Starting phenix.real_space_refine on Thu Mar 13 00:47:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zl2_60216/03_2025/8zl2_60216.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zl2_60216/03_2025/8zl2_60216.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zl2_60216/03_2025/8zl2_60216.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zl2_60216/03_2025/8zl2_60216.map" model { file = "/net/cci-nas-00/data/ceres_data/8zl2_60216/03_2025/8zl2_60216.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zl2_60216/03_2025/8zl2_60216.cif" } resolution = 2.8 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= 0.003 sd= 0.018 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 91 5.16 5 C 5675 2.51 5 N 1346 2.21 5 O 1438 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 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: 8552 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4206 Classifications: {'peptide': 542} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 33, 'TRANS': 508} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 4190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4190 Classifications: {'peptide': 539} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 33, 'TRANS': 505} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 92 Unusual residues: {'4DS': 1, 'NAG': 1, 'PTY': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Unusual residues: {'NAG': 1, 'PTY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.72, per 1000 atoms: 0.67 Number of scatterers: 8552 At special positions: 0 Unit cell: (90.2312, 103, 115.768, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 91 16.00 P 2 15.00 O 1438 8.00 N 1346 7.00 C 5675 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 - 3.00 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: 2.63 Conformation dependent library (CDL) restraints added in 1.0 seconds 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2018 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 0 sheets defined 81.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 33 through 40 removed outlier: 3.720A pdb=" N PHE A 37 " --> pdb=" O CYS A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 54 removed outlier: 3.587A pdb=" N LEU A 44 " --> pdb=" O HIS A 40 " (cutoff:3.500A) Proline residue: A 50 - end of helix Processing helix chain 'A' and resid 54 through 60 removed outlier: 3.842A pdb=" N ASN A 60 " --> pdb=" O VAL A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 81 removed outlier: 3.823A pdb=" N ARG A 66 " --> pdb=" O GLY A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 89 Processing helix chain 'A' and resid 90 through 100 removed outlier: 4.237A pdb=" N VAL A 94 " --> pdb=" O MET A 90 " (cutoff:3.500A) Proline residue: A 97 - end of helix Processing helix chain 'A' and resid 103 through 111 removed outlier: 3.582A pdb=" N TYR A 111 " --> pdb=" O THR A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 132 removed outlier: 3.962A pdb=" N CYS A 132 " --> pdb=" O ALA A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 147 Processing helix chain 'A' and resid 149 through 166 Processing helix chain 'A' and resid 169 through 191 Proline residue: A 179 - end of helix Processing helix chain 'A' and resid 220 through 239 removed outlier: 4.026A pdb=" N CYS A 239 " --> pdb=" O SER A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 259 removed outlier: 3.717A pdb=" N LEU A 249 " --> pdb=" O THR A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 296 Proline residue: A 277 - end of helix removed outlier: 3.622A pdb=" N GLY A 296 " --> pdb=" O TRP A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 314 removed outlier: 3.687A pdb=" N GLN A 306 " --> pdb=" O SER A 302 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY A 314 " --> pdb=" O ARG A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 329 removed outlier: 4.034A pdb=" N LYS A 320 " --> pdb=" O ASP A 316 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU A 329 " --> pdb=" O ARG A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 353 removed outlier: 3.873A pdb=" N ARG A 353 " --> pdb=" O MET A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 365 removed outlier: 3.761A pdb=" N LEU A 364 " --> pdb=" O GLY A 360 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A 365 " --> pdb=" O TRP A 361 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 360 through 365' Processing helix chain 'A' and resid 372 through 386 removed outlier: 4.008A pdb=" N THR A 376 " --> pdb=" O ASN A 372 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE A 384 " --> pdb=" O VAL