pdb=" N ASN A 695 " pdb=" CA ASN A 695 " ideal model delta sigma weight residual 122.83 127.56 -4.73 1.08e+00 8.57e-01 1.91e+01 angle pdb=" CA SER B 24 " pdb=" C SER B 24 " pdb=" O SER B 24 " ideal model delta sigma weight residual 121.87 117.24 4.63 1.16e+00 7.43e-01 1.59e+01 angle pdb=" N SER A 24 " pdb=" CA SER A 24 " pdb=" C SER A 24 " ideal model delta sigma weight residual 110.53 105.46 5.07 1.29e+00 6.01e-01 1.54e+01 angle pdb=" CA SER A 24 " pdb=" C SER A 24 " pdb=" O SER A 24 " ideal model delta sigma weight residual 121.94 117.49 4.45 1.15e+00 7.56e-01 1.50e+01 ... (remaining 14555 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 5760 17.92 - 35.85: 482 35.85 - 53.77: 80 53.77 - 71.69: 4 71.69 - 89.62: 8 Dihedral angle restraints: 6334 sinusoidal: 2428 harmonic: 3906 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 180.00 154.89 25.11 0 5.00e+00 4.00e-02 2.52e+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 180.00 154.93 25.07 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA VAL B 268 " pdb=" C VAL B 268 " pdb=" N PHE B 269 " pdb=" CA PHE B 269 " ideal model delta harmonic sigma weight residual 180.00 158.22 21.78 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 6331 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1145 0.040 - 0.080: 392 0.080 - 0.120: 167 0.120 - 0.160: 17 0.160 - 0.200: 5 Chirality restraints: 1726 Sorted by residual: chirality pdb=" CB THR B 128 " pdb=" CA THR B 128 " pdb=" OG1 THR B 128 " pdb=" CG2 THR B 128 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 9.97e-01 chirality pdb=" CB THR A 128 " pdb=" CA THR A 128 " pdb=" OG1 THR A 128 " pdb=" CG2 THR A 128 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 9.92e-01 chirality pdb=" CA VAL A 27 " pdb=" N VAL A 27 " pdb=" C VAL A 27 " pdb=" CB VAL A 27 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.06e-01 ... (remaining 1723 not shown) Planarity restraints: 1816 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 288 " 0.029 5.00e-02 4.00e+02 4.45e-02 3.17e+00 pdb=" N PRO A 289 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 289 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 289 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 288 " 0.029 5.00e-02 4.00e+02 4.44e-02 3.15e+00 pdb=" N PRO B 289 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 289 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 289 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 21 " 0.009 2.00e-02 2.50e+03 1.75e-02 3.06e+00 pdb=" C PRO A 21 " -0.030 2.00e-02 2.50e+03 pdb=" O PRO A 21 " 0.011 2.00e-02 2.50e+03 pdb=" N ILE A 22 " 0.010 2.00e-02 2.50e+03 ... (remaining 1813 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 990 2.74 - 3.28: 11442 3.28 - 3.82: 17388 3.82 - 4.36: 20002 4.36 - 4.90: 34045 Nonbonded interactions: 83867 Sorted by model distance: nonbonded pdb=" OG SER B 167 " pdb=" OE1 GLU B 169 " model vdw 2.202 3.040 nonbonded pdb=" OG SER A 167 " pdb=" OE1 GLU A 169 " model vdw 2.202 3.040 nonbonded pdb=" OG SER B 41 " pdb=" O ASP B 44 " model vdw 2.214 3.040 nonbonded pdb=" OG SER A 41 " pdb=" O ASP A 44 " model vdw 2.215 3.040 nonbonded pdb=" O PHE B 101 " pdb=" OG SER B 141 " model vdw 2.225 3.040 ... (remaining 83862 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: 0.06 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: 1.040 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: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 28.410 Find NCS groups from input model: 0.210 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:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 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 : 0.004 0.038 10712 Z= 0.205 Angle : 0.721 9.226 14560 Z= 0.411 Chirality : 0.047 0.200 1726 Planarity : 0.004 0.045 1816 Dihedral : 13.528 89.618 3834 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.23), residues: 1346 helix: 0.73 (0.18), residues: 838 sheet: 1.28 (0.94), residues: 36 loop : -2.17 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 472 HIS 0.004 0.001 HIS B 25 PHE 0.021 0.002 PHE B 198 TYR 0.012 0.001 TYR A 16 ARG 0.007 0.001 ARG B 716 Details of bonding type rmsd hydrogen bonds : bond 0.12910 ( 622) hydrogen bonds : angle 5.75772 ( 1806) covalent geometry : bond 0.00368 (10712) covalent geometry : angle 0.72119 (14560) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 1.276 Fit side-chains revert: symmetry clash REVERT: A 125 PHE cc_start: 0.8118 (m-10) cc_final: 0.7696 (m-10) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.2115 time to fit residues: 46.2793 Evaluate side-chains 111 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 1.225 ------------------------------------------------------------------------------- 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: 1.9990 chunk 101 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 121 optimal weight: 0.6980 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.121995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.091794 restraints weight = 17265.