Starting phenix.real_space_refine on Mon Mar 11 06:09:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wbx_37426/03_2024/8wbx_37426_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wbx_37426/03_2024/8wbx_37426.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wbx_37426/03_2024/8wbx_37426.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wbx_37426/03_2024/8wbx_37426.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wbx_37426/03_2024/8wbx_37426_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wbx_37426/03_2024/8wbx_37426_updated.pdb" } resolution = 3.23 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= -0.002 sd= 0.052 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 44 5.16 5 C 4809 2.51 5 N 1202 2.21 5 O 1276 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 294": "OD1" <-> "OD2" Residue "A ASP 314": "OD1" <-> "OD2" Residue "A PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 469": "OE1" <-> "OE2" Residue "A PHE 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 159": "OE1" <-> "OE2" Residue "B GLU 188": "OE1" <-> "OE2" Residue "B PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 407": "OD1" <-> "OD2" Residue "B TYR 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 432": "OD1" <-> "OD2" Residue "B PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 462": "OE1" <-> "OE2" Residue "B TYR 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7331 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3656 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 16, 'TRANS': 450} Chain breaks: 3 Chain: "B" Number of atoms: 3656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3656 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 16, 'TRANS': 450} Chain breaks: 3 Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'A8S': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.33, per 1000 atoms: 0.59 Number of scatterers: 7331 At special positions: 0 Unit cell: (80.3, 94.6, 116.6, 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 44 16.00 O 1276 8.00 N 1202 7.00 C 4809 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 2.88 Conformation dependent library (CDL) restraints added in 1.4 seconds 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1724 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 39 helices and 2 sheets defined 62.5% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'A' and resid 107 through 110 No H-bonds generated for 'chain 'A' and resid 107 through 110' Processing helix chain 'A' and resid 137 through 140 No H-bonds generated for 'chain 'A' and resid 137 through 140' Processing helix chain 'A' and resid 157 through 168 removed outlier: 3.572A pdb=" N LEU A 161 " --> pdb=" O VAL A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 188 Processing helix chain 'A' and resid 209 through 221 removed outlier: 3.671A pdb=" N GLU A 220 " --> pdb=" O SER A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 255 Processing helix chain 'A' and resid 269 through 274 removed outlier: 4.055A pdb=" N MET A 274 " --> pdb=" O ARG A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 302 removed outlier: 4.333A pdb=" N MET A 296 " --> pdb=" O GLY A 292 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ALA A 297 " --> pdb=" O ARG A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 319 Processing helix chain 'A' and resid 380 through 403 removed outlier: 3.917A pdb=" N LYS A 399 " --> pdb=" O HIS A 395 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLU A 400 " --> pdb=" O ARG A 396 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N HIS A 403 " --> pdb=" O LYS A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 424 removed outlier: 4.207A pdb=" N GLN A 413 " --> pdb=" O LEU A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 471 Proline residue: A 451 - end of helix removed outlier: 3.810A pdb=" N PHE A 457 " --> pdb=" O PHE A 453 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR A 458 " --> pdb=" O ASN A 454 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N PHE A 459 " --> pdb=" O ALA A 455 " (cutoff:3.500A) Proline residue: A 460 - end of helix removed outlier: 4.509A pdb=" N ALA A 464 " --> pdb=" O PRO A 460 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N ILE A 465 " --> pdb=" O GLN A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 491 Processing helix chain 'A' and resid 494 through 507 removed outlier: 3.691A pdb=" N TRP A 505 " --> pdb=" O THR A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 540 