A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 396 Processing helix chain 'A' and resid 413 through 421 Processing helix chain 'A' and resid 424 through 443 removed outlier: 4.035A pdb=" N GLY A 432 " --> pdb=" O LEU A 428 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 453 removed outlier: 3.844A pdb=" N ILE A 453 " --> pdb=" O GLY A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 458 removed outlier: 4.321A pdb=" N VAL A 457 " --> pdb=" O GLY A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 477 removed outlier: 4.321A pdb=" N PHE A 477 " --> pdb=" O PHE A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 499 Proline residue: A 489 - end of helix Processing helix chain 'A' and resid 501 through 513 removed outlier: 4.157A pdb=" N LEU A 505 " --> pdb=" O HIS A 501 " (cutoff:3.500A) Proline residue: A 508 - end of helix Processing helix chain 'A' and resid 523 through 533 Processing helix chain 'A' and resid 536 through 544 removed outlier: 3.604A pdb=" N MET A 540 " --> pdb=" O ARG A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 567 removed outlier: 3.611A pdb=" N THR A 548 " --> pdb=" O GLY A 544 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEU A 564 " --> pdb=" O GLN A 560 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL A 565 " --> pdb=" O THR A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 584 removed outlier: 3.573A pdb=" N GLN A 578 " --> pdb=" O PRO A 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 40 removed outlier: 3.610A pdb=" N PHE B 37 " --> pdb=" O CYS B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 60 removed outlier: 3.512A pdb=" N LEU B 44 " --> pdb=" O HIS B 40 " (cutoff:3.500A) Proline residue: B 50 - end of helix Proline residue: B 55 - end of helix removed outlier: 3.873A pdb=" N ASN B 60 " --> pdb=" O VAL B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 81 removed outlier: 3.908A pdb=" N ARG B 66 " --> pdb=" O GLY B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 89 Processing helix chain 'B' and resid 90 through 99 removed outlier: 4.150A pdb=" N VAL B 94 " --> pdb=" O MET B 90 " (cutoff:3.500A) Proline residue: B 97 - end of helix Processing helix chain 'B' and resid 103 through 111 removed outlier: 3.741A pdb=" N TYR B 111 " --> pdb=" O THR B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 131 Processing helix chain 'B' and resid 133 through 146 removed outlier: 4.002A pdb=" N ARG B 137 " --> pdb=" O ASN B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 166 Processing helix chain 'B' and resid 169 through 192 Proline residue: B 179 - end of helix Processing helix chain 'B' and resid 220 through 238 Processing helix chain 'B' and resid 239 through 244 removed outlier: 5.960A pdb=" N ILE B 242 " --> pdb=" O CYS B 239 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ILE B 243 " --> pdb=" O GLY B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 259 removed outlier: 3.877A pdb=" N LEU B 249 " --> pdb=" O THR B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 296 Proline residue: B 277 - end of helix Processing helix chain 'B' and resid 304 through 314 removed outlier: 3.803A pdb=" N VAL B 308 " --> pdb=" O GLU B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 327 Processing helix chain 'B' and resid 333 through 352 Processing helix chain 'B' and resid 373 through 386 removed outlier: 3.603A pdb=" N ILE B 377 " --> pdb=" O SER B 373 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE B 384 " --> pdb=" O VAL B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 395 removed outlier: 3.589A pdb=" N LEU B 393 " --> pdb=" O TYR B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 421 Processing helix chain 'B' and resid 423 through 443 removed outlier: 4.533A pdb=" N PHE B 427 " --> pdb=" O TRP B 423 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY B 443 " --> pdb=" O SER B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 452 removed outlier: 3.886A pdb=" N LEU B 447 " --> pdb=" O GLY B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 458 removed outlier: 3.708A pdb=" N VAL B 457 " --> pdb=" O GLY B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 476 Processing helix chain 'B' and resid 479 through 498 Proline residue: B 489 - end of helix Processing helix chain 'B' and resid 501 through 513 removed outlier: 3.942A pdb=" N LEU B 505 " --> pdb=" O HIS B 501 " (cutoff:3.500A) Proline residue: B 508 - end of helix Processing helix chain 'B' and resid 523 through 534 Processing helix chain 'B' and resid 536 through 544 removed outlier: 3.557A pdb=" N MET B 540 " --> pdb=" O ARG B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 567 removed outlier: 3.527A pdb=" N THR B 548 " --> pdb=" O GLY B 544 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLN B 560 " --> pdb=" O PHE B 556 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LEU B 564 " --> pdb=" O GLN B 560 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL B 565 " --> pdb=" O THR B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 584 552 hydrogen bonds defined for protein. 