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.093020 restraints weight = 15508.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.093822 restraints weight = 12279.094| |-----------------------------------------------------------------------------| r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 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 : 0.005 0.046 10712 Z= 0.223 Angle : 0.668 6.072 14560 Z= 0.345 Chirality : 0.047 0.158 1726 Planarity : 0.005 0.048 1816 Dihedral : 5.289 52.703 1450 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 1.66 % Allowed : 7.67 % Favored : 90.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.23), residues: 1346 helix: 0.81 (0.18), residues: 848 sheet: 1.62 (0.96), residues: 36 loop : -2.11 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 472 HIS 0.006 0.001 HIS A 131 PHE 0.019 0.002 PHE B 111 TYR 0.015 0.002 TYR A 16 ARG 0.003 0.000 ARG A 572 Details of bonding type rmsd hydrogen bonds : bond 0.05325 ( 622) hydrogen bonds : angle 4.71694 ( 1806) covalent geometry : bond 0.00526 (10712) covalent geometry : angle 0.66773 (14560) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 1.179 Fit side-chains revert: symmetry clash REVERT: B 326 LEU cc_start: 0.8460 (mt) cc_final: 0.8034 (mt) outliers start: 19 outliers final: 15 residues processed: 127 average time/residue: 0.1968 time to fit residues: 37.7521 Evaluate side-chains 124 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 192 CYS Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 423 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 95 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 2 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 105 optimal weight: 0.0870 chunk 36 optimal weight: 1.9990 chunk 133 optimal weight: 0.8980 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 HIS ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 548 ASN B 365 HIS ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 548 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.125746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.094723 restraints weight = 17304.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.096469 restraints weight = 13754.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.096963 restraints weight = 9119.736| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10712 Z= 0.130 Angle : 0.573 5.368 14560 Z= 0.295 Chirality : 0.044 0.145 1726 Planarity : 0.004 0.045 1816 Dihedral : 5.031 48.764 1450 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 1.92 % Allowed : 11.24 % Favored : 86.85 % 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: 0.19 (0.24), residues: 1346 helix: 1.14 (0.18), residues: 848 sheet: 1.80 (0.99), residues: 36 loop : -2.01 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 472 HIS 0.003 0.001 HIS B 33 PHE 0.014 0.001 PHE A 111 TYR 0.016 0.001 TYR B 578 ARG 0.003 0.000 ARG B 631 Details of bonding type rmsd hydrogen bonds : bond 0.04506 ( 622) hydrogen bonds : angle 4.37969 ( 1806) covalent geometry : bond 0.00288 (10712) covalent geometry : angle 0.57293 (14560) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 132 time to evaluate : 1.244 Fit side-chains revert: symmetry clash REVERT: A 527 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.7318 (pt0) REVERT: B 326 LEU cc_start: 0.8389 (mt) cc_final: 0.7975 (mt) outliers start: 22 outliers final: 13 residues processed: 141 average time/residue: 0.2203 time to fit residues: 46.8557 Evaluate side-chains 132 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 423 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 87 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 72 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 16 optimal weight: 8.9990 chunk 43 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 129 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 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 = 0.3523 r_free = 0.3523 target = 0.123209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.093014 restraints weight = 17461.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.092232 restraints weight = 13615.