Starting phenix.real_space_refine on Tue Jan 14 18:17:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x06_37970/01_2025/8x06_37970.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x06_37970/01_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_37970/01_2025/8x06_37970.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x06_37970/01_2025/8x06_37970.map" model { file = "/net/cci-nas-00/data/ceres_data/8x06_37970/01_2025/8x06_37970.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x06_37970/01_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-5571/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: 6.14, per 1000 atoms: 0.87 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: 1.63 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.76 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: 1.90 Time building geometry restraints manager: 1.97 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: 9.370 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: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 20.810 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.550 ------------------------------------------------------------------------------- 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 7203 Z= 0.152 Angle : 0.580 10.354 9718 Z= 0.324 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 *********************** 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 : 0.804 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: 0.1950 time to fit residues: 17.9889 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 : 0.763 ------------------------------------------------------------------------------- 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 7203 Z= 0.288 Angle : 0.572 8.451 9718 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 *********************** 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 : 0.702 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: 0.1777 time to fit residues: 25.0244 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 : 0.803 ------------------------------------------------------------------------------- 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: 8.9990 chunk 52 optimal weight: 8.9990 chunk 58 optimal weight: 5.9990 chunk 19 optimal weight: 0.0370 chunk 6 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 56 optimal weight: 10.0000 chunk 61 optimal weight: 9.9990 overall best weight: 1.2062 ------------------------------------------------------------------------------- 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 = 0.3815 r_free = 0.3815 target = 0.096264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.070877 restraints weight = 20080.874| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 3.83 r_work: 0.3124 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7203 Z= 0.246 Angle : 0.543 8.861 9718 Z= 0.272 Chirality : 0.042 0.143 1061 Planarity : 0.004 0.049 1233 Dihedral : 3.765 14.879 931 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 3.69 % Allowed : 28.54 % 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: -1.38 (0.29), residues: 816 helix: -0.14 (0.50), residues: 128 sheet: -0.43 (0.59), residues: 90 loop : -1.24 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 604 HIS 0.003 0.001 HIS B 619 PHE 0.017 0.001 PHE B 696 TYR 0.011 0.001 TYR B 697 ARG 0.006 0.000 ARG C 56 *********************** 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 103 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 74 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 412 TRP cc_start: 0.9149 (OUTLIER) cc_final: 0.7907 (m-90) REVERT: C 55 ARG cc_start: 0.9217 (tmt-80) cc_final: 0.8904 (tpt90) REVERT: B 626 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8586 (mm) outliers start: 29 outliers final: 15 residues processed: 96 average time/residue: 0.1845 time to fit residues: 24.8486 Evaluate side-chains 80 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 63 time to evaluate : 0.788 ------------------------------------------------------------------------------- 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 626 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: 0.9980 chunk 57 optimal weight: 4.9990 chunk 65 optimal weight: 0.0270 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 5 optimal weight: 0.0870 chunk 27 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 31 optimal weight: 0.0980 chunk 18 optimal weight: 4.9990 chunk 2 optimal weight: 0.0770 overall best weight: 0.2574 ------------------------------------------------------------------------------- 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 = 0.3838 r_free = 0.3838 target = 0.097158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.072117 restraints weight = 20039.753| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 3.78 r_work: 0.3153 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7203 Z= 0.131 Angle : 0.470 6.758 9718 Z= 0.232 Chirality : 0.041 0.167 1061 Planarity : 0.003 0.048 1233 Dihedral : 3.407 14.277 931 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.68 % Allowed : 29.81 % 