Starting phenix.real_space_refine on Wed Mar 12 02:41:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x06_37970/03_2025/8x06_37970.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x06_37970/03_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_37970/03_2025/8x06_37970.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x06_37970/03_2025/8x06_37970.map" model { file = "/net/cci-nas-00/data/ceres_data/8x06_37970/03_2025/8x06_37970.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x06_37970/03_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 7.21, per 1000 atoms: 1.02 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: 1.70 Conformation dependent library (CDL) restraints added in 1.2 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: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 17 through 24 removed outlier: 3.546A pdb=" N LEU A 20 " --> pdb=" O LEU A 17 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N HIS A 21 " --> pdb=" O THR A 18 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N GLU A 22 " --> pdb=" O ARG A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 46 Processing helix chain 'A' and resid 127 through 131 removed outlier: 3.544A pdb=" N THR A 130 " --> pdb=" O TYR A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 268 removed outlier: 3.663A pdb=" N CYS A 266 " --> pdb=" O LEU A 262 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASN A 268 " --> pdb=" O HIS A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 329 removed outlier: 3.597A pdb=" N ALA A 327 " --> pdb=" O SER A 323 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLU A 329 " --> pdb=" O THR A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 358 Processing helix chain 'A' and resid 394 through 396 No H-bonds generated for 'chain 'A' and resid 394 through 396' Processing helix chain 'A' and resid 435 through 447 removed outlier: 3.780A pdb=" N ILE A 439 " --> pdb=" O CYS A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 removed outlier: 3.535A pdb=" N GLN A 452 " --> pdb=" O LYS A 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 18 removed outlier: 3.717A pdb=" N VAL C 11 " --> pdb=" O GLY C 7 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU C 14 " --> pdb=" O LEU C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 48 Processing helix chain 'C' and resid 53 through 58 Processing helix chain 'C' and resid 59 through 61 No H-bonds generated for 'chain 'C' and resid 59 through 61' Processing helix chain 'D' and resid 9 through 15 Processing helix chain 'D' and resid 53 through 57 removed outlier: 3.819A pdb=" N ARG D 56 " --> pdb=" O ASP D 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 546 removed outlier: 4.052A pdb=" N ALA B 546 " --> pdb=" O ALA B 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 542 through 546' Processing helix chain 'B' and resid 625 through 631 removed outlier: 3.984A pdb=" N ILE B 629 " --> pdb=" O CYS B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 634 No H-bonds generated for 'chain 'B' and resid 632 through 634' Processing helix chain 'B' and resid 882 through 904 Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 8 removed outlier: 3.668A pdb=" N ILE A 29 " --> pdb=" O MET A 56 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE A 57 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE A 82 " --> pdb=" O ASN A 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 38 removed outlier: 3.919A pdb=" N PHE A 64 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N VAL A 66 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU A 61 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N PHE A 96 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LEU A 63 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N LEU A 93 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N GLU A 120 " --> pdb=" O LEU A 93 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ILE A 95 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR A 144 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE A 119 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 231 through 233 Processing sheet with id=AA4, first strand: chain 'A' and resid 245 through 246 Processing sheet with id=AA5, first strand: chain 'A' and resid 292 through 293 Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 313 removed outlier: 3.796A pdb=" N ASN A 337 " --> pdb=" O CYS A 312 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ILE A 336 " --> pdb=" O SER A 365 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILE A 364 " --> pdb=" O ARG A 389 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 320 through 321 Processing sheet with id=AA8, first strand: chain 'A' and resid 368 through 370 removed outlier: 4.280A pdb=" N TYR A 398 " --> pdb=" O LYS A 425 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N PHE A 427 " --> pdb=" O TYR A 398 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N PHE A 400 " --> pdb=" O PHE A 427 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 484 through 487 removed outlier: 3.905A pdb=" N ILE A 485 " --> pdb=" O MET A 553 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N MET A 553 " --> pdb=" O ILE A 485 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU A 487 " --> pdb=" O TRP A 551 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 531 through 534 removed outlier: 3.640A pdb=" N PHE A 506 " --> pdb=" O PHE A 565 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N PHE A 565 " --> pdb=" O PHE A 506 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 525 through 526 removed outlier: 3.510A pdb=" N ILE B 526 " --> pdb=" O GLU B 553 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE B 554 " --> pdb=" O LEU B 577 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 558 through 560 Processing sheet with id=AB4, first strand: chain 'B' and resid 665 through 670 removed outlier: 3.550A pdb=" N ARG B 678 " --> pdb=" O SER B 666 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N ILE B 668 " --> pdb=" O LEU B 676 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N LEU B 676 " --> pdb=" O ILE B 668 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 722 through 724 removed outlier: 4.145A pdb=" N GLY B 692 " --> pdb=" O LEU B 759 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU B 759 " --> pdb=" O GLY B 692 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE B 755 " --> pdb=" O PHE B 696 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS B 698 " --> pdb=" O ALA B 753 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA B 753 " --> pdb=" O LYS B 698 " (cutoff:3.500A) 103 hydrogen bonds defined for protein. 