Starting phenix.real_space_refine on Mon Apr 28 06:26:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x06_37970/04_2025/8x06_37970.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x06_37970/04_2025/8x06_37970.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x06_37970/04_2025/8x06_37970.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x06_37970/04_2025/8x06_37970.map" model { file = "/net/cci-nas-00/data/ceres_data/8x06_37970/04_2025/8x06_37970.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x06_37970/04_2025/8x06_37970.cif" } resolution = 3.24 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= 0.006 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 59 5.16 5 C 4514 2.51 5 N 1197 2.21 5 O 1283 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 7053 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4320 Classifications: {'peptide': 536} Link IDs: {'PTRANS': 26, 'TRANS': 509} Chain breaks: 10 Chain: "C" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 359 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain breaks: 1 Chain: "D" Number of atoms: 261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 261 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 1, 'TRANS': 31} Chain breaks: 2 Chain: "B" Number of atoms: 2113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2113 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 10, 'TRANS': 243} Chain breaks: 10 Time building chain proxies: 6.38, per 1000 atoms: 0.90 Number of scatterers: 7053 At special positions: 0 Unit cell: (77.88, 92.4, 110.88, 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 59 16.00 O 1283 8.00 N 1197 7.00 C 4514 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS A 26 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 169 " - pdb=" SG CYS A 188 " distance=2.03 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 208 " - pdb=" SG CYS A 216 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 225 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 253 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 284 " distance=2.03 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 312 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 435 " - pdb=" SG CYS A 468 " distance=2.03 Simple disulfide: pdb=" SG CYS C 6 " - pdb=" SG CYS C 48 " distance=2.03 Simple disulfide: pdb=" SG CYS C 18 " - pdb=" SG CYS C 61 " distance=2.03 Simple disulfide: pdb=" SG CYS C 47 " - pdb=" SG CYS C 52 " distance=2.03 Simple disulfide: pdb=" SG CYS D 6 " - pdb=" SG CYS D 48 " distance=2.03 Simple disulfide: pdb=" SG CYS D 18 " - pdb=" SG CYS D 61 " distance=2.03 Simple disulfide: pdb=" SG CYS B 625 " - pdb=" SG CYS B 658 " distance=2.03 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: 1.52 Conformation dependent library (CDL) restraints added in 936.6 milliseconds 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1634 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 14 sheets defined 16.6% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 17 through 24 removed outlier: 3.546A pdb=" N LEU A 20 " --> pdb=" O LEU A 17 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N HIS A 21 " --> pdb=" O THR A 18 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N GLU A 22 " --> pdb=" O ARG A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 46 Processing helix chain 'A' and resid 127 through 131 removed outlier: 3.544A pdb=" N THR A 130 " --> pdb=" O TYR A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 268 removed outlier: 3.663A pdb=" N CYS A 266 " --> pdb=" O LEU A 262 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASN A 268 " --> pdb=" O HIS A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 329 removed outlier: 3.597A pdb=" N ALA A 327 " --> pdb=" O SER A 323 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLU A 329 " --> pdb=" O THR A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 358 Processing helix chain 'A' and resid 394 through 396 No H-bonds generated for 'chain 'A' and resid 394 through 396' Processing helix chain 'A' and resid 435 through 447 removed outlier: 3.780A pdb=" N ILE A 439 " --> pdb=" O CYS A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 removed outlier: 3.535A pdb=" N GLN A 452 " --> pdb=" O LYS A 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 18 removed outlier: 3.717A pdb=" N VAL C 11 " --> pdb=" O GLY C 7 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU C 14 " --> pdb=" O LEU C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 48 Processing helix chain 'C' and resid 53 through 58 Processing helix chain 'C' and resid 59 through 61 No H-bonds generated for 'chain 'C' and resid 59 through 61' Processing helix chain 'D' and resid 9 through 15 Processing helix chain 'D' and resid 53 through 57 removed outlier: 3.819A pdb=" N ARG D 56 " --> pdb=" O ASP D 