Starting phenix.real_space_refine on Sat May 10 23:54:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x06_37970/05_2025/8x06_37970.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x06_37970/05_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_37970/05_2025/8x06_37970.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x06_37970/05_2025/8x06_37970.map" model { file = "/net/cci-nas-00/data/ceres_data/8x06_37970/05_2025/8x06_37970.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x06_37970/05_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-5687/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: 6.06, per 1000 atoms: 0.86 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: 1.51 Conformation dependent library (CDL) restraints added in 869.2 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: 0.73 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: 1.71 Time building geometry restraints manager: 1.82 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: 6.770 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: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 20.100 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.270 ------------------------------------------------------------------------------- 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 : 0.820 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: 0.1864 time to fit residues: 17.1398 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 : 0.897 ------------------------------------------------------------------------------- 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 = 0.3877 r_free = 0.3877 target = 0.099381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.074514 restraints weight = 19983.822| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 3.87 r_work: 0.3203 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7223 Z= 0.195 Angle : 0.573 8.451 9758 Z= 0.293 Chirality : 0.043 0.196 1061 Planarity : 0.004 0.050 1233 Dihedral : 3.501 14.418 931 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % 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: -1.20 (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 0.027 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 0.03621 ( 103) hydrogen bonds : angle 4.90463 ( 258) SS BOND : bond 0.00314 ( 20) SS BOND : angle 0.77100 ( 40) covalent geometry : bond 0.00439 ( 7203) covalent geometry : angle 0.57215 ( 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 : 0.838 Fit side-chains revert: symmetry clash REVERT: A 412 TRP cc_start: 0.9070 (OUTLIER) cc_final: 0.8389 (m-90) REVERT: C 15 GLN cc_start: 0.8655 (tp-100) cc_final: 0.8297 (tp-100) outliers start: 36 outliers final: 16 residues processed: 102 average time/residue: 0.1735 time to fit residues: 24.4043 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 : 0.819 ------------------------------------------------------------------------------- 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: 8.9990 chunk 58 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 56 optimal weight: 10.0000 chunk 61 optimal weight: 9.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3826 r_free = 0.3826 target = 0.096934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.071671 restraints weight = 20040.864| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 3.84 r_work: 0.3131 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7223 Z= 0.155 Angle : 0.526 8.969 9758 Z= 0.260 Chirality : 0.042 0.195 1061 Planarity : 0.004 0.049 1233 Dihedral : 3.648 14.800 931 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.57 % Allowed : 28.79 % Favored : 67.64 % 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: -1.34 (0.29), residues: 816 helix: -0.11 (0.51), residues: 128 sheet: -0.40 (0.60), residues: 90 loop : -1.22 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 604 HIS 0.003 0.001 HIS A 417 PHE 0.017 0.001 PHE B 696 TYR 0.013 0.001 TYR B 697 ARG 0.004 0.000 ARG C 56 Details of bonding type rmsd hydrogen bonds : bond 0.03146 ( 103) hydrogen bonds : angle 4.83261 ( 258) SS BOND : bond 0.00253 ( 20) SS BOND : angle 0.60599 ( 40) covalent geometry : bond 0.00361 ( 7203) covalent geometry : angle 0.52563 ( 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 101 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 73 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 412 TRP cc_start: 0.9120 (OUTLIER) cc_final: 0.7959 (m-90) REVERT: C 55 ARG cc_start: 0.9225 (tmt-80) cc_final: 0.8876 (tpt90) outliers start: 28 outliers final: 15 residues processed: 94 average time/residue: 0.1975 time to fit residues: 25.7617 Evaluate side-chains 80 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 125 LEU 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 