258 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.38 Time building geometry restraints manager: 2.06 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: 11.150 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: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 23.420 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.050 ------------------------------------------------------------------------------- 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 : 0.871 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: 0.1874 time to fit residues: 17.3906 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 : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 0.2980 chunk 64 optimal weight: 8.9990 chunk 35 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 43 optimal weight: 0.2980 chunk 34 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 77 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.099462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.074553 restraints weight = 19998.716| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 3.88 r_work: 0.3204 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7203 Z= 0.285 Angle : 0.567 8.319 9718 Z= 0.290 Chirality : 0.043 0.192 1061 Planarity : 0.004 0.049 1233 Dihedral : 3.490 14.433 931 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 4.59 % Allowed : 28.15 % Favored : 67.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.30), residues: 816 helix: -0.17 (0.51), residues: 126 sheet: -0.34 (0.53), residues: 112 loop : -1.08 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 604 HIS 0.003 0.001 HIS A 21 PHE 0.028 0.002 PHE B 696 TYR 0.017 0.001 TYR B 591 ARG 0.004 0.001 ARG A 371 *********************** 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 : 0.853 Fit side-chains revert: symmetry clash REVERT: A 412 TRP cc_start: 0.9068 (OUTLIER) cc_final: 0.8385 (m-90) REVERT: C 15 GLN cc_start: 0.8659 (tp-100) cc_final: 0.8305 (tp-100) outliers start: 36 outliers final: 16 residues processed: 102 average time/residue: 0.1731 time to fit residues: 24.4530 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 : 0.750 ------------------------------------------------------------------------------- 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: 7.9990 chunk 52 optimal weight: 9.9990 chunk 58 optimal weight: 4.9990 chunk 19 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 56 optimal weight: 9.9990 chunk 61 optimal weight: 9.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN A 410 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.091381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.065686 restraints weight = 20417.416| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 3.78 r_work: 0.3004 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.4802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.064 7203 Z= 0.517 Angle : 0.721 9.096 9718 Z= 0.371 Chirality : 0.048 0.185 1061 Planarity : 0.005 0.075 1233 Dihedral : 4.929 22.128 931 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 5.48 % Allowed : 26.50 % 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: -1.82 (0.28), residues: 816 helix: -0.46 (0.47), residues: 127 sheet: -1.00 (0.54), residues: 100 loop : -1.50 (0.24), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 604 HIS 0.007 0.001 HIS A 100 PHE 0.025 0.002 PHE B 696 TYR 0.017 0.002 TYR B 697 ARG 0.005 0.001 ARG A 371 *********************** 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 113 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 70 time to evaluate : 0.825 Fit side-chains revert: symmetry clash REVERT: A 62 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.9091 (tp) REVERT: A 412 TRP cc_start: 0.9291 (OUTLIER) cc_final: 0.8092 (m-90) REVERT: B 626 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8672 (mm) outliers start: 43 outliers final: 26 residues processed: 107 average time/residue: 0.1734 time to fit residues: 25.9042 Evaluate side-chains 89 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 60 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 PHE Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 412 TRP Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 535 ASP Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain B residue 518 GLN Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 547 ASN Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 775 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 51 optimal weight: 20.0000 chunk 57 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN C 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.092952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.067397 restraints weight = 20236.749| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 3.81 r_work: 0.3044 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.4820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7203 Z= 0.228 Angle : 0.540 6.778 9718 Z= 0.271 Chirality : 0.043 0.172 1061 Planarity : 0.004 0.047 1233 Dihedral : 4.215 17.430 