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 546 removed outlier: 4.052A pdb=" N ALA B 546 " --> pdb=" O ALA B 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 542 through 546' Processing helix chain 'B' and resid 625 through 631 removed outlier: 3.984A pdb=" N ILE B 629 " --> pdb=" O CYS B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 634 No H-bonds generated for 'chain 'B' and resid 632 through 634' Processing helix chain 'B' and resid 882 through 904 Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 8 removed outlier: 3.668A pdb=" N ILE A 29 " --> pdb=" O MET A 56 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE A 57 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE A 82 " --> pdb=" O ASN A 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 38 removed outlier: 3.919A pdb=" N PHE A 64 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N VAL A 66 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU A 61 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N PHE A 96 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LEU A 63 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N LEU A 93 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N GLU A 120 " --> pdb=" O LEU A 93 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ILE A 95 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR A 144 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE A 119 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 231 through 233 Processing sheet with id=AA4, first strand: chain 'A' and resid 245 through 246 Processing sheet with id=AA5, first strand: chain 'A' and resid 292 through 293 Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 313 removed outlier: 3.796A pdb=" N ASN A 337 " --> pdb=" O CYS A 312 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ILE A 336 " --> pdb=" O SER A 365 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILE A 364 " --> pdb=" O ARG A 389 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 320 through 321 Processing sheet with id=AA8, first strand: chain 'A' and resid 368 through 370 removed outlier: 4.280A pdb=" N TYR A 398 " --> pdb=" O LYS A 425 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N PHE A 427 " --> pdb=" O TYR A 398 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N PHE A 400 " --> pdb=" O PHE A 427 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 484 through 487 removed outlier: 3.905A pdb=" N ILE A 485 " --> pdb=" O MET A 553 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N MET A 553 " --> pdb=" O ILE A 485 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU A 487 " --> pdb=" O TRP A 551 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 531 through 534 removed outlier: 3.640A pdb=" N PHE A 506 " --> pdb=" O PHE A 565 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N PHE A 565 " --> pdb=" O PHE A 506 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 525 through 526 removed outlier: 3.510A pdb=" N ILE B 526 " --> pdb=" O GLU B 553 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE B 554 " --> pdb=" O LEU B 577 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 558 through 560 Processing sheet with id=AB4, first strand: chain 'B' and resid 665 through 670 removed outlier: 3.550A pdb=" N ARG B 678 " --> pdb=" O SER B 666 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N ILE B 668 " --> pdb=" O LEU B 676 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N LEU B 676 " --> pdb=" O ILE B 668 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 722 through 724 removed outlier: 4.145A pdb=" N GLY B 692 " --> pdb=" O LEU B 759 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU B 759 " --> pdb=" O GLY B 692 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE B 755 " --> pdb=" O PHE B 696 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS B 698 " --> pdb=" O ALA B 753 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA B 753 " --> pdb=" O LYS B 698 " (cutoff:3.500A) 103 hydrogen bonds defined for protein. 258 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: 2.05 Time building geometry restraints manager: 1.