360 LEU Chi-restraints excluded: chain A residue 387 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 C residue 5 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain B residue 593 LEU 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: 9.9990 chunk 57 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 40 optimal weight: 0.0040 chunk 5 optimal weight: 0.2980 chunk 27 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 overall best weight: 0.5392 ------------------------------------------------------------------------------- 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 = 0.3830 r_free = 0.3830 target = 0.096748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.071610 restraints weight = 20177.060| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 3.80 r_work: 0.3144 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7223 Z= 0.100 Angle : 0.476 8.395 9758 Z= 0.235 Chirality : 0.040 0.129 1061 Planarity : 0.003 0.048 1233 Dihedral : 3.443 14.629 931 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 3.06 % Allowed : 28.92 % Favored : 68.03 % 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: -1.34 (0.29), residues: 816 helix: -0.06 (0.51), residues: 127 sheet: -0.42 (0.60), residues: 90 loop : -1.22 (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 619 PHE 0.015 0.001 PHE B 696 TYR 0.010 0.001 TYR B 697 ARG 0.003 0.000 ARG A 454 Details of bonding type rmsd hydrogen bonds : bond 0.02455 ( 103) hydrogen bonds : angle 4.69650 ( 258) SS BOND : bond 0.00190 ( 20) SS BOND : angle 0.45853 ( 40) covalent geometry : bond 0.00236 ( 7203) covalent geometry : angle 0.47624 ( 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 90 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 66 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 412 TRP cc_start: 0.9088 (OUTLIER) cc_final: 0.8007 (m-90) outliers start: 24 outliers final: 19 residues processed: 83 average time/residue: 0.1728 time to fit residues: 20.3170 Evaluate side-chains 84 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 64 time to evaluate : 0.871 ------------------------------------------------------------------------------- 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 140 VAL 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 341 ILE Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 412 TRP Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 676 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 25 optimal weight: 0.0040 chunk 42 optimal weight: 0.2980 chunk 69 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 23 optimal weight: 0.0470 chunk 38 optimal weight: 3.9990 overall best weight: 0.6292 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.096189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.071127 restraints weight = 19886.433| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 3.76 r_work: 0.3132 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7223 Z= 0.108 Angle : 0.489 7.023 9758 Z= 0.241 Chirality : 0.041 0.163 1061 Planarity : 0.003 0.048 1233 Dihedral : 3.510 15.284 931 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 3.69 % Allowed : 28.92 % 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: -1.35 (0.29), residues: 816 helix: -0.02 (0.50), residues: 127 sheet: -0.42 (0.60), residues: 90 loop : -1.24 (0.25), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 604 HIS 0.003 0.000 HIS B 630 PHE 0.017 0.001 PHE B 696 TYR 0.009 0.001 TYR B 697 ARG 0.002 0.000 ARG D 21 Details of bonding type rmsd hydrogen bonds : bond 0.02421 ( 103) hydrogen bonds : angle 4.68290 ( 258) SS BOND : bond 0.00165 ( 20) SS BOND : angle 0.48080 ( 40) covalent geometry : bond 0.00254 ( 7203) covalent geometry : angle 0.48895 ( 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: 29 poor density : 67 time to evaluate : 0.835 Fit side-chains revert: symmetry clash REVERT: A 412 TRP cc_start: 0.9104 (OUTLIER) cc_final: 0.7959 (m-90) REVERT: C 55 ARG cc_start: 0.9147 (tmt-80) cc_final: 0.8946 (tpt90) outliers start: 29 outliers final: 21 residues processed: 90 average time/residue: 0.1742 time to fit residues: 22.4131 Evaluate side-chains 83 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 61 time to evaluate : 0.908 ------------------------------------------------------------------------------- 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 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 360 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 412 TRP Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain D residue 60 TYR 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 647 ILE Chi-restraints excluded: chain B residue 676 LEU 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: 8.9990 chunk 80 