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.093398 restraints weight = 12809.409| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10712 Z= 0.196 Angle : 0.621 9.744 14560 Z= 0.316 Chirality : 0.045 0.151 1726 Planarity : 0.004 0.047 1816 Dihedral : 5.034 48.572 1450 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 3.05 % Allowed : 12.28 % Favored : 84.67 % 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: 0.24 (0.24), residues: 1346 helix: 1.19 (0.18), residues: 848 sheet: 1.70 (0.99), residues: 36 loop : -1.97 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 472 HIS 0.003 0.001 HIS A 707 PHE 0.016 0.002 PHE B 111 TYR 0.014 0.001 TYR B 16 ARG 0.002 0.000 ARG B 502 Details of bonding type rmsd hydrogen bonds : bond 0.04654 ( 622) hydrogen bonds : angle 4.34943 ( 1806) covalent geometry : bond 0.00465 (10712) covalent geometry : angle 0.62089 (14560) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 118 time to evaluate : 1.697 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.7932 (mmmt) cc_final: 0.7662 (mppt) REVERT: A 206 THR cc_start: 0.8685 (OUTLIER) cc_final: 0.8478 (m) REVERT: A 225 MET cc_start: 0.8329 (mmm) cc_final: 0.8092 (mmm) REVERT: A 527 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7381 (pt0) REVERT: A 577 LYS cc_start: 0.8025 (tmtt) cc_final: 0.7765 (tmtt) REVERT: B 55 LYS cc_start: 0.7917 (mmmt) cc_final: 0.7647 (mppt) REVERT: B 206 THR cc_start: 0.8692 (OUTLIER) cc_final: 0.8491 (m) REVERT: B 225 MET cc_start: 0.8340 (mmm) cc_final: 0.8108 (mmm) REVERT: B 326 LEU cc_start: 0.8418 (mt) cc_final: 0.7986 (mt) outliers start: 35 outliers final: 22 residues processed: 141 average time/residue: 0.2528 time to fit residues: 53.5132 Evaluate side-chains 143 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 118 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 70 TRP Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 70 TRP Chi-restraints excluded: chain B residue 103 MET Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 532 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 83 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 45 optimal weight: 0.0970 chunk 70 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 114 optimal weight: 7.9990 chunk 82 optimal weight: 0.0970 chunk 127 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 ASN ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.126700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.097519 restraints weight = 17312.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.096369 restraints weight = 13017.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.097106 restraints weight = 12631.859| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10712 Z= 0.120 Angle : 0.553 7.651 14560 Z= 0.281 Chirality : 0.043 0.152 1726 Planarity : 0.004 0.045 1816 Dihedral : 4.818 44.397 1450 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 3.48 % Allowed : 13.07 % Favored : 83.45 % 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: 0.55 (0.24), residues: 1346 helix: 1.47 (0.18), residues: 848 sheet: 1.85 (1.00), residues: 36 loop : -1.93 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 472 HIS 0.003 0.001 HIS B 337 PHE 0.013 0.001 PHE B 111 TYR 0.017 0.001 TYR A 578 ARG 0.002 0.000 ARG B 399 Details of bonding type rmsd hydrogen bonds : bond 0.04111 ( 622) hydrogen bonds : angle 4.13473 ( 1806) covalent geometry : bond 0.00264 (10712) covalent geometry : angle 0.55318 (14560) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 132 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.7927 (mmmt) cc_final: 0.7648 (mppt) REVERT: A 225 MET cc_start: 0.8397 (mmm) cc_final: 0.7639 (mmm) REVERT: A 527 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7251 (pt0) REVERT: B 55 LYS cc_start: 0.7904 (mmmt) cc_final: 0.7627 (mppt) REVERT: B 326 LEU cc_start: 0.8308 (mt) cc_final: 0.7892 (mt) outliers start: 40 outliers final: 23 residues processed: 156 average time/residue: 0.2594 time to fit residues: 61.4652 Evaluate side-chains 150 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 1.