931 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 4.20 % Allowed : 28.79 % 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: -1.71 (0.29), residues: 816 helix: -0.28 (0.49), residues: 127 sheet: -0.77 (0.55), residues: 95 loop : -1.48 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 604 HIS 0.003 0.000 HIS A 100 PHE 0.024 0.002 PHE B 696 TYR 0.012 0.001 TYR B 697 ARG 0.003 0.000 ARG B 669 *********************** 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 98 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 65 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 294 MET cc_start: 0.8008 (tpp) cc_final: 0.7732 (tpp) REVERT: A 412 TRP cc_start: 0.9186 (OUTLIER) cc_final: 0.7802 (m-90) REVERT: C 55 ARG cc_start: 0.9165 (tmt-80) cc_final: 0.8919 (tpt90) REVERT: B 599 ARG cc_start: 0.8892 (OUTLIER) cc_final: 0.8607 (ttp80) outliers start: 33 outliers final: 23 residues processed: 91 average time/residue: 0.2161 time to fit residues: 26.4112 Evaluate side-chains 87 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 62 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 PHE Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 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 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 599 ARG Chi-restraints excluded: chain B residue 619 HIS Chi-restraints excluded: chain B residue 657 SER Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 775 ILE Chi-restraints excluded: chain B residue 905 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 25 optimal weight: 10.0000 chunk 42 optimal weight: 0.4980 chunk 69 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 7 optimal weight: 0.2980 chunk 31 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.092959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.067480 restraints weight = 20104.354| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 3.78 r_work: 0.3050 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.4902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7203 Z= 0.214 Angle : 0.528 8.876 9718 Z= 0.263 Chirality : 0.042 0.156 1061 Planarity : 0.004 0.047 1233 Dihedral : 4.091 17.592 931 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 5.10 % Allowed : 28.28 % 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: -1.66 (0.29), residues: 816 helix: -0.21 (0.49), residues: 129 sheet: -0.63 (0.58), residues: 90 loop : -1.48 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 604 HIS 0.002 0.000 HIS A 100 PHE 0.024 0.002 PHE B 696 TYR 0.013 0.001 TYR B 697 ARG 0.008 0.000 ARG D 55 *********************** 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 107 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 67 time to evaluate : 0.874 Fit side-chains revert: symmetry clash REVERT: A 46 PHE cc_start: 0.9217 (OUTLIER) cc_final: 0.8927 (t80) REVERT: A 412 TRP cc_start: 0.9183 (OUTLIER) cc_final: 0.7969 (m-90) REVERT: A 559 TRP cc_start: 0.5821 (p90) cc_final: 0.5526 (p90) REVERT: C 55 ARG cc_start: 0.9153 (tmt-80) cc_final: 0.8870 (tpt90) REVERT: B 545 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8001 (mm-30) REVERT: B 599 ARG cc_start: 0.8911 (OUTLIER) cc_final: 0.8647 (ttp80) outliers start: 40 outliers final: 25 residues processed: 99 average time/residue: 0.1915 time to fit residues: 25.7771 Evaluate side-chains 91 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 63 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 PHE Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 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 25 PHE Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain B residue 518 GLN Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 599 ARG 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 722 VAL Chi-restraints excluded: chain B residue 775 ILE Chi-restraints excluded: chain B residue 905 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 56 optimal weight: 9.9990 chunk 80 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 59 optimal weight: 0.3980 chunk 81 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 79 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3746 r_free = 0.3746 target = 0.092265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.066793 restraints weight = 20319.329| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 3.79 r_work: 0.3034 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.5155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7203 Z= 0.250 Angle : 0.545 8.270 9718 Z= 0.275 Chirality : 0.042 0.151 1061 Planarity : 0.004 0.046 1233 Dihedral : 4.231 18.637 931 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 5.35 % Allowed : 27.90 % 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: -1.72 (0.29), residues: 816 helix: -0.18 (0.49), residues: 129 sheet: -0.64 (0.58), residues: 90 loop : -1.55 (0.25), residues: 597 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 0.024 0.002 PHE B 696 TYR 0.015 0.001 TYR B 697 ARG 0.005 0.000 ARG D 55 *********************** 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 104 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 62 time to evaluate : 0.829 Fit side-chains revert: symmetry clash REVERT: A 46 PHE cc_start: 0.9204 (OUTLIER) cc_final: 0.8942 (t80) REVERT: A 294 MET cc_start: 0.8026 (tpp) cc_final: 0.7809 (tpp) REVERT: A 412 TRP cc_start: 0.9195 (OUTLIER) cc_final: 0.7890 (m-90) REVERT: A 508 LYS cc_start: 0.7473 (OUTLIER) cc_final: 0.7252 (mmmm) REVERT: A 559 TRP cc_start: 0.5759 (p90) cc_final: 0.5553 (p90) REVERT: C 24 TYR cc_start: 0.8816 (t80) cc_final: 0.8611 (t80) REVERT: B 545 GLU cc_start: 0.8692 (mm-30) cc_final: 0.7980 (mm-30) REVERT: B 599 ARG cc_start: 0.8927 (OUTLIER) cc_final: 0.8654 (ttp80) REVERT: B 631 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7963 (tppp) outliers start: 42 outliers final: 