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2264 1.35 - 1.46: 1718 1.46 - 1.58: 3148 1.58 - 1.70: 0 1.70 - 1.82: 73 Bond restraints: 7203 Sorted by residual: bond pdb=" CA LYS B 631 " pdb=" C LYS B 631 " ideal model delta sigma weight residual 1.523 1.570 -0.047 1.41e-02 5.03e+03 1.11e+01 bond pdb=" C PRO A 243 " pdb=" N PRO A 244 " ideal model delta sigma weight residual 1.335 1.361 -0.027 1.28e-02 6.10e+03 4.33e+00 bond pdb=" CB PRO A 307 " pdb=" CG PRO A 307 " ideal model delta sigma weight residual 1.492 1.542 -0.050 5.00e-02 4.00e+02 9.88e-01 bond pdb=" CB TRP B 604 " pdb=" CG TRP B 604 " ideal model delta sigma weight residual 1.498 1.524 -0.026 3.10e-02 1.04e+03 7.14e-01 bond pdb=" CA TYR D 60 " pdb=" CB TYR D 60 " ideal model delta sigma weight residual 1.524 1.535 -0.011 1.31e-02 5.83e+03 6.91e-01 ... (remaining 7198 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 9575 2.07 - 4.14: 128 4.14 - 6.21: 10 6.21 - 8.28: 2 8.28 - 10.35: 3 Bond angle restraints: 9718 Sorted by residual: angle pdb=" CB MET A 294 " pdb=" CG MET A 294 " pdb=" SD MET A 294 " ideal model delta sigma weight residual 112.70 122.46 -9.76 3.00e+00 1.11e-01 1.06e+01 angle pdb=" CA LEU B 550 " pdb=" CB LEU B 550 " pdb=" CG LEU B 550 " ideal model delta sigma weight residual 116.30 126.65 -10.35 3.50e+00 8.16e-02 8.75e+00 angle pdb=" CA LYS B 631 " pdb=" C LYS B 631 " pdb=" O LYS B 631 " ideal model delta sigma weight residual 119.28 122.83 -3.55 1.21e+00 6.83e-01 8.60e+00 angle pdb=" N GLY D 19 " pdb=" CA GLY D 19 " pdb=" C GLY D 19 " ideal model delta sigma weight residual 111.35 114.80 -3.45 1.20e+00 6.94e-01 8.27e+00 angle pdb=" CB ARG C 55 " pdb=" CG ARG C 55 " pdb=" CD ARG C 55 " ideal model delta sigma weight residual 111.30 117.54 -6.24 2.30e+00 1.89e-01 7.36e+00 ... (remaining 9713 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.10: 3560 17.10 - 34.20: 533 34.20 - 51.31: 188 51.31 - 68.41: 42 68.41 - 85.51: 19 Dihedral angle restraints: 4342 sinusoidal: 1827 harmonic: 2515 Sorted by residual: dihedral pdb=" CB CYS A 169 " pdb=" SG CYS A 169 " pdb=" SG CYS A 188 " pdb=" CB CYS A 188 " ideal model delta sinusoidal sigma weight residual -86.00 -171.51 85.51 1 1.00e+01 1.00e-02 8.85e+01 dihedral pdb=" CB CYS A 259 " pdb=" SG CYS A 259 " pdb=" SG CYS A 284 " pdb=" CB CYS A 284 " ideal model delta sinusoidal sigma weight residual -86.00 -164.02 78.02 1 1.00e+01 1.00e-02 7.61e+01 dihedral pdb=" CB CYS A 266 " pdb=" SG CYS A 266 " pdb=" SG CYS A 274 " pdb=" CB CYS A 274 " ideal model delta sinusoidal sigma weight residual 93.00 165.29 -72.29 1 1.00e+01 1.00e-02 6.68e+01 ... (remaining 4339 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 635 0.026 - 0.051: 249 0.051 - 0.077: 93 0.077 - 0.102: 44 0.102 - 0.128: 40 Chirality restraints: 1061 Sorted by residual: chirality pdb=" CA ILE A 585 " pdb=" N ILE A 585 " pdb=" C ILE A 585 " pdb=" CB ILE A 585 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.08e-01 chirality pdb=" CA ILE A 95 " pdb=" N ILE A 95 " pdb=" C ILE A 95 " pdb=" CB ILE A 95 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.91e-01 chirality pdb=" CA ILE A 370 " pdb=" N ILE A 370 " pdb=" C ILE A 370 " pdb=" CB ILE A 370 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.62e-01 ... (remaining 1058 not shown) Planarity restraints: 1233 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 306 " -0.042 5.00e-02 4.00e+02 6.30e-02 6.34e+00 pdb=" N PRO A 307 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 307 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 307 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 243 " 0.035 5.00e-02 4.00e+02 5.23e-02 4.38e+00 pdb=" N PRO A 244 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 244 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 244 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 316 " 0.007 2.00e-02 2.50e+03 1.38e-02 1.89e+00 pdb=" C GLU A 316 " -0.024 2.00e-02 2.50e+03 pdb=" O GLU A 316 " 0.009 2.00e-02 2.50e+03 pdb=" N GLY A 317 " 0.008 2.00e-02 2.50e+03 ... (remaining 1230 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1567 2.79 - 3.32: 5823 3.32 - 3.84: 10999 3.84 - 4.37: 12266 4.37 - 4.90: 21398 Nonbonded interactions: 52053 Sorted by model distance: nonbonded pdb=" O ILE A 29 " pdb=" OG1 THR A 58 " model vdw 2.261 3.040 nonbonded pdb=" OG1 THR A 41 " pdb=" O TYR A 67 " model vdw 2.262 3.040 nonbonded pdb=" O TYR B 697 " pdb=" OG1 THR B 720 " model vdw 2.288 3.040 nonbonded pdb=" O LYS B 747 " pdb=" OG1 THR B 750 " model vdw 2.293 3.040 nonbonded pdb=" O ILE A 336 " pdb=" OG SER A 365 " model vdw 2.306 3.040 ... (remaining 52048 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.030 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: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.530 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 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 : 0.002 0.050 7223 Z= 0.123 Angle : 0.579 10.354 9758 Z= 0.323 Chirality : 0.040 0.128 1061 Planarity : 0.003 0.063 1233 Dihedral : 18.499 82.436 2648 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.25 % Allowed : 34.39 % Favored : 65.35 % 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: -0.94 (0.30), residues: 816 helix: 0.05 (0.55), residues: 118 sheet: 0.45 (0.68), residues: 77 loop : -0.96 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 604 HIS 0.002 0.000 HIS A 100 PHE 0.012 0.000 PHE B 696 TYR 0.012 0.001 TYR A 477 ARG 0.009 0.000 ARG C 55 Details of bonding type rmsd hydrogen bonds : bond 0.20241 ( 