1626 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: 2.28 Time building geometry restraints manager: 2.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1314 1.32 - 1.44: 2306 1.44 - 1.57: 5002 1.57 - 1.69: 6 1.69 - 1.81: 147 Bond restraints: 8775 Sorted by residual: bond pdb=" CAT 4DS A 601 " pdb=" NAS 4DS A 601 " ideal model delta sigma weight residual 1.170 1.315 -0.145 2.00e-02 2.50e+03 5.28e+01 bond pdb=" CBA 4DS A 601 " pdb=" NAZ 4DS A 601 " ideal model delta sigma weight residual 1.170 1.313 -0.143 2.00e-02 2.50e+03 5.14e+01 bond pdb=" N VAL A 146 " pdb=" CA VAL A 146 " ideal model delta sigma weight residual 1.460 1.497 -0.038 1.21e-02 6.83e+03 9.62e+00 bond pdb=" N VAL B 457 " pdb=" CA VAL B 457 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.19e-02 7.06e+03 8.24e+00 bond pdb=" N VAL A 142 " pdb=" CA VAL A 142 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.19e-02 7.06e+03 8.19e+00 ... (remaining 8770 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.84: 11926 10.84 - 21.69: 0 21.69 - 32.53: 0 32.53 - 43.38: 0 43.38 - 54.22: 2 Bond angle restraints: 11928 Sorted by residual: angle pdb=" CAP 4DS A 601 " pdb=" NAS 4DS A 601 " pdb=" CAT 4DS A 601 " ideal model delta sigma weight residual 180.00 125.78 54.22 3.00e+00 1.11e-01 3.27e+02 angle pdb=" CAG 4DS A 601 " pdb=" NAZ 4DS A 601 " pdb=" CBA 4DS A 601 " ideal model delta sigma weight residual 177.62 124.15 53.47 3.00e+00 1.11e-01 3.18e+02 angle pdb=" N GLU B 304 " pdb=" CA GLU B 304 " pdb=" C GLU B 304 " ideal model delta sigma weight residual 114.04 107.10 6.94 1.24e+00 6.50e-01 3.13e+01 angle pdb=" CA TYR A 282 " pdb=" CB TYR A 282 " pdb=" CG TYR A 282 " ideal model delta sigma weight residual 113.90 122.67 -8.77 1.80e+00 3.09e-01 2.37e+01 angle pdb=" N LYS B 303 " pdb=" CA LYS B 303 " pdb=" C LYS B 303 " ideal model delta sigma weight residual 113.56 107.00 6.56 1.39e+00 5.18e-01 2.23e+01 ... (remaining 11923 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.82: 5047 24.82 - 49.63: 149 49.63 - 74.45: 21 74.45 - 99.27: 3 99.27 - 124.09: 2 Dihedral angle restraints: 5222 sinusoidal: 2089 harmonic: 3133 Sorted by residual: dihedral pdb=" CA PHE B 47 " pdb=" C PHE B 47 " pdb=" N LEU B 48 " pdb=" CA LEU B 48 " ideal model delta harmonic sigma weight residual -180.00 -158.62 -21.38 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" C3 PTY B 601 " pdb=" O11 PTY B 601 " pdb=" P1 PTY B 601 " pdb=" O12 PTY B 601 " ideal model delta sinusoidal sigma weight residual 300.23 176.14 124.09 1 3.00e+01 1.11e-03 1.66e+01 dihedral pdb=" N1 PTY B 601 " pdb=" C2 PTY B 601 " pdb=" C3 PTY B 601 " pdb=" O11 PTY B 601 " ideal model delta sinusoidal sigma weight residual 65.33 -177.99 -116.68 1 3.00e+01 1.11e-03 1.55e+01 ... (remaining 5219 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 950 0.043 - 0.085: 312 0.085 - 0.128: 102 0.128 - 0.171: 18 0.171 - 0.213: 5 Chirality restraints: 1387 Sorted by residual: chirality pdb=" CA MET B 444 " pdb=" N MET B 444 " pdb=" C MET B 444 " pdb=" CB MET B 444 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA TYR B 282 " pdb=" N TYR B 282 " pdb=" C TYR B 282 " pdb=" CB TYR B 282 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.70e-01 chirality pdb=" CA GLU B 304 " pdb=" N GLU B 304 " pdb=" C GLU B 304 " pdb=" CB GLU B 304 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.19 2.00e-01 2.50e+01 9.47e-01 ... (remaining 1384 not shown) Planarity restraints: 1452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 421 " 0.048 5.00e-02 4.00e+02 7.39e-02 8.75e+00 pdb=" N PRO B 422 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO B 422 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 422 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 546 " 0.047 5.00e-02 4.00e+02 7.20e-02 8.29e+00 pdb=" N PRO A 547 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 547 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 547 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 559 " 0.014 2.00e-02 2.50e+03 2.75e-02 7.56e+00 pdb=" C CYS A 559 " -0.048 2.00e-02 2.50e+03 pdb=" O CYS A 559 " 0.018 2.00e-02 2.50e+03 pdb=" N GLN A 560 " 0.016 2.00e-02 2.50e+03 ... (remaining 1449 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 