Processing helix chain 'A' and resid 544 through 560 Processing helix chain 'A' and resid 574 through 576 No H-bonds generated for 'chain 'A' and resid 574 through 576' Processing helix chain 'A' and resid 582 through 593 Processing helix chain 'A' and resid 625 through 629 Processing helix chain 'A' and resid 635 through 659 removed outlier: 3.794A pdb=" N ARG A 650 " --> pdb=" O PHE A 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 110 No H-bonds generated for 'chain 'B' and resid 107 through 110' Processing helix chain 'B' and resid 137 through 140 No H-bonds generated for 'chain 'B' and resid 137 through 140' Processing helix chain 'B' and resid 157 through 168 Processing helix chain 'B' and resid 175 through 188 Processing helix chain 'B' and resid 209 through 221 removed outlier: 3.671A pdb=" N GLU B 220 " --> pdb=" O SER B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 255 Processing helix chain 'B' and resid 269 through 274 removed outlier: 3.967A pdb=" N MET B 274 " --> pdb=" O ARG B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 302 Processing helix chain 'B' and resid 312 through 319 Processing helix chain 'B' and resid 380 through 405 removed outlier: 4.125A pdb=" N LYS B 399 " --> pdb=" O HIS B 395 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLU B 400 " --> pdb=" O ARG B 396 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N HIS B 403 " --> pdb=" O LYS B 399 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLU B 404 " --> pdb=" O GLU B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 424 Processing helix chain 'B' and resid 433 through 471 Proline residue: B 451 - end of helix removed outlier: 3.907A pdb=" N PHE B 457 " --> pdb=" O PHE B 453 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N THR B 458 " --> pdb=" O ASN B 454 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N PHE B 459 " --> pdb=" O ALA B 455 " (cutoff:3.500A) Proline residue: B 460 - end of helix removed outlier: 4.547A pdb=" N ALA B 464 " --> pdb=" O PRO B 460 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ILE B 465 " --> pdb=" O GLN B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 507 removed outlier: 4.076A pdb=" N SER B 490 " --> pdb=" O LEU B 486 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N MET B 491 " --> pdb=" O GLY B 487 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU B 495 " --> pdb=" O MET B 491 " (cutoff:3.500A) Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 513 through 540 Processing helix chain 'B' and resid 544 through 561 Processing helix chain 'B' and resid 571 through 578 removed outlier: 3.833A pdb=" N VAL B 574 " --> pdb=" O SER B 571 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N TRP B 575 " --> pdb=" O GLY B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 594 Processing helix chain 'B' and resid 625 through 628 No H-bonds generated for 'chain 'B' and resid 625 through 628' Processing helix chain 'B' and resid 635 through 659 Processing sheet with id= A, first strand: chain 'A' and resid 285 through 290 removed outlier: 6.724A pdb=" N LEU A 280 " --> pdb=" O LEU A 287 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N VAL A 289 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL A 278 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N VAL A 260 " --> pdb=" O MET A 97 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N VAL A 99 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N THR A 262 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 285 through 290 removed outlier: 6.587A pdb=" N LEU B 280 " --> pdb=" O LEU B 287 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N VAL B 289 " --> pdb=" O VAL B 278 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL B 278 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL B 260 " --> pdb=" O MET B 97 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N VAL B 99 " --> pdb=" O VAL B 260 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N THR B 262 " --> pdb=" O VAL B 99 " (cutoff:3.500A) 414 hydrogen bonds defined for protein. 1221 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: 2.25 Time building geometry restraints manager: 3.