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: -1.31 (0.29), residues: 816 helix: -0.07 (0.51), residues: 127 sheet: -0.40 (0.60), residues: 90 loop : -1.19 (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 0.014 0.001 PHE B 696 TYR 0.010 0.001 TYR B 697 ARG 0.003 0.000 ARG A 454 *********************** 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 89 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 68 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 412 TRP cc_start: 0.9064 (OUTLIER) cc_final: 0.7875 (m-90) outliers start: 21 outliers final: 16 residues processed: 82 average time/residue: 0.1807 time to fit residues: 20.6705 Evaluate side-chains 81 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.875 ------------------------------------------------------------------------------- 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 412 TRP Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain B residue 593 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: 0.4980 chunk 42 optimal weight: 0.0470 chunk 69 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 23 optimal weight: 0.2980 chunk 38 optimal weight: 3.9990 overall best weight: 0.7480 ------------------------------------------------------------------------------- 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 = 0.3811 r_free = 0.3811 target = 0.095672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.070492 restraints weight = 19954.447| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 3.77 r_work: 0.3121 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7203 Z= 0.181 Angle : 0.493 8.563 9718 Z= 0.245 Chirality : 0.041 0.128 1061 Planarity : 0.003 0.048 1233 Dihedral : 3.534 15.842 931 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 3.31 % Allowed : 28.92 % 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: -1.33 (0.29), residues: 816 helix: -0.02 (0.50), residues: 127 sheet: -0.45 (0.59), residues: 90 loop : -1.22 (0.25), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 559 HIS 0.002 0.000 HIS B 619 PHE 0.018 0.001 PHE B 696 TYR 0.009 0.001 TYR B 697 ARG 0.002 0.000 ARG A 554 *********************** 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 94 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 68 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 412 TRP cc_start: 0.9116 (OUTLIER) cc_final: 0.7999 (m-90) REVERT: A 559 TRP cc_start: 0.5907 (p90) cc_final: 0.5649 (p90) REVERT: C 55 ARG cc_start: 0.9131 (tmt-80) cc_final: 0.8924 (tpt90) outliers start: 26 outliers final: 22 residues processed: 90 average time/residue: 0.1875 time to fit residues: 23.4606 Evaluate side-chains 89 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 66 time to evaluate : 0.832 ------------------------------------------------------------------------------- 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 A residue 478 ILE 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 593 LEU 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 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: 0.0970 chunk 59 optimal weight: 8.9990 chunk 81 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 2 optimal weight: 0.1980 chunk 23 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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 = 0.3768 r_free = 0.3768 target = 0.093615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.068181 restraints weight = 20332.165| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 3.82 r_work: 0.3057 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.4521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7203 Z= 0.259 Angle : 0.535 7.682 9718 Z= 0.271 Chirality : 0.042 0.176 1061 Planarity : 0.004 0.047 1233 Dihedral : 3.988 17.225 931 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 3.57 % Allowed : 29.17 % 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: -1.48 (0.29), residues: 816 helix: -0.04 (0.49), residues: 128 sheet: -0.80 (0.57), residues: 95 loop : -1.30 (0.25), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 604 HIS 0.005 0.001 HIS B 630 PHE 0.020 0.002 PHE D 25 TYR 0.017 0.001 TYR D 24 ARG 0.003 0.000 ARG A 454 *********************** 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 94 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 66 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 SER cc_start: 0.9290 (OUTLIER) cc_final: 0.8731 (t) REVERT: A 412 TRP cc_start: 0.9201 (OUTLIER) cc_final: 0.8152 (m-90) REVERT: A 559 TRP cc_start: 0.5885 (p90) cc_final: 0.5656 (p90) REVERT: C 55 ARG cc_start: 0.9165 (tmt-80) cc_final: 0.8896 (tpt90) REVERT: B 545 GLU cc_start: 0.8709 (tp30) cc_final: 0.8300 (mm-30) outliers start: 28 outliers final: 20 residues processed: 88 average time/residue: 0.1668 time to fit residues: 21.0993 Evaluate side-chains 85 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 63 time to evaluate : 0.910 ------------------------------------------------------------------------------- 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 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 24 TYR Chi-restraints excluded: chain D residue 60 