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 59 optimal weight: 7.9990 chunk 81 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.3764 r_free = 0.3764 target = 0.092898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.067496 restraints weight = 20377.551| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 3.77 r_work: 0.3052 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.4563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7223 Z= 0.193 Angle : 0.572 10.494 9758 Z= 0.291 Chirality : 0.043 0.136 1061 Planarity : 0.004 0.046 1233 Dihedral : 4.166 20.168 931 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 4.33 % Allowed : 28.03 % Favored : 67.64 % 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: -1.55 (0.29), residues: 816 helix: -0.13 (0.48), residues: 129 sheet: -0.63 (0.56), residues: 95 loop : -1.39 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 412 HIS 0.003 0.001 HIS B 619 PHE 0.021 0.002 PHE A 258 TYR 0.016 0.002 TYR B 591 ARG 0.005 0.000 ARG D 21 Details of bonding type rmsd hydrogen bonds : bond 0.03141 ( 103) hydrogen bonds : angle 4.92390 ( 258) SS BOND : bond 0.00455 ( 20) SS BOND : angle 0.81520 ( 40) covalent geometry : bond 0.00450 ( 7203) covalent geometry : angle 0.57033 ( 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 95 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 61 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 SER cc_start: 0.9315 (OUTLIER) cc_final: 0.8741 (t) REVERT: A 412 TRP cc_start: 0.9234 (OUTLIER) cc_final: 0.8071 (m-90) REVERT: C 55 ARG cc_start: 0.9174 (tmt-80) cc_final: 0.8925 (tpt90) REVERT: B 545 GLU cc_start: 0.8677 (tp30) cc_final: 0.8300 (mm-30) REVERT: B 550 LEU cc_start: 0.9064 (tp) cc_final: 0.8568 (pp) outliers start: 34 outliers final: 26 residues processed: 89 average time/residue: 0.1675 time to fit residues: 21.1960 Evaluate side-chains 86 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 58 time to evaluate : 0.730 ------------------------------------------------------------------------------- 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 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 395 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 A residue 586 ILE Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain D residue 21 ARG Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain B residue 516 SER 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 647 ILE Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain B residue 705 VAL 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: 1.9990 chunk 75 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3779 r_free = 0.3779 target = 0.093641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.068465 restraints weight = 20076.633| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 3.75 r_work: 0.3075 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.4609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7223 Z= 0.124 Angle : 0.515 10.664 9758 Z= 0.255 Chirality : 0.041 0.134 1061 Planarity : 0.003 0.047 1233 Dihedral : 3.925 17.151 931 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 4.08 % Allowed : 28.41 % 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: -0.01 (0.49), residues: 128 sheet: -0.90 (0.55), residues: 100 loop : -1.35 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 604 HIS 0.002 0.000 HIS B 619 PHE 0.017 0.001 PHE B 696 TYR 0.013 0.001 TYR B 697 ARG 0.002 0.000 ARG A 454 Details of bonding type rmsd hydrogen bonds : bond 0.02768 ( 103) hydrogen bonds : angle 4.85980 ( 258) SS BOND : bond 0.00184 ( 20) SS BOND : angle 0.56377 ( 40) covalent geometry : bond 0.00293 ( 7203) covalent geometry : angle 0.51478 ( 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 97 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 65 time to evaluate : 0.822 Fit side-chains REVERT: A 116 SER cc_start: 0.9283 (OUTLIER) cc_final: 0.8734 (t) REVERT: A 412 TRP cc_start: 0.9150 (OUTLIER) cc_final: 0.7984 (m-90) REVERT: A 559 TRP cc_start: 0.5891 (p90) cc_final: 0.5583 (p90) REVERT: C 55 ARG cc_start: 0.9155 (tmt-80) cc_final: 0.8889 (tpt90) REVERT: B 655 GLN cc_start: 0.8566 (mp10) cc_final: 0.8297 (mp10) outliers start: 32 outliers final: 26 residues processed: 90 average time/residue: 0.1560 time to fit residues: 20.1712 Evaluate side-chains 88 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 60 time to evaluate : 0.845 ------------------------------------------------------------------------------- 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 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 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 46 GLU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain B residue 516 SER 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 