103) hydrogen bonds : angle 6.48183 ( 258) SS BOND : bond 0.00083 ( 20) SS BOND : angle 0.24514 ( 40) covalent geometry : bond 0.00220 ( 7203) covalent geometry : angle 0.58035 ( 9718) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 66 time to evaluate : 0.753 Fit side-chains revert: symmetry clash REVERT: A 487 LEU cc_start: 0.7393 (tp) cc_final: 0.6991 (pp) outliers start: 2 outliers final: 0 residues processed: 66 average time/residue: 0.1831 time to fit residues: 16.8399 Evaluate side-chains 65 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 0.2980 chunk 64 optimal weight: 8.9990 chunk 35 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 43 optimal weight: 0.2980 chunk 34 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 77 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.099462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.074553 restraints weight = 19998.716| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 3.88 r_work: 0.3204 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7223 Z= 0.193 Angle : 0.567 8.319 9758 Z= 0.291 Chirality : 0.043 0.192 1061 Planarity : 0.004 0.049 1233 Dihedral : 3.490 14.433 931 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 4.59 % Allowed : 28.15 % Favored : 67.26 % 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: -1.20 (0.30), residues: 816 helix: -0.17 (0.51), residues: 126 sheet: -0.34 (0.53), residues: 112 loop : -1.08 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 604 HIS 0.003 0.001 HIS A 21 PHE 0.028 0.002 PHE B 696 TYR 0.017 0.001 TYR B 591 ARG 0.004 0.001 ARG A 371 Details of bonding type rmsd hydrogen bonds : bond 0.03595 ( 103) hydrogen bonds : angle 4.89270 ( 258) SS BOND : bond 0.00313 ( 20) SS BOND : angle 0.75616 ( 40) covalent geometry : bond 0.00434 ( 7203) covalent geometry : angle 0.56655 ( 9718) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 75 time to evaluate : 0.859 Fit side-chains revert: symmetry clash REVERT: A 412 TRP cc_start: 0.9068 (OUTLIER) cc_final: 0.8385 (m-90) REVERT: C 15 GLN cc_start: 0.8659 (tp-100) cc_final: 0.8305 (tp-100) outliers start: 36 outliers final: 16 residues processed: 102 average time/residue: 0.1806 time to fit residues: 25.6261 Evaluate side-chains 85 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 PHE Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 412 TRP Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain D residue 21 ARG Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 905 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 40 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 52 optimal weight: 9.9990 chunk 58 optimal weight: 5.9990 chunk 19 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 56 optimal weight: 10.0000 chunk 61 optimal weight: 9.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN A 410 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.092875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.067279 restraints weight = 20440.661| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 3.82 r_work: 0.3031 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.4508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 7223 Z= 0.264 Angle : 0.654 9.524 9758 Z= 0.332 Chirality : 0.045 0.151 1061 Planarity : 0.005 0.072 1233 Dihedral : 4.566 20.354 931 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 5.10 % Allowed : 26.50 % Favored : 68.41 % 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 (0.29), residues: 816 helix: -0.31 (0.49), residues: 128 sheet: -0.71 (0.56), residues: 94 loop : -1.41 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 604 HIS 0.006 0.001 HIS A 100 PHE 0.022 0.002 PHE B 696 TYR 0.015 0.002 TYR B 697 ARG 0.005 0.001 ARG C 56 Details of bonding type rmsd hydrogen bonds : bond 0.04234 ( 103) hydrogen bonds : angle 5.21557 ( 258) SS BOND : bond 0.00593 ( 20) SS BOND : angle 0.96127 ( 40) covalent geometry : bond 0.00614 ( 7203) covalent geometry : angle 0.65227 ( 9718) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 74 time to evaluate : 0.741 Fit side-chains revert: symmetry clash REVERT: A 412 TRP cc_start: 0.9255 (OUTLIER) cc_final: 0.7947 (m-90) REVERT: C 55 ARG cc_start: 0.9270 (tmt-80) cc_final: 0.9041 (tpt90) REVERT: B 545 GLU cc_start: 0.8657 (tp30) cc_final: 0.8311 (mm-30) REVERT: B 626 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8644 (mm) outliers start: 40 outliers final: 25 residues processed: 106 average time/residue: 0.1725 time to fit residues: 25.2818 Evaluate side-chains 89 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 62 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 PHE Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 412 TRP Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 535 ASP Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain B residue 518 