982 2.74 - 3.28: 8434 3.28 - 3.82: 13197 3.82 - 4.36: 15262 4.36 - 4.90: 27313 Nonbonded interactions: 65188 Sorted by model distance: nonbonded pdb=" O LYS A 260 " pdb=" OH TYR A 580 " model vdw 2.203 3.040 nonbonded pdb=" O ALA B 492 " pdb=" OG SER B 495 " model vdw 2.341 3.040 nonbonded pdb=" O PRO A 404 " pdb=" OG1 THR A 405 " model vdw 2.386 3.040 nonbonded pdb=" O MET B 279 " pdb=" OG1 THR B 283 " model vdw 2.419 3.040 nonbonded pdb=" O ILE B 76 " pdb=" OG1 THR B 80 " model vdw 2.474 3.040 ... (remaining 65183 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 32 through 147 or (resid 148 and (name N or name CA or nam \ e C or name O or name CB )) or resid 149 through 200 or (resid 215 and (name N o \ r name CA or name C or name O or name CB )) or resid 216 through 584)) selection = (chain 'B' and (resid 32 through 298 or (resid 299 and (name N or name CA or nam \ e C or name O or name CB )) or resid 300 through 302 or (resid 303 through 305 a \ nd (name N or name CA or name C or name O or name CB )) or resid 306 through 584 \ )) } 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: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.470 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.050 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:13.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 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 : 0.007 0.145 8775 Z= 0.482 Angle : 1.051 54.224 11928 Z= 0.519 Chirality : 0.048 0.213 1387 Planarity : 0.006 0.074 1452 Dihedral : 12.491 124.086 3204 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.22 (0.25), residues: 1073 helix: 1.59 (0.18), residues: 787 sheet: None (None), residues: 0 loop : -1.40 (0.33), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP B 78 HIS 0.017 0.002 HIS B 335 PHE 0.024 0.002 PHE A 251 TYR 0.032 0.002 TYR A 282 ARG 0.006 0.001 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.960 Fit side-chains revert: symmetry clash REVERT: A 349 MET cc_start: 0.8809 (mmt) cc_final: 0.8455 (mmm) outliers start: 0 outliers final: 1 residues processed: 104 average time/residue: 1.2195 time to fit residues: 135.9142 Evaluate side-chains 81 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 80 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 45 optimal weight: 0.0070 chunk 27 optimal weight: 5.9990 chunk 54 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 62 optimal weight: 0.4980 chunk 97 optimal weight: 0.9980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 GLN ** B 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.069706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.051565 restraints weight = 21771.997| |-----------------------------------------------------------------------------| r_work (start): 0.2766 rms_B_bonded: 3.02 r_work: 0.2638 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8775 Z= 0.159 Angle : 0.569 7.201 11928 Z= 0.308 Chirality : 0.040 0.162 1387 Planarity : 0.006 0.062 1452 Dihedral : 8.775 128.385 1285 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.88 % Allowed : 5.40 % Favored : 93.72 % 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 (0.25), residues: 1073 helix: 1.96 (0.18), residues: 789 sheet: None (None), residues: 0 loop : -1.28 (0.33), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 562 HIS 0.009 0.001 HIS B 335 PHE 0.029 0.001 PHE A 251 TYR 0.025 0.001 TYR B 282 ARG 0.004 0.000 ARG B 398 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.996 Fit side-chains revert: symmetry clash REVERT: A 295 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.8527 (mtm) REVERT: A 316 ASP cc_start: 0.8941 (t0) cc_final: 0.8434 (p0) REVERT: A 328 ASP cc_start: 0.8871 (m-30) cc_final: 0.8536 (m-30) REVERT: B 295 MET cc_start: 0.8085 (OUTLIER) cc_final: 0.7801 (mtt) outliers start: 8 outliers final: 0 residues processed: 88 average time/residue: 1.2455 time to fit residues: 117.2638 Evaluate side-chains 76 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 74 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain B residue 295 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 72 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 chunk 94 optimal weight: 8.9990 chunk 79 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 41 optimal weight: 8.9990 chunk 42 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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 = 0.3099 r_free = 0.3099 target = 0.066201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.047726 restraints weight = 22634.995| |-----------------------------------------------------------------------------| r_work (start): 0.2674 rms_B_bonded: 3.04 r_work: 0.2544 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8775 Z= 0.251 Angle : 0.549 6.993 11928 Z= 0.297 Chirality : 0.040 0.177 1387 Planarity : 0.005 0.065 1452 Dihedral : 7.278 62.818 1282 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.21 % Allowed : 7.05 % Favored : 91.74 % 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: 2.02 (0.25), residues: 1073 helix: 2.19 (0.18), residues: 784 sheet: None (None), residues: 0 loop : -1.12 (0.34), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 414 HIS 0.011 0.001 HIS B 335 PHE 0.025 0.001 PHE A 251 TYR 0.024 0.001 TYR B 282 ARG 0.011 0.000 ARG B 398 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.901 Fit side-chains REVERT: A 328 ASP cc_start: 0.8841 (m-30) cc_final: 0.8316 (m-30) REVERT: B 260 LYS cc_start: 0.9362 (tttt) cc_final: 0.9106 (mttp) REVERT: B 370 ILE cc_start: 0.8163 (OUTLIER) cc_final: 0.7909 (mp) outliers start: 11 outliers final: 1 residues processed: 81 average time/residue: 1.2969 time to fit residues: 112.0781 Evaluate side-chains 77 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 75 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 370 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 17 optimal weight: 0.0870 chunk 62 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 52 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 overall best weight: 1.5762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.067546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.049370 restraints weight = 22333.412| |-----------------------------------------------------------------------------| r_work (start): 0.2717 rms_B_bonded: 3.04 r_work: 0.2587 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8775 Z= 0.196 Angle : 0.527 8.569 11928 Z= 0.280 Chirality : 0.039 0.168 1387 Planarity : 0.005 0.060 1452 Dihedral : 6.950 55.907 1282 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.99 % Allowed : 9.03 % Favored : 89.98 % 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: 2.12 (0.26), residues: 1073 helix: 2.28 (0.18), residues: 779 sheet: None (None), residues: 0 loop : -1.07 (0.34), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 562 HIS 0.010 0.001 HIS B 335 PHE 0.022 0.001 PHE A 251 TYR 0.023 0.001 TYR B 282 ARG 0.002 0.000 ARG A 109 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.896 Fit side-chains REVERT: A 328 ASP cc_start: 0.8888 (m-30) cc_final: 0.8337 (m-30) REVERT: B 260 LYS cc_start: 0.9374 (tttt) cc_final: 0.9153 (mttp) REVERT: B 295 MET cc_start: 0.7896 (OUTLIER) cc_final: 0.7476 (mtt) REVERT: B 370 ILE cc_start: 0.8275 (OUTLIER) cc_final: 0.8009 (mp) outliers start: 9 outliers final: 3 residues processed: 83 average time/residue: 1.4306 time to fit residues: 127.3945 Evaluate side-chains 82 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 77 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 370 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 38 optimal weight: 0.9990 chunk 17 optimal weight: 0.0970 chunk 13 optimal weight: 0.4980 chunk 48 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 19 optimal weight: 7.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.3174 r_free = 0.3174 target = 0.069898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.051790 restraints weight = 22058.172| |-----------------------------------------------------------------------------| r_work (start): 0.2772 rms_B_bonded: 3.01 r_work: 0.2646 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8775 Z= 0.141 Angle : 0.489 7.810 11928 Z= 0.259 Chirality : 0.038 0.156 1387 Planarity : 0.005 0.059 1452 Dihedral : 6.594 55.598 1282 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.65 % Allowed : 9.47 % Favored : 88.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.26), residues: 1073 helix: 2.34 (0.18), residues: 779 sheet: None (None), residues: 0 loop : -1.00 (0.35), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 562 HIS 0.007 0.001 HIS B 335 PHE 0.018 0.001 PHE A 268 TYR 0.024 0.001 TYR B 282 ARG 0.001 0.000 ARG B 151 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.919 Fit side-chains revert: symmetry clash REVERT: A 328 ASP cc_start: 0.8882 (m-30) cc_final: 0.8313 (m-30) REVERT: B 260 LYS cc_start: 0.9336 (tttt) cc_final: 0.9134 (mttp) REVERT: B 295 MET cc_start: 0.7778 (OUTLIER) cc_final: 0.7370 (mtt) outliers start: 15 outliers final: 3 residues processed: 86 average time/residue: 1.3232 time to fit residues: 121.8172 Evaluate side-chains 80 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 295 