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 70 TRP Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 64 PHE Chi-restraints excluded: chain B residue 70 TRP Chi-restraints excluded: chain B residue 103 MET Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 192 CYS Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 620 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 103 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 49 optimal weight: 0.0370 chunk 87 optimal weight: 0.7980 chunk 101 optimal weight: 0.8980 chunk 46 optimal weight: 0.0770 chunk 50 optimal weight: 0.1980 chunk 58 optimal weight: 0.9990 chunk 114 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 ASN ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 GLN ** B 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.128331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.098825 restraints weight = 17483.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.097871 restraints weight = 14479.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.098810 restraints weight = 12218.672| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10712 Z= 0.120 Angle : 0.581 11.964 14560 Z= 0.288 Chirality : 0.044 0.165 1726 Planarity : 0.004 0.048 1816 Dihedral : 4.694 42.106 1450 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 2.70 % Allowed : 14.63 % Favored : 82.67 % 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: 0.68 (0.24), residues: 1346 helix: 1.55 (0.19), residues: 848 sheet: 1.94 (1.00), residues: 36 loop : -1.85 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 472 HIS 0.002 0.001 HIS A 337 PHE 0.012 0.001 PHE A 111 TYR 0.010 0.001 TYR A 546 ARG 0.002 0.000 ARG A 399 Details of bonding type rmsd hydrogen bonds : bond 0.03961 ( 622) hydrogen bonds : angle 4.05090 ( 1806) covalent geometry : bond 0.00272 (10712) covalent geometry : angle 0.58126 (14560) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 129 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.7913 (mmmt) cc_final: 0.7627 (mppt) REVERT: A 225 MET cc_start: 0.8404 (mmm) cc_final: 0.7676 (mmm) REVERT: A 527 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7240 (pt0) REVERT: B 55 LYS cc_start: 0.7922 (mmmt) cc_final: 0.7642 (mppt) REVERT: B 326 LEU cc_start: 0.8289 (mt) cc_final: 0.7915 (mt) outliers start: 31 outliers final: 30 residues processed: 145 average time/residue: 0.2329 time to fit residues: 50.8505 Evaluate side-chains 148 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 117 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 70 TRP Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 70 TRP Chi-restraints excluded: chain B residue 103 MET Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 192 CYS Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 527 GLU Chi-restraints excluded: chain B residue 532 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 42 optimal weight: 7.9990 chunk 46 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 54 optimal weight: 0.3980 chunk 9 optimal weight: 0.0980 chunk 27 optimal weight: 9.9990 chunk 61 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 126 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 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 = 0.3590 r_free = 0.3590 target = 0.128322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.098926 restraints weight = 17612.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.098499 restraints weight = 14151.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.099116 restraints weight = 12348.569| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10712 Z= 0.121 Angle : 0.578 10.104 14560 Z= 0.286 Chirality : 0.044 0.154 1726 Planarity : 0.004 0.046 1816 Dihedral : 4.642 41.001 1450 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.96 % Allowed : 16.20 % Favored : 80.84 % 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: 0.68 (0.24), residues: 1346 helix: 1.56 (0.18), residues: 856 sheet: 1.80 (0.99), residues: 36 loop : -1.91 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 472 HIS 0.002 0.001 HIS A 337 PHE 0.012 0.001 PHE A 111 TYR 0.019 0.001 TYR A 578 ARG 0.002 0.000 ARG A 399 Details of bonding type rmsd hydrogen bonds : bond 0.03943 ( 622) hydrogen bonds : angle 4.00978 ( 1806) covalent geometry : bond 0.00278 (10712) covalent geometry : angle 0.57769 (14560) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 121 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.7898 (mmmt) cc_final: 0.7601 (mppt) REVERT: A 497 MET cc_start: 0.7645 (mmp) cc_final: 0.6446 (tpt) REVERT: B 55 LYS cc_start: 0.7909 (mmmt) cc_final: 0.7628 (mppt) REVERT: B 326 LEU cc_start: 0.8274 (mt) cc_final: 0.7944 (mt) REVERT: B 497 MET cc_start: 0.7703 (mmp) cc_final: 0.6470 (tpt) outliers start: 34 outliers final: 31 residues processed: 140 average time/residue: 0.1891 time to fit residues: 40.3089 Evaluate side-chains 148 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 117 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 64 PHE Chi-restraints excluded: chain B residue 103 MET Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 192 CYS Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 527 GLU Chi-restraints excluded: chain B residue 532 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 127 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 chunk 62 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** 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 = 0.3560 r_free = 0.3560 target = 0.126096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.096518 restraints weight = 17402.