GLN Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 775 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 51 optimal weight: 20.0000 chunk 57 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 31 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.092187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.066900 restraints weight = 20203.278| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 3.78 r_work: 0.3039 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.4820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 7223 Z= 0.194 Angle : 0.570 8.024 9758 Z= 0.287 Chirality : 0.043 0.166 1061 Planarity : 0.004 0.046 1233 Dihedral : 4.264 17.528 931 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 4.59 % Allowed : 28.15 % Favored : 67.26 % 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: -1.70 (0.29), residues: 816 helix: -0.28 (0.49), residues: 129 sheet: -0.68 (0.58), residues: 90 loop : -1.49 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 604 HIS 0.002 0.000 HIS A 100 PHE 0.019 0.002 PHE A 39 TYR 0.013 0.001 TYR B 697 ARG 0.005 0.000 ARG A 454 Details of bonding type rmsd hydrogen bonds : bond 0.03291 ( 103) hydrogen bonds : angle 5.12226 ( 258) SS BOND : bond 0.00291 ( 20) SS BOND : angle 0.75042 ( 40) covalent geometry : bond 0.00458 ( 7203) covalent geometry : angle 0.56933 ( 9718) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 65 time to evaluate : 0.794 Fit side-chains revert: symmetry clash REVERT: A 56 MET cc_start: 0.9252 (OUTLIER) cc_final: 0.8397 (ttp) REVERT: A 294 MET cc_start: 0.7995 (tpp) cc_final: 0.7650 (tpp) REVERT: A 412 TRP cc_start: 0.9223 (OUTLIER) cc_final: 0.7965 (m-90) REVERT: B 545 GLU cc_start: 0.8629 (tp30) cc_final: 0.8271 (mm-30) REVERT: B 599 ARG cc_start: 0.8910 (OUTLIER) cc_final: 0.8653 (ttp80) outliers start: 36 outliers final: 26 residues processed: 96 average time/residue: 0.1945 time to fit residues: 25.2786 Evaluate side-chains 90 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 61 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 PHE Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 208 CYS Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 412 TRP Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain B residue 518 GLN Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 547 ASN Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 599 ARG Chi-restraints excluded: chain B residue 619 HIS Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 657 SER Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 775 ILE Chi-restraints excluded: chain B residue 905 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 25 optimal weight: 9.9990 chunk 42 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.3759 r_free = 0.3759 target = 0.092614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.067340 restraints weight = 19950.286| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 3.77 r_work: 0.3053 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.4886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7223 Z= 0.139 Angle : 0.529 8.907 9758 Z= 0.263 Chirality : 0.042 0.149 1061 Planarity : 0.004 0.046 1233 Dihedral : 4.026 17.290 931 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 3.82 % Allowed : 29.30 % Favored : 66.88 % 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 (0.29), residues: 816 helix: -0.19 (0.50), residues: 128 sheet: -0.66 (0.59), residues: 90 loop : -1.46 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 604 HIS 0.002 0.000 HIS A 100 PHE 0.017 0.001 PHE B 755 TYR 0.013 0.001 TYR B 697 ARG 0.006 0.000 ARG D 55 Details of bonding type rmsd hydrogen bonds : bond 0.02944 ( 103) hydrogen bonds : angle 4.99046 ( 258) SS BOND : bond 0.00220 ( 20) SS BOND : angle 0.61256 ( 40) covalent geometry : bond 0.00329 ( 7203) covalent geometry : angle 0.52842 ( 9718) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 66 time to evaluate : 0.833 Fit side-chains REVERT: A 46 PHE cc_start: 0.9208 (OUTLIER) cc_final: 0.8920 (t80) REVERT: A 294 MET cc_start: 0.8013 (tpp) cc_final: 0.7734 (tpp) REVERT: A 412 TRP cc_start: 0.9160 (OUTLIER) cc_final: 0.7900 (m-90) REVERT: C 56 ARG cc_start: 0.8992 (tpm170) cc_final: 0.8789 (tpm170) outliers start: 30 outliers final: 20 residues processed: 90 average time/residue: 0.1772 time to fit residues: 22.2551 Evaluate side-chains 84 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 62 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 PHE Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 412 TRP Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 619 HIS Chi-restraints excluded: chain B residue 657 SER Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 775 ILE Chi-restraints excluded: chain B residue 905 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 56 optimal weight: 7.9990 chunk 80 optimal