Starting phenix.real_space_refine on Thu Jun 5 10:04:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wm9_37646/06_2025/8wm9_37646_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wm9_37646/06_2025/8wm9_37646.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wm9_37646/06_2025/8wm9_37646.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wm9_37646/06_2025/8wm9_37646.map" model { file = "/net/cci-nas-00/data/ceres_data/8wm9_37646/06_2025/8wm9_37646_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wm9_37646/06_2025/8wm9_37646_neut.cif" } resolution = 3.53 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= 0.001 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: 4 Type Number sf(0) Gaussians S 38 5.16 5 C 3958 2.51 5 N 884 2.21 5 O 999 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 5879 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2492 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 313} Chain breaks: 1 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 47 Chain: "B" Number of atoms: 2377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2377 Classifications: {'peptide': 310} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 303} Chain breaks: 3 Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 160 Unresolved non-hydrogen dihedrals: 105 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 2, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 82 Chain: "C" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 660 Classifications: {'peptide': 89} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 3, 'TRANS': 85} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 175 Unusual residues: {'Y01': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 175 Unusual residues: {'Y01': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 4.47, per 1000 atoms: 0.76 Number of scatterers: 5879 At special positions: 0 Unit cell: (90.2, 94.6, 90.2, 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 38 16.00 O 999 8.00 N 884 7.00 C 3958 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 204 " - pdb=" SG CYS A 282 " distance=2.03 Simple disulfide: pdb=" SG CYS A 302 " - pdb=" SG CYS A 377 " distance=2.04 Simple disulfide: pdb=" SG CYS B 204 " - pdb=" SG CYS B 282 " distance=2.03 Simple disulfide: pdb=" SG CYS B 302 " - pdb=" SG CYS B 377 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.61 Conformation dependent library (CDL) restraints added in 741.3 milliseconds 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1360 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 4 sheets defined 72.9% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 212 through 244 removed outlier: 3.890A pdb=" N ASP A 244 " --> pdb=" O THR A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 276 removed outlier: 3.886A pdb=" N PHE A 257 " --> pdb=" O ARG A 253 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA A 268 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N TYR A 269 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE A 270 " --> pdb=" O SER A 266 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG A 272 " --> pdb=" O ALA A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 281 removed outlier: 3.568A pdb=" N ILE A 280 " --> pdb=" O GLY A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 298 Processing helix chain 'A' and resid 299 through 332 removed outlier: 3.510A pdb=" N ALA A 303 " --> pdb=" O ASN A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 342 No H-bonds generated for 'chain 'A' and resid 340 through 342' Processing helix chain 'A' and resid 343 through 366 removed outlier: 3.771A pdb=" N PHE A 347 " --> pdb=" O HIS A 343 " (cutoff:3.500A) Proline residue: A 355 - end of helix Processing helix chain 'A' and resid 383 through 391 removed outlier: 3.686A pdb=" N VAL A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 421 removed outlier: 3.530A pdb=" N LEU A 395 " --> pdb=" O VAL