27 residues processed: 98 average time/residue: 0.1775 time to fit residues: 24.1417 Evaluate side-chains 91 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 59 time to evaluate : 0.771 ------------------------------------------------------------------------------- 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 412 TRP Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain D residue 21 ARG Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 518 GLN Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 599 ARG Chi-restraints excluded: chain B residue 619 HIS Chi-restraints excluded: chain B residue 631 LYS Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 775 ILE Chi-restraints excluded: chain B residue 905 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 39 optimal weight: 0.0670 chunk 75 optimal weight: 0.1980 chunk 1 optimal weight: 1.9990 chunk 15 optimal weight: 0.0870 chunk 67 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 10 optimal weight: 0.0980 chunk 44 optimal weight: 0.0010 overall best weight: 0.0902 ------------------------------------------------------------------------------- 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 = 0.3790 r_free = 0.3790 target = 0.094652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.069640 restraints weight = 20016.471| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 3.79 r_work: 0.3101 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.4924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7203 Z= 0.129 Angle : 0.506 9.091 9718 Z= 0.250 Chirality : 0.041 0.141 1061 Planarity : 0.003 0.046 1233 Dihedral : 3.781 15.983 931 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 4.71 % Allowed : 28.66 % 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: -1.60 (0.29), residues: 816 helix: -0.02 (0.50), residues: 127 sheet: -0.61 (0.58), residues: 90 loop : -1.47 (0.25), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 493 HIS 0.002 0.000 HIS A 263 PHE 0.017 0.001 PHE B 696 TYR 0.013 0.001 TYR B 697 ARG 0.002 0.000 ARG A 371 *********************** 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 103 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 66 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 412 TRP cc_start: 0.9032 (OUTLIER) cc_final: 0.7790 (m-90) REVERT: A 454 ARG cc_start: 0.7759 (tpt170) cc_final: 0.7539 (tpt90) REVERT: C 55 ARG cc_start: 0.9057 (tmt-80) cc_final: 0.8812 (tpt90) REVERT: C 56 ARG cc_start: 0.9023 (tpm170) cc_final: 0.8795 (tpm170) REVERT: B 629 ILE cc_start: 0.8484 (mm) cc_final: 0.8074 (pt) REVERT: B 631 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7947 (tppp) outliers start: 37 outliers final: 27 residues processed: 93 average time/residue: 0.1918 time to fit residues: 24.2017 Evaluate side-chains 90 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 61 time to evaluate : 0.811 ------------------------------------------------------------------------------- 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 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 25 PHE Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 59 MET Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 518 GLN Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 631 LYS Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain B residue 657 SER Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 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: 1.9990 chunk 4 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 25 optimal weight: 8.9990 chunk 11 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 50 optimal weight: 0.0770 overall best weight: 1.4144 ------------------------------------------------------------------------------- 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 = 0.3734 r_free = 0.3734 target = 0.091824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.066134 restraints weight = 20452.704| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 3.81 r_work: 0.3025 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.5301 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= 0.288 Angle : 0.561 7.724 9718 Z= 0.283 Chirality : 0.043 0.149 1061 Planarity : 0.004 0.046 1233 Dihedral : 4.257 18.693 931 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 4.97 % Allowed : 27.64 % 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: -1.66 (0.29), residues: 816 helix: -0.06 (0.49), residues: 129 sheet: -0.59 (0.58), residues: 90 loop : -1.53 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 604 HIS 0.002 0.000 HIS A 548 PHE 0.024 0.002 PHE B 696 TYR 0.015 0.001 TYR B 697 ARG 0.003 0.000 ARG D 21 *********************** 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 103 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 64 time to evaluate : 0.749 Fit side-chains revert: symmetry clash REVERT: A 412 TRP cc_start: 0.9179 (OUTLIER) cc_final: 0.8023 (m-90) REVERT: C 24 TYR cc_start: 0.8864 (t80) cc_final: 0.8647 (t80) REVERT: C 55 ARG cc_start: 0.9097 (tmt-80) cc_final: 0.8502 (tpt90) REVERT: B 545 GLU cc_start: 0.8729 (mm-30) cc_final: 0.8029 (mm-30) REVERT: B 631 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.8063 (tppp) outliers start: 39 outliers final: 27 residues processed: 95 average time/residue: 0.1600 time to fit residues: 21.4585 Evaluate side-chains 90 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 61 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 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 25 PHE Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain B residue 518 GLN Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 619 HIS Chi-restraints excluded: chain B residue 631 LYS Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 905 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 16 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 