weight: 0.6980 chunk 42 optimal weight: 0.0470 chunk 59 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 48 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 23 optimal weight: 0.0370 chunk 79 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 overall best weight: 0.5156 ------------------------------------------------------------------------------- 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 = 0.3777 r_free = 0.3777 target = 0.093553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.068445 restraints weight = 20088.757| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 3.73 r_work: 0.3079 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.4869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7223 Z= 0.100 Angle : 0.511 7.824 9758 Z= 0.253 Chirality : 0.041 0.143 1061 Planarity : 0.004 0.047 1233 Dihedral : 3.888 16.525 931 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 4.59 % Allowed : 28.92 % Favored : 66.50 % 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: -1.58 (0.29), residues: 816 helix: -0.08 (0.50), residues: 127 sheet: -0.61 (0.58), residues: 90 loop : -1.43 (0.25), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 604 HIS 0.002 0.000 HIS B 630 PHE 0.015 0.001 PHE B 755 TYR 0.014 0.001 TYR D 24 ARG 0.005 0.000 ARG D 55 Details of bonding type rmsd hydrogen bonds : bond 0.02654 ( 103) hydrogen bonds : angle 4.86471 ( 258) SS BOND : bond 0.00167 ( 20) SS BOND : angle 0.53984 ( 40) covalent geometry : bond 0.00238 ( 7203) covalent geometry : angle 0.51118 ( 9718) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 65 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 PHE cc_start: 0.9200 (OUTLIER) cc_final: 0.8982 (t80) REVERT: A 294 MET cc_start: 0.8005 (tpp) cc_final: 0.7790 (tpp) REVERT: A 412 TRP cc_start: 0.9116 (OUTLIER) cc_final: 0.7871 (m-90) outliers start: 36 outliers final: 29 residues processed: 96 average time/residue: 0.1680 time to fit residues: 22.7121 Evaluate side-chains 91 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 60 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 PHE Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 208 CYS Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 412 TRP Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 518 GLN Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 619 HIS Chi-restraints excluded: chain B residue 657 SER Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 775 ILE Chi-restraints excluded: chain B residue 905 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 39 optimal weight: 0.0030 chunk 75 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 15 optimal weight: 0.0670 chunk 67 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 43 optimal weight: 0.0970 chunk 73 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 overall best weight: 0.5728 ------------------------------------------------------------------------------- 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 = 0.3777 r_free = 0.3777 target = 0.093495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.068321 restraints weight = 20045.620| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 3.73 r_work: 0.3079 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.4863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7223 Z= 0.104 Angle : 0.506 8.327 9758 Z= 0.251 Chirality : 0.041 0.141 1061 Planarity : 0.003 0.047 1233 Dihedral : 3.804 16.838 931 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 5.10 % Allowed : 27.64 % Favored : 67.26 % 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: -1.52 (0.29), residues: 816 helix: 0.04 (0.50), residues: 127 sheet: -0.61 (0.58), residues: 90 loop : -1.39 (0.25), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 493 HIS 0.001 0.000 HIS A 100 PHE 0.015 0.001 PHE B 755 TYR 0.013 0.001 TYR B 697 ARG 0.003 0.000 ARG D 55 Details of bonding type rmsd hydrogen bonds : bond 0.02580 ( 103) hydrogen bonds : angle 4.79115 ( 258) SS BOND : bond 0.00181 ( 20) SS BOND : angle 0.53483 ( 40) covalent geometry : bond 0.00248 ( 7203) covalent geometry : angle 0.50609 ( 9718) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 64 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 PHE cc_start: 0.9226 (OUTLIER) cc_final: 0.9015 (t80) REVERT: A 116 SER cc_start: 0.9148 (OUTLIER) cc_final: 0.8865 (t) REVERT: A 412 TRP cc_start: 0.9106 (OUTLIER) cc_final: 0.7888 (m-90) REVERT: A 559 TRP cc_start: 0.5829 (p90) cc_final: 0.5597 (p90) REVERT: B 545 GLU cc_start: 0.8648 (mm-30) cc_final: 0.7971 (mm-30) REVERT: B 631 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7976 (tppp) outliers start: 40 outliers final: 28 residues processed: 95 average time/residue: 0.1683 time to fit residues: 22.3652 Evaluate side-chains 93 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 61 