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.096507 restraints weight = 13144.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.097608 restraints weight = 12205.092| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10712 Z= 0.155 Angle : 0.600 9.970 14560 Z= 0.297 Chirality : 0.044 0.158 1726 Planarity : 0.004 0.048 1816 Dihedral : 4.676 41.756 1450 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 2.96 % Allowed : 16.81 % Favored : 80.23 % 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: 0.78 (0.24), residues: 1346 helix: 1.63 (0.18), residues: 848 sheet: 1.73 (0.98), residues: 36 loop : -1.77 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 70 HIS 0.002 0.001 HIS B 707 PHE 0.014 0.001 PHE A 111 TYR 0.013 0.001 TYR A 546 ARG 0.002 0.000 ARG A 399 Details of bonding type rmsd hydrogen bonds : bond 0.04109 ( 622) hydrogen bonds : angle 4.04209 ( 1806) covalent geometry : bond 0.00371 (10712) covalent geometry : angle 0.60013 (14560) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 123 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.7909 (mmmt) cc_final: 0.7651 (mppt) REVERT: A 225 MET cc_start: 0.8333 (mmm) cc_final: 0.7349 (mmm) REVERT: A 527 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7226 (pt0) REVERT: B 55 LYS cc_start: 0.7917 (mmmt) cc_final: 0.7664 (mppt) REVERT: B 225 MET cc_start: 0.8363 (mmm) cc_final: 0.7539 (mmm) REVERT: B 326 LEU cc_start: 0.8287 (mt) cc_final: 0.7952 (mt) outliers start: 34 outliers final: 32 residues processed: 141 average time/residue: 0.1933 time to fit residues: 41.6696 Evaluate side-chains 151 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 118 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 70 TRP Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 64 PHE Chi-restraints excluded: chain B residue 103 MET Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 192 CYS Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 527 GLU Chi-restraints excluded: chain B residue 532 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 58 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 89 optimal weight: 6.9990 chunk 110 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** 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 = 0.3543 r_free = 0.3543 target = 0.124868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.095088 restraints weight = 17690.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.094928 restraints weight = 15292.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.096091 restraints weight = 11579.993| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10712 Z= 0.166 Angle : 0.617 9.940 14560 Z= 0.306 Chirality : 0.045 0.163 1726 Planarity : 0.004 0.046 1816 Dihedral : 4.765 42.510 1450 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 3.48 % Allowed : 16.81 % Favored : 79.70 % 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: 0.76 (0.24), residues: 1346 helix: 1.64 (0.18), residues: 846 sheet: 1.63 (0.95), residues: 36 loop : -1.82 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 70 HIS 0.002 0.001 HIS A 707 PHE 0.014 0.001 PHE A 111 TYR 0.015 0.001 TYR B 546 ARG 0.003 0.000 ARG A 399 Details of bonding type rmsd hydrogen bonds : bond 0.04272 ( 622) hydrogen bonds : angle 4.06964 ( 1806) covalent geometry : bond 0.00399 (10712) covalent geometry : angle 0.61676 (14560) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 113 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.7902 (mmmt) cc_final: 0.7665 (mppt) REVERT: A 225 MET cc_start: 0.8354 (mmm) cc_final: 0.7743 (mmm) REVERT: A 527 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7220 (pt0) REVERT: B 55 LYS cc_start: 0.7898 (mmmt) cc_final: 0.7664 (mppt) REVERT: B 326 LEU cc_start: 0.8367 (mt) cc_final: 0.8013 (mt) outliers start: 40 outliers final: 32 residues processed: 136 average time/residue: 0.2015 time to fit residues: 41.9632 Evaluate side-chains 145 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 