18 optimal weight: 0.2980 chunk 49 optimal weight: 0.5980 chunk 78 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.3747 r_free = 0.3747 target = 0.092487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.066992 restraints weight = 20494.946| |-----------------------------------------------------------------------------| r_work (start): 0.3198 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: 0.8233 moved from start: 0.5254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7203 Z= 0.181 Angle : 0.556 12.460 9718 Z= 0.271 Chirality : 0.042 0.156 1061 Planarity : 0.003 0.046 1233 Dihedral : 4.072 17.700 931 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 4.20 % Allowed : 28.41 % 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: -1.65 (0.29), residues: 816 helix: -0.04 (0.49), residues: 129 sheet: -0.57 (0.58), residues: 90 loop : -1.52 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 493 HIS 0.001 0.000 HIS B 630 PHE 0.021 0.001 PHE B 696 TYR 0.014 0.001 TYR B 697 ARG 0.006 0.000 ARG C 55 *********************** 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 93 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 60 time to evaluate : 0.817 Fit side-chains revert: symmetry clash REVERT: A 412 TRP cc_start: 0.9128 (OUTLIER) cc_final: 0.7938 (m-90) REVERT: B 545 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8013 (mm-30) REVERT: B 631 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.8048 (tppp) outliers start: 33 outliers final: 28 residues processed: 86 average time/residue: 0.1773 time to fit residues: 21.3237 Evaluate side-chains 89 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 59 time to evaluate : 0.756 ------------------------------------------------------------------------------- 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 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 25 PHE Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain B residue 518 GLN Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 619 HIS Chi-restraints excluded: chain B residue 631 LYS Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 905 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 82 optimal weight: 0.8980 chunk 72 optimal weight: 0.4980 chunk 74 optimal weight: 0.8980 chunk 61 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 chunk 3 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3732 r_free = 0.3732 target = 0.091745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.066230 restraints weight = 20739.576| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 3.84 r_work: 0.3027 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.5394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7203 Z= 0.235 Angle : 0.579 11.970 9718 Z= 0.281 Chirality : 0.042 0.149 1061 Planarity : 0.003 0.046 1233 Dihedral : 4.150 18.056 931 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 4.08 % Allowed : 28.28 % 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: -1.67 (0.29), residues: 816 helix: -0.03 (0.50), residues: 129 sheet: -0.62 (0.58), residues: 89 loop : -1.54 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 493 HIS 0.002 0.000 HIS B 630 PHE 0.022 0.001 PHE B 696 TYR 0.014 0.001 TYR B 697 ARG 0.004 0.000 ARG C 55 ********************** 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 92 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 60 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 412 TRP cc_start: 0.9168 (OUTLIER) cc_final: 0.7893 (m-90) REVERT: C 24 TYR cc_start: 0.8836 (t80) cc_final: 0.8602 (t80) REVERT: C 55 ARG cc_start: 0.9031 (tpt90) cc_final: 0.8674 (tpt90) REVERT: B 545 GLU cc_start: 0.8683 (mm-30) cc_final: 0.7998 (mm-30) outliers start: 32 outliers final: 28 residues processed: 85 average time/residue: 0.1747 time to fit residues: 20.7725 Evaluate side-chains 89 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 60 time to evaluate : 0.758 ------------------------------------------------------------------------------- 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 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 25 PHE Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain B residue 518 GLN Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 619 HIS Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 905 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 15 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 13 optimal weight: 0.0970 chunk 64 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 18 optimal weight: 0.0370 chunk 2 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 56 optimal weight: 8.9990 chunk 58 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 overall best weight: 0.5658 ------------------------------------------------------------------------------- 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 = 0.3752 r_free = 0.3752 target = 0.092718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.067394 restraints weight = 20289.453| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 3.81 r_work: 0.3057 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.5320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7203 Z= 0.166 Angle : 0.563 11.847 9718 Z= 0.274 Chirality : 0.042 0.144 1061 Planarity : 0.004 0.046 1233 Dihedral : 3.967 17.012 931 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 3.82 % Allowed : 28.54 % 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: -1.57 (0.29), residues: 816 helix: 0.25 (0.52), residues: 122 sheet: -0.86 (0.54), residues: 99 loop : -1.45 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 604 HIS 0.005 0.000 HIS B 630 PHE 0.019 0.001 PHE B 696 TYR 0.013 0.001 TYR B 697 ARG 0.008 0.000 ARG C 55 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4093.76 seconds wall clock time: 70 minutes 50.99 seconds (4250.99 seconds total)