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1991 1.34 - 1.45: 1304 1.45 - 1.57: 4124 1.57 - 1.69: 0 1.69 - 1.81: 76 Bond restraints: 7495 Sorted by residual: bond pdb=" N PRO A 460 " pdb=" CD PRO A 460 " ideal model delta sigma weight residual 1.473 1.536 -0.063 1.40e-02 5.10e+03 1.99e+01 bond pdb=" N TYR B 504 " pdb=" CA TYR B 504 " ideal model delta sigma weight residual 1.459 1.491 -0.031 1.19e-02 7.06e+03 6.89e+00 bond pdb=" N LEU A 280 " pdb=" CA LEU A 280 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.19e-02 7.06e+03 6.06e+00 bond pdb=" N PHE A 275 " pdb=" CA PHE A 275 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.29e-02 6.01e+03 6.01e+00 bond pdb=" N GLN B 593 " pdb=" CA GLN B 593 " ideal model delta sigma weight residual 1.458 1.489 -0.032 1.30e-02 5.92e+03 5.90e+00 ... (remaining 7490 not shown) Histogram of bond angle deviations from ideal: 98.50 - 105.64: 142 105.64 - 112.78: 4056 112.78 - 119.92: 2476 119.92 - 127.06: 3409 127.06 - 134.20: 82 Bond angle restraints: 10165 Sorted by residual: angle pdb=" N PHE B 583 " pdb=" CA PHE B 583 " pdb=" C PHE B 583 " ideal model delta sigma weight residual 110.97 105.67 5.30 1.09e+00 8.42e-01 2.37e+01 angle pdb=" N PHE B 315 " pdb=" CA PHE B 315 " pdb=" C PHE B 315 " ideal model delta sigma weight residual 111.36 106.34 5.02 1.09e+00 8.42e-01 2.12e+01 angle pdb=" C ASP B 314 " pdb=" N PHE B 315 " pdb=" CA PHE B 315 " ideal model delta sigma weight residual 120.29 114.12 6.17 1.42e+00 4.96e-01 1.89e+01 angle pdb=" CA GLU B 159 " pdb=" CB GLU B 159 " pdb=" CG GLU B 159 " ideal model delta sigma weight residual 114.10 121.29 -7.19 2.00e+00 2.50e-01 1.29e+01 angle pdb=" O PHE B 583 " pdb=" C PHE B 583 " pdb=" N TYR B 584 " ideal model delta sigma weight residual 122.03 125.37 -3.34 1.04e+00 9.25e-01 1.03e+01 ... (remaining 10160 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.41: 3966 22.41 - 44.82: 377 44.82 - 67.23: 46 67.23 - 89.64: 3 89.64 - 112.04: 10 Dihedral angle restraints: 4402 sinusoidal: 1720 harmonic: 2682 Sorted by residual: dihedral pdb=" C10 A8S A 701 " pdb=" C11 A8S A 701 " pdb=" C12 A8S A 701 " pdb=" C7 A8S A 701 " ideal model delta sinusoidal sigma weight residual 55.84 -56.20 112.04 1 3.00e+01 1.11e-03 1.47e+01 dihedral pdb=" C15 A8S A 701 " pdb=" C12 A8S A 701 " pdb=" C7 A8S A 701 " pdb=" C5 A8S A 701 " ideal model delta sinusoidal sigma weight residual -49.34 58.90 -108.24 1 3.00e+01 1.11e-03 1.40e+01 dihedral pdb=" C11 A8S A 701 " pdb=" C12 A8S A 701 " pdb=" C7 A8S A 701 " pdb=" C5 A8S A 701 " ideal model delta sinusoidal sigma weight residual -169.52 -62.40 -107.12 1 3.00e+01 1.11e-03 1.38e+01 ... (remaining 4399 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 954 0.047 - 0.095: 196 0.095 - 0.142: 43 0.142 - 0.189: 4 0.189 - 0.236: 2 Chirality restraints: 1199 Sorted by residual: chirality pdb=" CA PHE B 583 " pdb=" N PHE B 583 " pdb=" C PHE B 583 " pdb=" CB PHE B 583 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA ILE A 660 " pdb=" N ILE A 660 " pdb=" C ILE A 660 " pdb=" CB ILE A 660 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.96e-01 chirality pdb=" CA LEU A 652 " pdb=" N LEU A 652 " pdb=" C LEU A 652 " pdb=" CB LEU A 652 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.49e-01 ... (remaining 1196 not shown) Planarity restraints: 1242 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 92 " -0.040 5.00e-02 4.00e+02 6.07e-02 5.89e+00 pdb=" N PRO A 93 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 93 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 93 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR B 582 " 0.010 2.00e-02 2.50e+03 2.15e-02 4.60e+00 pdb=" C THR B 582 " -0.037 2.00e-02 2.50e+03 pdb=" O THR B 582 " 0.014 2.00e-02 2.50e+03 pdb=" N PHE B 583 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 232 " 0.033 5.00e-02 4.00e+02 4.97e-02 3.96e+00 pdb=" N PRO B 233 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 233 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 233 " 0.028 5.00e-02 4.00e+02 ... (remaining 1239 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2220 2.82 - 3.34: 7409 3.34 - 3.86: 12627 3.86 - 4.38: 14086 4.38 - 4.90: 24002 Nonbonded interactions: 60344 Sorted by model distance: nonbonded pdb=" O THR B 156 " pdb=" OG1 THR B 160 " model vdw 2.305 2.440 nonbonded pdb=" N ASP B 432 " pdb=" OD1 ASP B 432 " model vdw 2.368 2.520 nonbonded pdb=" OE1 GLU B 462 " pdb=" OH TYR B 480 " model vdw 2.402 2.440 nonbonded pdb=" O LEU A 528 " pdb=" NH2 ARG A 650 " model vdw 2.410 2.520 nonbonded pdb=" O SER A 444 " pdb=" OH TYR A 526 " model vdw 2.424 2.440 ... (remaining 60339 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 90 through 660) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.850 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: 3.850 