112 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 103 MET Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 192 CYS Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 527 GLU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 620 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 123 optimal weight: 9.9990 chunk 68 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 121 optimal weight: 0.0970 chunk 66 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 128 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** 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 = 0.3572 r_free = 0.3572 target = 0.127009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.097691 restraints weight = 17491.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.098801 restraints weight = 13094.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.099668 restraints weight = 11297.269| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10712 Z= 0.129 Angle : 0.602 9.742 14560 Z= 0.296 Chirality : 0.044 0.162 1726 Planarity : 0.004 0.047 1816 Dihedral : 4.706 40.992 1450 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 2.87 % Allowed : 17.16 % Favored : 79.97 % 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: 0.86 (0.24), residues: 1346 helix: 1.69 (0.18), residues: 850 sheet: 1.69 (0.95), residues: 36 loop : -1.76 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 70 HIS 0.002 0.001 HIS A 337 PHE 0.012 0.001 PHE A 111 TYR 0.010 0.001 TYR A 16 ARG 0.007 0.000 ARG A 631 Details of bonding type rmsd hydrogen bonds : bond 0.04037 ( 622) hydrogen bonds : angle 4.01481 ( 1806) covalent geometry : bond 0.00297 (10712) covalent geometry : angle 0.60216 (14560) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 114 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.7932 (mmmt) cc_final: 0.7666 (mppt) REVERT: A 225 MET cc_start: 0.8346 (mmm) cc_final: 0.7754 (mmm) REVERT: A 497 MET cc_start: 0.7853 (mmp) cc_final: 0.7647 (mmp) REVERT: A 527 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.7147 (pt0) REVERT: B 55 LYS cc_start: 0.7933 (mmmt) cc_final: 0.7673 (mppt) REVERT: B 225 MET cc_start: 0.8395 (mmm) cc_final: 0.7557 (mmm) REVERT: B 262 LEU cc_start: 0.8075 (mm) cc_final: 0.7771 (mt) REVERT: B 316 ASP cc_start: 0.8305 (t0) cc_final: 0.8080 (t0) REVERT: B 326 LEU cc_start: 0.8359 (mt) cc_final: 0.8033 (mt) REVERT: B 497 MET cc_start: 0.7911 (mmp) cc_final: 0.7701 (mmp) outliers start: 33 outliers final: 31 residues processed: 133 average time/residue: 0.2481 time to fit residues: 51.0787 Evaluate side-chains 142 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 110 time to evaluate : 2.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 70 TRP Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 64 PHE Chi-restraints excluded: chain B residue 70 TRP Chi-restraints excluded: chain B residue 103 MET Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 192 CYS Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 527 GLU Chi-restraints excluded: chain B residue 532 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 8 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 82 optimal weight: 9.9990 chunk 114 optimal weight: 3.9990 chunk 97 optimal weight: 0.1980 chunk 62 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** 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 = 0.3567 r_free = 0.3567 target = 0.126593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.097214 restraints weight = 17361.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.096956 restraints weight = 15444.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.098258 restraints weight = 11810.920| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10712 Z= 0.133 Angle : 0.594 9.609 14560 Z= 0.292 Chirality : 0.044 0.163 1726 Planarity : 0.004 0.048 1816 Dihedral : 4.647 40.242 1450 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 2.87 % Allowed : 17.51 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.24), residues: 1346 helix: 1.68 (0.18), residues: 852 sheet: 1.53 (0.96), residues: 36 loop : -1.71 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 70 HIS 0.002 0.001 HIS A 337 PHE 0.012 0.001 PHE A 111 TYR 0.011 0.001 TYR B 546 ARG 0.002 0.000 ARG B 399 Details of bonding type rmsd hydrogen bonds : bond 0.04026 ( 622) hydrogen bonds : angle 4.00259 ( 1806) covalent geometry : bond 0.00313 (10712) covalent geometry : angle 0.59425 (14560) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3553.81 seconds wall clock time: 67 minutes 42.57 seconds (4062.57 seconds total)