A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 461 removed outlier: 3.969A pdb=" N GLU A 431 " --> pdb=" O THR A 427 " (cutoff:3.500A) Proline residue: A 447 - end of helix Processing helix chain 'A' and resid 462 through 465 Processing helix chain 'A' and resid 471 through 490 removed outlier: 3.503A pdb=" N ALA A 475 " --> pdb=" O ASP A 471 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLY A 488 " --> pdb=" O SER A 484 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR A 490 " --> pdb=" O LEU A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 496 removed outlier: 3.516A pdb=" N TRP A 496 " --> pdb=" O MET A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 511 removed outlier: 3.870A pdb=" N LEU A 511 " --> pdb=" O PHE A 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 244 removed outlier: 3.846A pdb=" N LYS B 216 " --> pdb=" O SER B 212 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP B 244 " --> pdb=" O THR B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 248 Processing helix chain 'B' and resid 253 through 276 removed outlier: 3.675A pdb=" N PHE B 257 " --> pdb=" O ARG B 253 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA B 268 " --> pdb=" O ILE B 264 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N TYR B 269 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE B 270 " --> pdb=" O SER B 266 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG B 272 " --> pdb=" O ALA B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 281 removed outlier: 3.647A pdb=" N ILE B 280 " --> pdb=" O GLY B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 332 removed outlier: 3.633A pdb=" N ALA B 303 " --> pdb=" O ASN B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 342 removed outlier: 3.595A pdb=" N ILE B 340 " --> pdb=" O GLY B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 366 removed outlier: 3.696A pdb=" N PHE B 347 " --> pdb=" O HIS B 343 " (cutoff:3.500A) Proline residue: B 355 - end of helix removed outlier: 3.635A pdb=" N MET B 365 " --> pdb=" O VAL B 361 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG B 366 " --> pdb=" O ILE B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 391 Processing helix chain 'B' and resid 391 through 418 Processing helix chain 'B' and resid 432 through 461 removed outlier: 4.047A pdb=" N VAL B 446 " --> pdb=" O VAL B 442 " (cutoff:3.500A) Proline residue: B 447 - end of helix Processing helix chain 'B' and resid 461 through 468 removed outlier: 3.520A pdb=" N TYR B 467 " --> pdb=" O ALA B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 490 removed outlier: 3.842A pdb=" N ALA B 475 " --> pdb=" O ASP B 471 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N VAL B 487 " --> pdb=" O MET B 483 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N GLY B 488 " --> pdb=" O SER B 484 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE B 489 " --> pdb=" O LEU B 485 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR B 490 " --> pdb=" O LEU B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 513 removed outlier: 3.639A pdb=" N LEU B 501 " --> pdb=" O SER B 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 431 Processing helix chain 'C' and resid 455 through 465 Processing helix chain 'C' and resid 474 through 485 removed outlier: 3.748A pdb=" N TYR C 478 " --> pdb=" O GLU C 474 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N SER C 480 " --> pdb=" O ARG C 476 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 191 through 193 Processing sheet with id=AA2, first strand: chain 'A' and resid 369 through 370 Processing sheet with id=AA3, first strand: chain 'B' and resid 368 through 370 Processing sheet with id=AA4, first strand: chain 'C' and resid 440 through 444 removed outlier: 6.750A pdb=" N ARG C 442 " --> pdb=" O PRO C 450 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N TRP C 444 " --> pdb=" O THR C 448 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N THR C 448 " --> pdb=" O TRP C 444 " (cutoff:3.500A) 367 hydrogen bonds defined for protein. 