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 PHE Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 208 CYS Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 412 TRP Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 59 MET Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 518 GLN Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 631 LYS Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 905 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 6 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 73 optimal weight: 0.3980 chunk 27 optimal weight: 0.0670 chunk 25 optimal weight: 8.9990 chunk 11 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 overall best weight: 0.6318 ------------------------------------------------------------------------------- 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 = 0.3773 r_free = 0.3773 target = 0.093780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.068627 restraints weight = 20274.339| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 3.80 r_work: 0.3074 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.4926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7223 Z= 0.109 Angle : 0.522 8.855 9758 Z= 0.258 Chirality : 0.041 0.138 1061 Planarity : 0.003 0.047 1233 Dihedral : 3.893 16.718 931 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 4.97 % Allowed : 27.77 % Favored : 67.26 % 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: -1.53 (0.29), residues: 816 helix: 0.04 (0.50), residues: 127 sheet: -0.57 (0.58), residues: 90 loop : -1.42 (0.25), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 493 HIS 0.001 0.000 HIS B 630 PHE 0.016 0.001 PHE D 23 TYR 0.013 0.001 TYR B 697 ARG 0.005 0.000 ARG C 55 Details of bonding type rmsd hydrogen bonds : bond 0.02603 ( 103) hydrogen bonds : angle 4.80068 ( 258) SS BOND : bond 0.00150 ( 20) SS BOND : angle 0.59151 ( 40) covalent geometry : bond 0.00258 ( 7203) covalent geometry : angle 0.52182 ( 9718) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 60 time to evaluate : 0.825 Fit side-chains revert: symmetry clash REVERT: A 116 SER cc_start: 0.9132 (OUTLIER) cc_final: 0.8843 (t) REVERT: A 412 TRP cc_start: 0.9094 (OUTLIER) cc_final: 0.7866 (m-90) REVERT: A 508 LYS cc_start: 0.7531 (OUTLIER) cc_final: 0.7304 (mmmm) REVERT: A 559 TRP cc_start: 0.5839 (p90) cc_final: 0.5623 (p90) REVERT: B 545 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8004 (mm-30) REVERT: B 629 ILE cc_start: 0.8525 (mm) cc_final: 0.8124 (pt) REVERT: B 631 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.8030 (tppp) outliers start: 39 outliers final: 29 residues processed: 90 average time/residue: 0.1807 time to fit residues: 22.6350 Evaluate side-chains 92 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 59 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 208 CYS Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 412 TRP Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 59 MET Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 518 GLN Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 619 HIS Chi-restraints excluded: chain B residue 631 LYS Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 905 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 16 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 11 optimal weight: 0.0970 chunk 22 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 78 optimal weight: 0.2980 chunk 70 optimal weight: 0.2980 overall best weight: 0.4778 ------------------------------------------------------------------------------- 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 = 0.3780 r_free = 0.3780 target = 0.094105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.068830 restraints weight = 20474.733| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 3.83 r_work: 0.3081 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.4934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7223 Z= 0.097 Angle : 0.514 8.973 9758 Z= 0.254 Chirality : 0.041 0.134 1061 Planarity : 0.003 0.047 1233 Dihedral : 3.798 16.589 931 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 4.59 % Allowed : 28.03 % Favored : 67.39 % 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: -1.52 (0.29), residues: 816 helix: 0.10 (0.51), residues: 127 sheet: -0.56 (0.58), residues: 90 loop : -1.42 (0.25), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 493 HIS 0.001 0.000 HIS B 630 PHE 0.014 0.001 PHE B 755 TYR 0.012 0.001 TYR B 697 ARG 0.004 0.000 ARG C 55 Details of bonding type rmsd hydrogen bonds : bond 0.02541 ( 103) hydrogen bonds : angle 4.75112 ( 258) SS BOND : bond 0.00122 ( 20) SS BOND : angle 0.54146 ( 40) covalent geometry : bond 0.00230 ( 7203) covalent geometry : angle 0.51404 ( 9718) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 60 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 