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 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: 0.9980 chunk 4 optimal weight: 0.0050 chunk 8 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 25 optimal weight: 0.0870 chunk 11 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 40 optimal weight: 0.1980 chunk 50 optimal weight: 2.9990 overall best weight: 0.4172 ------------------------------------------------------------------------------- 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 = 0.3796 r_free = 0.3796 target = 0.094628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.069204 restraints weight = 20258.326| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 3.83 r_work: 0.3092 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7223 Z= 0.093 Angle : 0.511 10.411 9758 Z= 0.249 Chirality : 0.041 0.138 1061 Planarity : 0.003 0.047 1233 Dihedral : 3.714 16.336 931 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 3.95 % Allowed : 29.30 % Favored : 66.75 % 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: -1.48 (0.29), residues: 816 helix: 0.13 (0.50), residues: 126 sheet: -0.82 (0.57), residues: 95 loop : -1.34 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 493 HIS 0.002 0.000 HIS B 630 PHE 0.016 0.001 PHE B 696 TYR 0.014 0.001 TYR B 697 ARG 0.002 0.000 ARG D 21 Details of bonding type rmsd hydrogen bonds : bond 0.02442 ( 103) hydrogen bonds : angle 4.81795 ( 258) SS BOND : bond 0.00126 ( 20) SS BOND : angle 0.50701 ( 40) covalent geometry : bond 0.00219 ( 7203) covalent geometry : angle 0.51093 ( 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 96 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 65 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 SER cc_start: 0.9336 (OUTLIER) cc_final: 0.8767 (t) REVERT: A 294 MET cc_start: 0.7982 (tpp) cc_final: 0.7762 (tpp) REVERT: A 412 TRP cc_start: 0.9072 (OUTLIER) cc_final: 0.8022 (m-90) REVERT: A 559 TRP cc_start: 0.5797 (p90) cc_final: 0.5559 (p90) REVERT: C 55 ARG cc_start: 0.9129 (tmt-80) cc_final: 0.8846 (tpt90) REVERT: C 56 ARG cc_start: 0.8957 (tpm170) cc_final: 0.8756 (tpm170) REVERT: B 655 GLN cc_start: 0.8557 (mp10) cc_final: 0.8299 (mp10) outliers start: 31 outliers final: 24 residues processed: 87 average time/residue: 0.1775 time to fit residues: 21.5972 Evaluate side-chains 87 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 61 time to evaluate : 0.816 ------------------------------------------------------------------------------- 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 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 46 GLU Chi-restraints excluded: chain C residue 54 LEU 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 647 ILE Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain B residue 705 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: 4.9990 chunk 35 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 21 optimal weight: 0.4980 chunk 11 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 78 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.093454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.068063 restraints weight = 20673.065| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 3.84 r_work: 0.3063 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.4749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7223 Z= 0.130 Angle : 0.528 9.700 9758 Z= 0.258 Chirality : 0.041 0.129 1061 Planarity : 0.003 0.047 1233 Dihedral : 3.870 18.165 931 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 4.46 % Allowed : 28.28 % 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: -1.49 (0.29), residues: 816 helix: 0.07 (0.50), residues: 129 sheet: -0.88 (0.57), residues: 95 loop : -1.33 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 493 HIS 0.001 0.000 HIS B 619 PHE 0.017 0.001 PHE B 696 TYR 0.014 0.001 TYR B 697 ARG 0.003 0.000 ARG D 21 Details of bonding type rmsd hydrogen bonds : bond 0.02634 ( 103) hydrogen bonds : angle 4.80971 ( 258) SS BOND : bond 0.00200 ( 20) SS BOND : angle 0.60132 ( 40) covalent geometry : bond 0.00306 ( 7203) covalent geometry : angle 0.52739 ( 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 99 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 64 time to evaluate : 0.841 Fit side-chains REVERT: A 116 SER cc_start: 0.9320 (OUTLIER) cc_final: 0.8760 (t) REVERT: A 412 TRP cc_start: 0.9146 (OUTLIER) cc_final: 0.8141 (m-90) REVERT: A 559 TRP cc_start: 0.5786 (p90) cc_final: 0.5558 (p90) REVERT: C 55 ARG cc_start: 0.9143 (tmt-80) cc_final: 0.8864 (tpt90) REVERT: C 56 ARG cc_start: 0.8961 (tpm170) cc_final: 0.8488 (tpt170) REVERT: B 545 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8017 (mm-30) outliers start: 35 outliers final: 25 residues