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 103 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 47 optimal weight: 0.1980 chunk 16 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.069830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.051439 restraints weight = 22230.035| |-----------------------------------------------------------------------------| r_work (start): 0.2771 rms_B_bonded: 3.05 r_work: 0.2645 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8775 Z= 0.148 Angle : 0.505 9.490 11928 Z= 0.263 Chirality : 0.038 0.158 1387 Planarity : 0.005 0.057 1452 Dihedral : 6.455 55.407 1282 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.99 % Allowed : 10.46 % Favored : 88.55 % 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: 2.29 (0.26), residues: 1073 helix: 2.38 (0.18), residues: 779 sheet: None (None), residues: 0 loop : -0.93 (0.35), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 562 HIS 0.008 0.001 HIS B 335 PHE 0.020 0.001 PHE A 268 TYR 0.023 0.001 TYR B 282 ARG 0.001 0.000 ARG B 109 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.879 Fit side-chains REVERT: A 328 ASP cc_start: 0.8904 (m-30) cc_final: 0.8334 (m-30) REVERT: B 295 MET cc_start: 0.7584 (OUTLIER) cc_final: 0.7198 (mtt) REVERT: B 316 ASP cc_start: 0.8667 (p0) cc_final: 0.8323 (p0) outliers start: 9 outliers final: 4 residues processed: 81 average time/residue: 1.3181 time to fit residues: 114.1960 Evaluate side-chains 79 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 523 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 70 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 17 optimal weight: 0.1980 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3171 r_free = 0.3171 target = 0.069708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.051416 restraints weight = 22257.357| |-----------------------------------------------------------------------------| r_work (start): 0.2767 rms_B_bonded: 3.04 r_work: 0.2639 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8775 Z= 0.154 Angle : 0.506 11.293 11928 Z= 0.261 Chirality : 0.038 0.158 1387 Planarity : 0.005 0.056 1452 Dihedral : 6.404 55.124 1282 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.99 % Allowed : 11.89 % Favored : 87.11 % 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: 2.30 (0.26), residues: 1073 helix: 2.38 (0.18), residues: 779 sheet: None (None), residues: 0 loop : -0.88 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 562 HIS 0.008 0.001 HIS B 335 PHE 0.023 0.001 PHE A 268 TYR 0.023 0.001 TYR B 282 ARG 0.001 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.936 Fit side-chains REVERT: A 295 MET cc_start: 0.8752 (OUTLIER) cc_final: 0.8526 (mtm) REVERT: A 328 ASP cc_start: 0.8885 (m-30) cc_final: 0.8396 (m-30) REVERT: B 295 MET cc_start: 0.7587 (OUTLIER) cc_final: 0.7200 (mtt) outliers start: 9 outliers final: 5 residues processed: 80 average time/residue: 1.7698 time to fit residues: 150.9427 Evaluate side-chains 82 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 272 MET Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 523 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 81 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 105 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.066317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.048212 restraints weight = 22509.313| |-----------------------------------------------------------------------------| r_work (start): 0.2687 rms_B_bonded: 3.02 r_work: 0.2556 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8775 Z= 0.262 Angle : 0.568 11.213 11928 Z= 0.294 Chirality : 0.040 0.175 1387 Planarity : 0.005 0.055 1452 Dihedral : 6.580 56.368 1282 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.99 % Allowed : 12.44 % Favored : 86.56 % 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: 2.31 (0.26), residues: 1073 helix: 2.40 (0.19), residues: 778 sheet: None (None), residues: 0 loop : -0.92 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 414 HIS 0.011 0.001 HIS B 335 PHE 0.021 0.001 PHE B 251 TYR 0.023 0.001 TYR A 282 ARG 0.003 0.000 ARG A 109 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.874 Fit side-chains REVERT: A 328 ASP cc_start: 0.8962 (m-30) cc_final: 0.8431 (m-30) REVERT: B 195 LYS cc_start: 0.9040 (mttp) cc_final: 0.8806 (mppt) outliers start: 9 outliers final: 3 residues processed: 80 average time/residue: 1.3072 time to fit residues: 111.7498 Evaluate side-chains 78 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 75 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain B residue 145 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 