SER cc_start: 0.9120 (OUTLIER) cc_final: 0.8828 (t) REVERT: A 412 TRP cc_start: 0.9073 (OUTLIER) cc_final: 0.7839 (m-90) REVERT: A 508 LYS cc_start: 0.7419 (OUTLIER) cc_final: 0.7161 (mmmm) REVERT: A 559 TRP cc_start: 0.5862 (p90) cc_final: 0.5645 (p90) REVERT: B 545 GLU cc_start: 0.8703 (mm-30) cc_final: 0.8044 (mm-30) REVERT: B 629 ILE cc_start: 0.8530 (mm) cc_final: 0.8141 (pt) outliers start: 36 outliers final: 30 residues processed: 87 average time/residue: 0.2067 time to fit residues: 25.3305 Evaluate side-chains 92 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 59 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 208 CYS Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 412 TRP Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 59 MET Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 518 GLN Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 619 HIS Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 905 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 82 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 61 optimal weight: 0.0270 chunk 45 optimal weight: 0.2980 chunk 3 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 chunk 47 optimal weight: 0.0670 chunk 5 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 overall best weight: 0.3776 ------------------------------------------------------------------------------- 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 = 0.3781 r_free = 0.3781 target = 0.094302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.068951 restraints weight = 20624.732| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 3.86 r_work: 0.3092 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.4926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7223 Z= 0.092 Angle : 0.549 14.076 9758 Z= 0.265 Chirality : 0.041 0.167 1061 Planarity : 0.003 0.047 1233 Dihedral : 3.707 16.148 931 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 4.20 % Allowed : 28.03 % Favored : 67.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.29), residues: 816 helix: 0.10 (0.51), residues: 126 sheet: -0.54 (0.58), residues: 90 loop : -1.40 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 604 HIS 0.004 0.000 HIS B 630 PHE 0.014 0.001 PHE B 755 TYR 0.012 0.001 TYR B 697 ARG 0.004 0.000 ARG D 55 Details of bonding type rmsd hydrogen bonds : bond 0.02448 ( 103) hydrogen bonds : angle 4.69623 ( 258) SS BOND : bond 0.00138 ( 20) SS BOND : angle 0.51882 ( 40) covalent geometry : bond 0.00217 ( 7203) covalent geometry : angle 0.54954 ( 9718) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 62 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 412 TRP cc_start: 0.9048 (OUTLIER) cc_final: 0.7914 (m-90) REVERT: A 454 ARG cc_start: 0.7768 (tpt170) cc_final: 0.7481 (tpt90) REVERT: A 559 TRP cc_start: 0.5869 (p90) cc_final: 0.5658 (p90) REVERT: B 629 ILE cc_start: 0.8553 (mm) cc_final: 0.8161 (pt) outliers start: 33 outliers final: 28 residues processed: 86 average time/residue: 0.2076 time to fit residues: 25.0242 Evaluate side-chains 90 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 61 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 208 CYS Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 412 TRP Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 59 MET Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 518 GLN Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 619 HIS Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 905 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 15 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3755 r_free = 0.3755 target = 0.092946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.067460 restraints weight = 20295.416| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 3.82 r_work: 0.3056 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.5135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7223 Z= 0.128 Angle : 0.556 12.604 9758 Z= 0.271 Chirality : 0.042 0.134 1061 Planarity : 0.004 0.047 1233 Dihedral : 3.928 17.439 931 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 4.20 % Allowed : 28.28 % Favored : 67.52 % 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: -1.53 (0.29), residues: 816 helix: 0.18 (0.51), residues: 126 sheet: -0.58 (0.58), residues: 89 loop : -1.45 (0.25), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 604 HIS 0.001 0.000 HIS B 630 PHE 0.014 0.001 PHE B 755 TYR 0.012 0.001 TYR B 697 ARG 0.009 0.000 ARG C 55 Details of bonding type rmsd hydrogen bonds : bond 0.02721 ( 103) hydrogen bonds : angle 4.75230 ( 258) SS BOND : bond 0.00202 ( 20) SS BOND : angle 0.63849 ( 40) covalent geometry : bond 0.00304 ( 7203) covalent geometry : angle 0.55540 ( 9718) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4685.16 seconds wall clock time: 83 minutes 9.31 seconds (4989.31 seconds total)