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 23.490 Find NCS groups from input model: 0.440 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6176 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 : 0.003 0.063 7495 Z= 0.204 Angle : 0.658 9.031 10165 Z= 0.351 Chirality : 0.040 0.236 1199 Planarity : 0.004 0.061 1242 Dihedral : 16.957 112.044 2678 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.38 % Allowed : 22.92 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.29), residues: 918 helix: 2.00 (0.21), residues: 608 sheet: 0.12 (0.66), residues: 46 loop : -0.58 (0.41), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 575 HIS 0.002 0.000 HIS B 219 PHE 0.015 0.001 PHE A 499 TYR 0.026 0.001 TYR B 504 ARG 0.008 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 167 time to evaluate : 0.842 Fit side-chains revert: symmetry clash REVERT: A 252 LEU cc_start: 0.7843 (mt) cc_final: 0.7549 (mp) REVERT: A 506 MET cc_start: 0.6127 (mmp) cc_final: 0.5685 (ttt) REVERT: B 97 MET cc_start: 0.5763 (ttm) cc_final: 0.5535 (ttp) REVERT: B 569 VAL cc_start: 0.7387 (t) cc_final: 0.7135 (t) REVERT: B 575 TRP cc_start: 0.7252 (p-90) cc_final: 0.6630 (t-100) outliers start: 3 outliers final: 1 residues processed: 168 average time/residue: 0.1704 time to fit residues: 39.4802 Evaluate side-chains 150 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 149 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 507 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 GLN ** B 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6404 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7495 Z= 0.209 Angle : 0.580 9.510 10165 Z= 0.271 Chirality : 0.038 0.150 1199 Planarity : 0.004 0.045 1242 Dihedral : 7.133 58.799 1035 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 4.66 % Allowed : 21.16 % Favored : 74.18 % 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: 1.76 (0.28), residues: 918 helix: 2.00 (0.21), residues: 612 sheet: -0.17 (0.66), residues: 48 loop : -0.58 (0.42), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP B 575 HIS 0.003 0.001 HIS B 219 PHE 0.020 0.002 PHE A 446 TYR 0.014 0.001 TYR A 475 ARG 0.003 0.000 ARG A 410 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 162 time to evaluate : 0.845 Fit side-chains REVERT: A 231 ASP cc_start: 0.6924 (t70) cc_final: 0.6621 (t0) REVERT: A 390 LEU cc_start: 0.7010 (OUTLIER) cc_final: 0.6740 (tt) REVERT: A 568 LYS cc_start: 0.8022 (tttt) cc_final: 0.7717 (tttt) REVERT: A 635 MET cc_start: 0.6772 (tpp) cc_final: 0.6545 (tpt) REVERT: A 652 LEU cc_start: 0.8332 (mm) cc_final: 0.7920 (tp) REVERT: B 161 LEU cc_start: 0.7799 (OUTLIER) cc_final: 0.7156 (mm) REVERT: B 390 LEU cc_start: 0.6904 (OUTLIER) cc_final: 0.6630 (tt) REVERT: B 432 ASP cc_start: 0.7607 (OUTLIER) cc_final: 0.7175 (p0) REVERT: B 508 TYR cc_start: 0.6166 (t80) cc_final: 0.5891 (t80) REVERT: B 635 MET cc_start: 0.6943 (mmm) cc_final: 0.6528 (tpt) REVERT: B 652 LEU cc_start: 0.8387 (mm) cc_final: 0.8086 (tp) outliers start: 37 outliers final: 21 residues processed: 183 average time/residue: 0.1848 time to fit residues: 45.8498 Evaluate side-chains 177 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 152 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 645 MET Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 430 TYR Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 580 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6524 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7495 Z= 0.262 Angle : 0.581 8.565 10165 Z= 0.278 Chirality : 0.039 0.126 1199 Planarity : 0.004 0.042 1242 Dihedral : 4.909 53.819 1034 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 4.91 % Allowed : 23.80 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.28), residues: 918 helix: 1.70 (0.20), residues: 608 sheet: -0.75 (0.70), residues: 46 loop : -0.63 (0.42), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 575 HIS 0.004 0.001 HIS A 219 PHE 0.024 0.002 PHE A 446 TYR 0.009 0.001 TYR B 475 ARG 0.004 0.000 ARG A 410 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 153 time to evaluate : 0.914 Fit side-chains REVERT: A 310 MET cc_start: 0.8172 (ppp) cc_final: 0.7906 (ppp) REVERT: A 432 ASP cc_start: 0.7940 (OUTLIER) cc_final: 0.7472 (p0) REVERT: A 568 LYS cc_start: 0.8008 (tttt) cc_final: 0.7681 (tttt) REVERT: B 159 GLU cc_start: 0.7487 (tp30) cc_final: 0.7246 (tp30) REVERT: B 161 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7502 (mm) REVERT: B 285 LYS cc_start: 0.7071 (mmmt) cc_final: 0.6842 (mmmt) REVERT: B 310 MET cc_start: 0.8198 (ppp) cc_final: 0.7744 (ppp) REVERT: B 432 ASP cc_start: 0.7808 (OUTLIER) cc_final: 0.7328 (p0) REVERT: B 652 LEU cc_start: 0.8361 (mm) cc_final: 0.7797 (tt) outliers start: 39 outliers final: 28 residues processed: 174 average time/residue: 0.2094 time to fit residues: 50.3448 Evaluate side-chains 180 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 149 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 430 TYR Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 645 MET Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 430 TYR Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain B residue 637 THR Chi-restraints excluded: chain B residue 646 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 43 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 39 optimal weight: 0.0980 chunk 56 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6523 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7495 Z= 0.205 Angle : 0.540 8.503 10165 Z= 0.254 Chirality : 0.037 0.117 1199 Planarity : 0.004 0.039 1242 Dihedral : 4.538 55.819 1034 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.91 % Allowed : 23.80 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.28), residues: 918 helix: 1.68 (0.20), residues: 608 sheet: -0.92 (0.67), residues: 46 loop : -0.59 (0.42), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 575 HIS 0.004 0.001 HIS A 219 PHE 0.018 0.001 PHE A 275 TYR 0.012 0.001 TYR B 504 ARG 0.003 0.000 ARG B 205 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 156 time to evaluate : 0.819 Fit side-chains revert: symmetry clash REVERT: A 161 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7650 (mm) REVERT: A 231 ASP cc_start: 0.7065 (t70) cc_final: 0.6783 (t0) REVERT: A 432 ASP cc_start: 0.7962 (OUTLIER) cc_final: 0.7507 (p0) REVERT: A 525 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7298 (tp) REVERT: A 635 MET cc_start: 0.6779 (tpp) cc_final: 0.6553 (tpt) REVERT: A 652 LEU cc_start: 0.8385 (mm) cc_final: 0.7972 (tt) REVERT: B 161 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7429 (mm) REVERT: B 285 LYS cc_start: 0.7145 (mmmt) cc_final: 0.6930 (mmmt) REVERT: B 387 PHE cc_start: 0.6299 (t80) cc_final: 0.6065 (t80) REVERT: B 432 ASP cc_start: 0.7822 (OUTLIER) cc_final: 0.7374 (p0) REVERT: B 462 GLU cc_start: 0.6667 (mm-30) cc_final: 0.6321 (mt-10) outliers start: 39 outliers final: 28 residues processed: 179 average time/residue: 0.1815 time to fit residues: 44.2393 Evaluate side-chains 179 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 146 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 430 TYR Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 645 MET Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 430 TYR Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 504 TYR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain B residue 637 THR Chi-restraints excluded: chain B residue 651 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 0.6980 chunk 1 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 79 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6581 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7495 Z= 0.260 Angle : 0.580 8.391 10165 Z= 0.275 Chirality : 0.039 0.125 1199 Planarity : 0.004 0.039 1242 Dihedral : 4.505 57.820 1034 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 6.05 % Allowed : 23.80 % Favored : 70.15 % 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: 1.07 (0.28), residues: 918 helix: 1.45 (0.20), residues: 618 sheet: -1.46 (0.64), residues: 46 loop : -0.62 (0.43), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 575 HIS 0.005 0.001 HIS A 219 PHE 0.020 0.002 PHE A 446 TYR 0.012 0.001 TYR B 504 ARG 0.003 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 153 time to evaluate : 0.854 Fit side-chains REVERT: A 161 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7540 (mm) REVERT: A 424 MET cc_start: 0.7008 (mmp) cc_final: 0.6740 (mmp) REVERT: A 432 ASP cc_start: 0.8000 (OUTLIER) cc_final: 0.7613 (p0) REVERT: A 525 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7362 (tp) REVERT: A 635 MET cc_start: 0.6713 (tpp) cc_final: 0.6453 (tpt) REVERT: A 652 LEU cc_start: 0.8447 (mm) cc_final: 0.7942 (tp) REVERT: B 161 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7663 (mm) REVERT: B 390 LEU cc_start: 0.7093 (OUTLIER) cc_final: 0.6872 (tt) REVERT: B 398 LEU cc_start: 0.7523 (mt) cc_final: 0.7206 (mt) REVERT: B 432 ASP cc_start: 