97 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 85 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.3140 r_free = 0.3140 target = 0.067852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.049438 restraints weight = 22517.637| |-----------------------------------------------------------------------------| r_work (start): 0.2717 rms_B_bonded: 3.06 r_work: 0.2587 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8775 Z= 0.177 Angle : 0.536 11.829 11928 Z= 0.277 Chirality : 0.039 0.163 1387 Planarity : 0.005 0.055 1452 Dihedral : 6.524 56.506 1282 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.88 % Allowed : 12.89 % Favored : 86.23 % 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: 2.27 (0.26), residues: 1073 helix: 2.34 (0.18), residues: 779 sheet: None (None), residues: 0 loop : -0.87 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 562 HIS 0.009 0.001 HIS B 335 PHE 0.020 0.001 PHE A 268 TYR 0.024 0.001 TYR A 282 ARG 0.002 0.000 ARG A 109 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.905 Fit side-chains REVERT: A 328 ASP cc_start: 0.8980 (m-30) cc_final: 0.8442 (m-30) REVERT: A 515 MET cc_start: 0.8848 (mmt) cc_final: 0.8509 (mmt) REVERT: B 195 LYS cc_start: 0.9027 (mttp) cc_final: 0.8790 (mppt) REVERT: B 295 MET cc_start: 0.7485 (mtt) cc_final: 0.7079 (mtt) outliers start: 8 outliers final: 3 residues processed: 81 average time/residue: 1.4910 time to fit residues: 129.2635 Evaluate side-chains 78 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 75 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain B residue 145 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 25 optimal weight: 0.1980 chunk 55 optimal weight: 4.9990 chunk 22 optimal weight: 8.9990 chunk 62 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 overall best weight: 1.4388 ------------------------------------------------------------------------------- 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 = 0.3141 r_free = 0.3141 target = 0.067724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.049595 restraints weight = 22117.238| |-----------------------------------------------------------------------------| r_work (start): 0.2723 rms_B_bonded: 3.01 r_work: 0.2594 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8775 Z= 0.186 Angle : 0.539 12.988 11928 Z= 0.276 Chirality : 0.039 0.163 1387 Planarity : 0.005 0.055 1452 Dihedral : 6.472 56.172 1282 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.55 % Allowed : 13.00 % Favored : 86.45 % 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: 2.31 (0.26), residues: 1073 helix: 2.37 (0.18), residues: 779 sheet: None (None), residues: 0 loop : -0.85 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 562 HIS 0.009 0.001 HIS B 335 PHE 0.019 0.001 PHE A 268 TYR 0.027 0.001 TYR A 282 ARG 0.002 0.000 ARG A 109 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.890 Fit side-chains REVERT: A 328 ASP cc_start: 0.9002 (m-30) cc_final: 0.8554 (m-30) REVERT: A 515 MET cc_start: 0.8853 (mmt) cc_final: 0.8491 (mmt) REVERT: B 195 LYS cc_start: 0.9034 (mttp) cc_final: 0.8797 (mppt) REVERT: B 295 MET cc_start: 0.7510 (mtt) cc_final: 0.7162 (mtt) outliers start: 5 outliers final: 5 residues processed: 79 average time/residue: 1.2970 time to fit residues: 109.3005 Evaluate side-chains 80 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 75 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 272 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 81 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 101 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 = 0.3134 r_free = 0.3134 target = 0.067383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.048886 restraints weight = 22643.349| |-----------------------------------------------------------------------------| r_work (start): 0.2722 rms_B_bonded: 3.08 r_work: 0.2594 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8775 Z= 0.204 Angle : 0.554 13.267 11928 Z= 0.283 Chirality : 0.039 0.165 1387 Planarity : 0.005 0.056 1452 Dihedral : 6.483 56.360 1282 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.44 % Allowed : 13.44 % Favored : 86.12 % 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: 2.30 (0.26), residues: 1073 helix: 2.36 (0.18), residues: 779 sheet: None (None), residues: 0 loop : -0.86 (0.37), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 562 HIS 0.009 0.001 HIS B 335 PHE 0.019 0.001 PHE A 268 TYR 0.028 0.001 TYR A 282 ARG 0.002 0.000 ARG A 109 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5067.89 seconds wall clock time: 90 minutes 4.38 seconds (5404.38 seconds total)