TYR 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 676 LEU 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: 2.9990 chunk 75 optimal weight: 0.9980 chunk 1 optimal weight: 0.0050 chunk 15 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.1998 ------------------------------------------------------------------------------- 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 = 0.092929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.067533 restraints weight = 20273.569| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 3.80 r_work: 0.3045 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.4805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7203 Z= 0.255 Angle : 0.543 10.398 9718 Z= 0.273 Chirality : 0.042 0.131 1061 Planarity : 0.004 0.047 1233 Dihedral : 4.046 17.608 931 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 3.95 % Allowed : 29.68 % Favored : 66.37 % 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: -1.56 (0.29), residues: 816 helix: -0.11 (0.49), residues: 129 sheet: -0.94 (0.54), residues: 100 loop : -1.35 (0.25), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 412 HIS 0.002 0.000 HIS B 619 PHE 0.018 0.002 PHE B 696 TYR 0.016 0.001 TYR D 24 ARG 0.003 0.000 ARG A 454 *********************** 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 96 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 65 time to evaluate : 0.805 Fit side-chains REVERT: A 116 SER cc_start: 0.9309 (OUTLIER) cc_final: 0.8776 (t) REVERT: A 412 TRP cc_start: 0.9171 (OUTLIER) cc_final: 0.8070 (m-90) REVERT: A 559 TRP cc_start: 0.5862 (p90) cc_final: 0.5592 (p90) REVERT: C 24 TYR cc_start: 0.8837 (t80) cc_final: 0.8608 (t80) REVERT: C 55 ARG cc_start: 0.9160 (tmt-80) cc_final: 0.8878 (tpt90) REVERT: B 550 LEU cc_start: 0.9143 (tp) cc_final: 0.8696 (pt) outliers start: 31 outliers final: 22 residues processed: 89 average time/residue: 0.1632 time to fit residues: 20.9099 Evaluate side-chains 84 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 60 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 387 LEU 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 46 GLU Chi-restraints excluded: chain C residue 54 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 6 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 4 optimal weight: 0.0370 chunk 8 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 overall best weight: 0.7458 ------------------------------------------------------------------------------- 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 = 0.3768 r_free = 0.3768 target = 0.093428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.068100 restraints weight = 20407.151| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 3.82 r_work: 0.3058 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.4875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7203 Z= 0.194 Angle : 0.536 10.135 9718 Z= 0.267 Chirality : 0.041 0.129 1061 Planarity : 0.003 0.047 1233 Dihedral : 3.964 20.923 931 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 3.95 % Allowed : 29.43 % Favored : 66.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.29), residues: 816 helix: 0.07 (0.50), residues: 128 sheet: -0.86 (0.57), residues: 95 loop : -1.37 (0.25), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 493 HIS 0.002 0.000 HIS A 100 PHE 0.017 0.001 PHE D 23 TYR 0.013 0.001 TYR B 697 ARG 0.002 0.000 ARG B 669 *********************** 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 : 0.879 Fit side-chains revert: symmetry clash REVERT: A 116 SER cc_start: 0.9298 (OUTLIER) cc_final: 0.8763 (t) REVERT: A 412 TRP cc_start: 0.9122 (OUTLIER) cc_final: 0.8018 (m-90) REVERT: A 559 TRP cc_start: 0.5838 (p90) cc_final: 0.5631 (p90) REVERT: C 55 ARG cc_start: 0.9154 (tmt-80) cc_final: 0.8847 (tpt90) REVERT: B 545 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8012 (mm-30) outliers start: 31 outliers final: 21 residues processed: 90 average time/residue: 0.1839 time to fit residues: 22.9055 Evaluate side-chains 86 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 63 time to evaluate : 0.813 ------------------------------------------------------------------------------- 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 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 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 619 HIS 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: 2.9990 chunk 35 optimal weight: 0.9990 chunk 13 optimal weight: 0.0770 chunk 21 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 56 optimal weight: 8.9990 chunk 18 optimal weight: 0.7980 chunk 49 optimal weight: 7.9990 chunk 78 optimal weight: 0.9980 chunk 70 optimal weight: 0.0770 overall best weight: 0.5896 ------------------------------------------------------------------------------- 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 = 0.3775 r_free = 0.3775 target = 0.093767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.068472 restraints weight = 20584.059| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 3.84 r_work: 0.3072 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.4892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7203 