0.7816 (OUTLIER) cc_final: 0.7377 (p0) REVERT: B 462 GLU cc_start: 0.6725 (mm-30) cc_final: 0.6331 (mt-10) REVERT: B 652 LEU cc_start: 0.8213 (mm) cc_final: 0.7773 (tp) outliers start: 48 outliers final: 34 residues processed: 181 average time/residue: 0.1814 time to fit residues: 45.0132 Evaluate side-chains 184 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 144 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 430 TYR Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 645 MET Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 430 TYR Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 504 TYR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain B residue 637 THR Chi-restraints excluded: chain B residue 651 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 0.8980 chunk 17 optimal weight: 0.0770 chunk 52 optimal weight: 0.1980 chunk 21 optimal weight: 10.0000 chunk 89 optimal weight: 0.0570 chunk 73 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6510 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7495 Z= 0.159 Angle : 0.530 8.487 10165 Z= 0.244 Chirality : 0.037 0.132 1199 Planarity : 0.004 0.037 1242 Dihedral : 4.200 59.632 1034 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.40 % Allowed : 26.32 % Favored : 70.28 % 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 (0.28), residues: 918 helix: 1.82 (0.21), residues: 608 sheet: -1.25 (0.63), residues: 46 loop : -0.50 (0.42), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 575 HIS 0.003 0.001 HIS A 219 PHE 0.016 0.001 PHE B 275 TYR 0.008 0.001 TYR B 504 ARG 0.004 0.000 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 154 time to evaluate : 0.769 Fit side-chains REVERT: A 161 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7616 (mm) REVERT: A 635 MET cc_start: 0.6731 (tpp) cc_final: 0.6470 (tpt) REVERT: A 652 LEU cc_start: 0.8323 (mm) cc_final: 0.7924 (tp) REVERT: B 161 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7326 (mm) REVERT: B 310 MET cc_start: 0.8222 (ppp) cc_final: 0.7903 (ppp) REVERT: B 398 LEU cc_start: 0.7472 (mt) cc_final: 0.7168 (mt) REVERT: B 432 ASP cc_start: 0.7743 (OUTLIER) cc_final: 0.7401 (p0) REVERT: B 462 GLU cc_start: 0.6681 (mm-30) cc_final: 0.6347 (mt-10) REVERT: B 506 MET cc_start: 0.6234 (mmp) cc_final: 0.5652 (ttt) REVERT: B 652 LEU cc_start: 0.8305 (mm) cc_final: 0.7789 (tp) outliers start: 27 outliers final: 19 residues processed: 171 average time/residue: 0.1867 time to fit residues: 44.6859 Evaluate side-chains 172 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 150 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 430 TYR Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 430 TYR Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 504 TYR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain B residue 637 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 65 optimal weight: 0.0050 chunk 74 optimal weight: 0.7980 chunk 49 optimal weight: 0.3980 chunk 88 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 52 optimal weight: 8.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6510 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7495 Z= 0.163 Angle : 0.532 8.372 10165 Z= 0.245 Chirality : 0.037 0.161 1199 Planarity : 0.004 0.035 1242 Dihedral : 4.123 59.497 1034 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 4.16 % Allowed : 26.32 % Favored : 69.52 % 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: 1.58 (0.28), residues: 918 helix: 1.89 (0.21), residues: 608 sheet: -1.17 (0.62), residues: 46 loop : -0.47 (0.42), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 575 HIS 0.004 0.001 HIS A 219 PHE 0.015 0.001 PHE A 275 TYR 0.008 0.001 TYR A 475 ARG 0.006 0.000 ARG A 410 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 153 time to evaluate : 0.928 Fit side-chains REVERT: A 161 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7628 (mm) REVERT: A 432 ASP cc_start: 0.7956 (OUTLIER) cc_final: 0.7579 (p0) REVERT: A 506 MET cc_start: 0.6006 (mmp) cc_final: 0.5508 (ttt) REVERT: A 568 LYS cc_start: 0.8066 (tttt) cc_final: 0.7631 (tttt) REVERT: A 635 MET cc_start: 0.6726 (tpp) cc_final: 0.6437 (tpt) REVERT: A 652 LEU cc_start: 0.8323 (mm) cc_final: 0.7950 (tt) REVERT: B 159 GLU cc_start: 0.7017 (mm-30) cc_final: 0.6731 (tp30) REVERT: B 161 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7287 (mm) REVERT: B 273 GLN cc_start: 0.5940 (pp30) cc_final: 0.5617 (tp40) REVERT: B 398 LEU cc_start: 0.7469 (mt) cc_final: 0.7169 (mt) REVERT: B 432 ASP cc_start: 0.7827 (OUTLIER) cc_final: 0.7419 (p0) REVERT: B 462 GLU cc_start: 0.6750 (mm-30) cc_final: 0.6401 (mt-10) REVERT: B 506 MET cc_start: 0.6294 (mmp) cc_final: 0.5952 (ttt) REVERT: B 652 LEU cc_start: 0.8313 (mm) cc_final: 0.7788 (tp) outliers start: 33 outliers final: 23 residues processed: 174 average time/residue: 0.1877 time to fit residues: 44.2124 Evaluate side-chains 176 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 149 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 430 TYR Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 430 TYR Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain B residue 637 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 chunk 60 optimal weight: 0.2980 chunk 43 optimal weight: 0.0770 chunk 8 optimal weight: 8.9990 chunk 69 optimal weight: 4.9990 chunk 80 optimal weight: 0.5980 chunk 84 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6495 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7495 Z= 0.154 Angle : 0.526 8.321 10165 Z= 0.241 Chirality : 0.037 0.149 1199 Planarity : 0.004 0.035 1242 Dihedral : 4.038 58.314 1034 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 4.16 % Allowed : 25.94 % Favored : 69.90 % 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: 1.61 (0.29), residues: 918 helix: 1.89 (0.21), residues: 618 sheet: -1.08 (0.62), residues: 46 loop : -0.52 (0.44), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 575 HIS 0.004 0.001 HIS A 219 PHE 0.014 0.001 PHE A 442 TYR 0.009 0.001 TYR B 504 ARG 0.006 0.000 ARG B 205 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 157 time to evaluate : 0.782 Fit side-chains REVERT: A 161 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7571 (mm) REVERT: A 432 ASP cc_start: 0.7952 (OUTLIER) cc_final: 0.7578 (p0) REVERT: A 506 MET cc_start: 0.5977 (mmp) cc_final: 0.5506 (ttt) REVERT: A 635 MET cc_start: 0.6643 (tpp) cc_final: 0.6364 (tpt) REVERT: A 652 LEU cc_start: 0.8314 (mm) cc_final: 0.7955 (tt) REVERT: B 159 GLU cc_start: 0.6990 (mm-30) cc_final: 0.6712 (tp30) REVERT: B 161 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7228 (mm) REVERT: B 273 GLN cc_start: 0.5915 (pp30) cc_final: 0.5623 (tp40) REVERT: B 398 LEU cc_start: 0.7457 (mt) cc_final: 0.7161 (mt) REVERT: B 432 ASP cc_start: 0.7836 (OUTLIER) cc_final: 0.7449 (p0) REVERT: B 462 GLU cc_start: 0.6847 (mm-30) cc_final: 0.6513 (mt-10) REVERT: B 506 MET cc_start: 0.6389 (mmp) cc_final: 0.5990 (ttt) REVERT: B 635 MET cc_start: 0.6768 (mmm) cc_final: 0.6551 (tpp) REVERT: B 652 LEU cc_start: 0.8320 (mm) cc_final: 0.7784 (tp) outliers start: 33 outliers final: 26 residues processed: 177 average time/residue: 0.1718 time to fit residues: 41.5412 Evaluate side-chains 180 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 150 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 430 TYR Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 430 TYR Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 504 TYR Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain B residue 637 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 64 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 chunk 78 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 87 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6530 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7495 Z= 0.189 Angle : 0.558 8.246 10165 Z= 0.259 Chirality : 0.037 0.131 1199 Planarity : 0.004 0.033 1242 Dihedral : 4.091 57.810 1034 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.28 % Allowed : 26.20 % Favored : 69.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.29), residues: 918 helix: 1.83 (0.21), residues: 616 sheet: -1.27 (0.62), residues: 46 loop : -0.50 (0.44), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 575 HIS 0.004 0.001 HIS A 219 PHE 0.014 0.001 PHE A 275 TYR 0.012 0.001 TYR B 504 ARG 0.006 0.000 ARG B 205 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 148 time to evaluate : 0.872 Fit side-chains REVERT: A 161 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7548 (mm) REVERT: A 432 ASP cc_start: 0.7964 (OUTLIER) cc_final: 0.7597 (p0) REVERT: A 506 MET cc_start: 0.6163 (mmp) cc_final: 0.5628 (ttt) REVERT: A 635 MET cc_start: 0.6617 (tpp) cc_final: 0.6336 (tpt) REVERT: A 652 LEU cc_start: 0.8327 (mm) cc_final: 0.7958 (tt) REVERT: B 161 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7339 (mm) REVERT: B 273 GLN cc_start: 0.6083 (pp30) cc_final: 0.5712 (tp40) REVERT: B 398 LEU cc_start: 0.7465 (mt) cc_final: 