processed: 90 average time/residue: 0.1922 time to fit residues: 24.0497 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 : 0.838 ------------------------------------------------------------------------------- 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 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 46 GLU Chi-restraints excluded: chain C residue 54 LEU 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 647 ILE Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain B residue 705 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: 1.9990 chunk 72 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 61 optimal weight: 0.0270 chunk 45 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 47 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 overall best weight: 1.1042 ------------------------------------------------------------------------------- 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 = 0.3751 r_free = 0.3751 target = 0.092672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.067321 restraints weight = 20830.770| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 3.85 r_work: 0.3048 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.4973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 7223 Z= 0.157 Angle : 0.571 12.878 9758 Z= 0.279 Chirality : 0.042 0.153 1061 Planarity : 0.004 0.068 1233 Dihedral : 4.079 23.506 931 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 3.69 % Allowed : 29.30 % Favored : 67.01 % 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: -1.54 (0.29), residues: 816 helix: 0.06 (0.50), residues: 129 sheet: -0.94 (0.57), residues: 95 loop : -1.37 (0.25), residues: 592 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 0.018 0.001 PHE B 696 TYR 0.015 0.001 TYR B 697 ARG 0.009 0.000 ARG D 21 Details of bonding type rmsd hydrogen bonds : bond 0.02823 ( 103) hydrogen bonds : angle 4.85112 ( 258) SS BOND : bond 0.00232 ( 20) SS BOND : angle 0.72637 ( 40) covalent geometry : bond 0.00371 ( 7203) covalent geometry : angle 0.57045 ( 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 93 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 64 time to evaluate : 0.885 Fit side-chains REVERT: A 116 SER cc_start: 0.9289 (OUTLIER) cc_final: 0.8688 (t) REVERT: A 412 TRP cc_start: 0.9155 (OUTLIER) cc_final: 0.8062 (m-90) REVERT: A 559 TRP cc_start: 0.5793 (p90) cc_final: 0.5564 (p90) REVERT: C 55 ARG cc_start: 0.9157 (tmt-80) cc_final: 0.8860 (tpt90) REVERT: C 56 ARG cc_start: 0.8968 (tpm170) cc_final: 0.8543 (tpt170) REVERT: B 545 GLU cc_start: 0.8718 (mm-30) cc_final: 0.8020 (mm-30) outliers start: 29 outliers final: 26 residues processed: 84 average time/residue: 0.1808 time to fit residues: 21.5840 Evaluate side-chains 90 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 62 time to evaluate : 0.899 ------------------------------------------------------------------------------- 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 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 46 GLU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 516 SER Chi-restraints excluded: chain B residue 518 GLN Chi-restraints excluded: chain B residue 593 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 905 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 15 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 13 optimal weight: 0.4980 chunk 64 optimal weight: 7.9990 chunk 34 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 58 optimal weight: 0.5980 chunk 51 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3772 r_free = 0.3772 target = 0.093738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.068318 restraints weight = 20402.138| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 3.86 r_work: 0.3070 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.4942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7223 Z= 0.108 Angle : 0.576 12.419 9758 Z= 0.276 Chirality : 0.041 0.128 1061 Planarity : 0.003 0.047 1233 Dihedral : 3.991 28.332 931 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 3.95 % Allowed : 28.79 % 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: 0.25 (0.51), residues: 126 sheet: -0.91 (0.57), residues: 95 loop : -1.40 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 493 HIS 0.002 0.000 HIS A 100 PHE 0.017 0.001 PHE B 696 TYR 0.014 0.001 TYR B 697 ARG 0.005 0.000 ARG D 21 Details of bonding type rmsd hydrogen bonds : bond 0.02576 ( 103) hydrogen bonds : angle 4.79248 ( 258) SS BOND : bond 0.00154 ( 20) SS BOND : angle 0.56599 ( 40) covalent geometry : bond 0.00258 ( 7203) covalent geometry : angle 0.57652 ( 9718) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4112.09 seconds wall clock time: 71 minutes 53.34 seconds (4313.34 seconds total)