Z= 0.170 Angle : 0.538 12.487 9718 Z= 0.262 Chirality : 0.041 0.128 1061 Planarity : 0.003 0.047 1233 Dihedral : 3.852 19.136 931 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 3.44 % Allowed : 29.68 % 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: -1.53 (0.29), residues: 816 helix: 0.22 (0.51), residues: 126 sheet: -0.89 (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 0.002 0.000 ARG A 454 *********************** 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 90 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 63 time to evaluate : 0.833 Fit side-chains revert: symmetry clash REVERT: A 116 SER cc_start: 0.9291 (OUTLIER) cc_final: 0.8732 (t) REVERT: A 294 MET cc_start: 0.7976 (tpp) cc_final: 0.7706 (tpp) REVERT: A 412 TRP cc_start: 0.9098 (OUTLIER) cc_final: 0.8006 (m-90) REVERT: C 55 ARG cc_start: 0.9138 (tmt-80) cc_final: 0.8838 (tpt90) REVERT: D 53 ASP cc_start: 0.6386 (p0) cc_final: 0.5646 (p0) REVERT: B 545 GLU cc_start: 0.8718 (mm-30) cc_final: 0.8038 (mm-30) REVERT: B 550 LEU cc_start: 0.9126 (mm) cc_final: 0.8905 (pp) outliers start: 27 outliers final: 22 residues processed: 83 average time/residue: 0.1835 time to fit residues: 21.2818 Evaluate side-chains 83 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 59 time to evaluate : 0.903 ------------------------------------------------------------------------------- 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 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 516 SER 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 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: 5.9990 chunk 74 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.1980 chunk 3 optimal weight: 0.0670 chunk 84 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 62 optimal weight: 0.4980 overall best weight: 0.4918 ------------------------------------------------------------------------------- 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 = 0.3775 r_free = 0.3775 target = 0.093802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.068349 restraints weight = 20591.447| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 3.88 r_work: 0.3078 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.4922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7203 Z= 0.160 Angle : 0.553 13.054 9718 Z= 0.270 Chirality : 0.041 0.151 1061 Planarity : 0.003 0.047 1233 Dihedral : 3.834 16.714 931 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 3.31 % Allowed : 30.32 % Favored : 66.37 % 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: -0.90 (0.57), residues: 95 loop : -1.39 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 604 HIS 0.002 0.000 HIS B 630 PHE 0.017 0.001 PHE D 23 TYR 0.014 0.001 TYR B 697 ARG 0.002 0.000 ARG D 21 ********************** 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 86 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 60 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 SER cc_start: 0.9325 (OUTLIER) cc_final: 0.8742 (t) REVERT: A 294 MET cc_start: 0.7975 (tpp) cc_final: 0.7717 (tpp) REVERT: A 412 TRP cc_start: 0.9074 (OUTLIER) cc_final: 0.7991 (m-90) REVERT: C 55 ARG cc_start: 0.9121 (tmt-80) cc_final: 0.8817 (tpt90) REVERT: D 53 ASP cc_start: 0.6235 (p0) cc_final: 0.5554 (p0) REVERT: B 545 GLU cc_start: 0.8722 (mm-30) cc_final: 0.8044 (mm-30) outliers start: 26 outliers final: 23 residues processed: 79 average time/residue: 0.1580 time to fit residues: 18.0054 Evaluate side-chains 84 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 59 time to evaluate : 0.789 ------------------------------------------------------------------------------- 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 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 516 SER 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 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: 10.0000 chunk 83 optimal weight: 1.9990 chunk 13 optimal weight: 0.1980 chunk 64 optimal weight: 7.9990 chunk 34 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 56 optimal weight: 0.4980 chunk 58 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.3754 r_free = 0.3754 target = 0.092819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.067412 restraints weight = 20318.187| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 3.83 r_work: 0.3055 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.5090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7203 Z= 0.208 Angle : 0.565 13.006 9718 Z= 0.277 Chirality : 0.041 0.131 1061 Planarity : 0.003 0.047 1233 Dihedral : 3.958 17.848 931 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 3.82 % Allowed : 29.81 % Favored : 66.37 % 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: 0.15 (0.50), residues: 127 sheet: -0.95 (0.57), residues: 95 loop : -1.43 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 604 HIS 0.001 0.000 HIS A 100 PHE 0.018 0.001 PHE B 696 TYR 0.014 0.001 TYR B 697 ARG 0.001 0.000 ARG B 669 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4119.47 seconds wall clock time: 75 minutes 42.77 seconds (4542.77 seconds total)