0.7161 (mt) REVERT: B 432 ASP cc_start: 0.7812 (OUTLIER) cc_final: 0.7400 (p0) REVERT: B 462 GLU cc_start: 0.6855 (mm-30) cc_final: 0.6525 (mt-10) REVERT: B 506 MET cc_start: 0.6361 (mmp) cc_final: 0.5885 (ttt) REVERT: B 635 MET cc_start: 0.6743 (mmm) cc_final: 0.6533 (tpp) REVERT: B 652 LEU cc_start: 0.8312 (mm) cc_final: 0.7761 (tp) outliers start: 34 outliers final: 26 residues processed: 167 average time/residue: 0.1760 time to fit residues: 40.4076 Evaluate side-chains 175 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 145 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 430 TYR Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 430 TYR Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 504 TYR Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain B residue 637 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 0.3980 chunk 60 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 57 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6521 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7495 Z= 0.187 Angle : 0.560 8.256 10165 Z= 0.260 Chirality : 0.037 0.155 1199 Planarity : 0.004 0.034 1242 Dihedral : 4.091 57.099 1034 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 4.53 % Allowed : 26.07 % Favored : 69.40 % 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: 1.50 (0.29), residues: 918 helix: 1.80 (0.21), residues: 616 sheet: -1.30 (0.62), residues: 46 loop : -0.47 (0.44), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 575 HIS 0.003 0.001 HIS A 219 PHE 0.015 0.001 PHE B 163 TYR 0.012 0.001 TYR B 504 ARG 0.007 0.000 ARG A 205 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 149 time to evaluate : 0.808 Fit side-chains REVERT: A 161 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7563 (mm) REVERT: A 432 ASP cc_start: 0.7968 (OUTLIER) cc_final: 0.7627 (p0) REVERT: A 506 MET cc_start: 0.6160 (mmp) cc_final: 0.5612 (ttt) REVERT: A 635 MET cc_start: 0.6614 (tpp) cc_final: 0.6332 (tpt) REVERT: A 652 LEU cc_start: 0.8327 (mm) cc_final: 0.7964 (tt) REVERT: B 161 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7201 (mm) REVERT: B 163 PHE cc_start: 0.7947 (OUTLIER) cc_final: 0.7718 (t80) REVERT: B 273 GLN cc_start: 0.6049 (pp30) cc_final: 0.5721 (tp40) REVERT: B 398 LEU cc_start: 0.7406 (mt) cc_final: 0.7081 (mt) REVERT: B 432 ASP cc_start: 0.7817 (OUTLIER) cc_final: 0.7426 (p0) REVERT: B 462 GLU cc_start: 0.6853 (mm-30) cc_final: 0.6517 (mt-10) REVERT: B 506 MET cc_start: 0.6378 (mmp) cc_final: 0.5919 (ttt) REVERT: B 652 LEU cc_start: 0.8309 (mm) cc_final: 0.7768 (tp) outliers start: 36 outliers final: 29 residues processed: 167 average time/residue: 0.1830 time to fit residues: 41.5710 Evaluate side-chains 181 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 147 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 430 TYR Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 645 MET Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 163 PHE Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 430 TYR Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 504 TYR Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain B residue 637 THR Chi-restraints excluded: chain B residue 646 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 75 optimal weight: 0.3980 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 64 optimal weight: 8.9990 chunk 4 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.4402 r_free = 0.4402 target = 0.172918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.146754 restraints weight = 10099.592| |-----------------------------------------------------------------------------| r_work (start): 0.4114 rms_B_bonded: 2.88 r_work: 0.3985 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6506 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7495 Z= 0.201 Angle : 0.576 8.877 10165 Z= 0.267 Chirality : 0.038 0.145 1199 Planarity : 0.004 0.034 1242 Dihedral : 4.136 56.396 1034 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 5.29 % Allowed : 25.31 % Favored : 69.40 % 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: 1.45 (0.29), residues: 918 helix: 1.75 (0.21), residues: 616 sheet: -1.41 (0.62), residues: 46 loop : -0.45 (0.44), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 575 HIS 0.004 0.001 HIS A 219 PHE 0.018 0.002 PHE B 163 TYR 0.012 0.001 TYR B 504 ARG 0.007 0.000 ARG A 205 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1825.49 seconds wall clock time: 33 minutes 58.94 seconds (2038.94 seconds total)