1083 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.39 Time building geometry restraints manager: 1.88 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: 1679 1.34 - 1.46: 1562 1.46 - 1.58: 2749 1.58 - 1.71: 1 1.71 - 1.83: 60 Bond restraints: 6051 Sorted by residual: bond pdb=" CAV Y01 B 603 " pdb=" CAZ Y01 B 603 " ideal model delta sigma weight residual 1.507 1.450 0.057 2.00e-02 2.50e+03 8.00e+00 bond pdb=" CBB Y01 B 603 " pdb=" CBE Y01 B 603 " ideal model delta sigma weight residual 1.535 1.591 -0.056 2.00e-02 2.50e+03 7.86e+00 bond pdb=" CAV Y01 B 603 " pdb=" CBC Y01 B 603 " ideal model delta sigma weight residual 1.523 1.467 0.056 2.00e-02 2.50e+03 7.83e+00 bond pdb=" CAY Y01 B 605 " pdb=" OAW Y01 B 605 " ideal model delta sigma weight residual 1.332 1.382 -0.050 2.00e-02 2.50e+03 6.18e+00 bond pdb=" CAZ Y01 B 604 " pdb=" CBH Y01 B 604 " ideal model delta sigma weight residual 1.519 1.470 0.049 2.00e-02 2.50e+03 5.92e+00 ... (remaining 6046 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 7855 1.70 - 3.40: 310 3.40 - 5.10: 92 5.10 - 6.81: 40 6.81 - 8.51: 6 Bond angle restraints: 8303 Sorted by residual: angle pdb=" N TYR A 206 " pdb=" CA TYR A 206 " pdb=" C TYR A 206 " ideal model delta sigma weight residual 111.02 107.35 3.67 1.22e+00 6.72e-01 9.05e+00 angle pdb=" CAJ Y01 B 603 " pdb=" CAO Y01 B 603 " pdb=" CBB Y01 B 603 " ideal model delta sigma weight residual 115.08 106.57 8.51 3.00e+00 1.11e-01 8.04e+00 angle pdb=" C TYR B 250 " pdb=" CA TYR B 250 " pdb=" CB TYR B 250 " ideal model delta sigma weight residual 109.46 113.98 -4.52 1.64e+00 3.72e-01 7.60e+00 angle pdb=" CAL Y01 B 604 " pdb=" CAM Y01 B 604 " pdb=" CAY Y01 B 604 " ideal model delta sigma weight residual 113.76 105.85 7.91 3.00e+00 1.11e-01 6.95e+00 angle pdb=" N ASP A 207 " pdb=" CA ASP A 207 " pdb=" C ASP A 207 " ideal model delta sigma weight residual 109.62 105.72 3.90 1.50e+00 4.44e-01 6.76e+00 ... (remaining 8298 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 3604 17.48 - 34.96: 290 34.96 - 52.45: 48 52.45 - 69.93: 14 69.93 - 87.41: 3 Dihedral angle restraints: 3959 sinusoidal: 1855 harmonic: 2104 Sorted by residual: dihedral pdb=" CB CYS B 302 " pdb=" SG CYS B 302 " pdb=" SG CYS B 377 " pdb=" CB CYS B 377 " ideal model delta sinusoidal sigma weight residual 93.00 31.72 61.28 1 1.00e+01 1.00e-02 4.99e+01 dihedral pdb=" CB CYS A 302 " pdb=" SG CYS A 302 " pdb=" SG CYS A 377 " pdb=" CB CYS A 377 " ideal model delta sinusoidal sigma weight residual 93.00 41.54 51.46 1 1.00e+01 1.00e-02 3.62e+01 dihedral pdb=" CA MET C 430 " pdb=" C MET C 430 " pdb=" N ALA C 431 " pdb=" CA ALA C 431 " ideal model delta harmonic sigma weight residual -180.00 -160.00 -20.00 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 3956 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 829 0.064 - 0.129: 111 0.129 - 0.193: 20 0.193 - 0.257: 17 0.257 - 0.321: 12 Chirality restraints: 989 Sorted by residual: chirality pdb=" CBG Y01 B 603 " pdb=" CAQ Y01 B 603 " pdb=" CBD Y01 B 603 " pdb=" CBI Y01 B 603 " both_signs ideal model delta sigma weight residual False -2.33 -2.65 0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" CBG Y01 A 605 " pdb=" CAQ Y01 A 605 " pdb=" CBD Y01 A 605 " pdb=" CBI Y01 A 605 " both_signs ideal model delta sigma weight residual False -2.33 -2.64 0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" CBG Y01 B 604 " pdb=" CAQ Y01 B 604 " pdb=" CBD Y01 B 604 " pdb=" CBI Y01 B 604 " both_signs ideal model delta sigma weight residual False -2.33 -2.63 0.30 2.00e-01 2.50e+01 2.25e+00 ... (remaining 986 not shown) Planarity restraints: 949 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 259 " -0.010 2.00e-02 2.50e+03 2.06e-02 4.24e+00 pdb=" C SER A 259 " 0.036 2.00e-02 2.50e+03 pdb=" O SER A 259 " -0.013 2.00e-02 2.50e+03 pdb=" N MET A 260 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 253 " 0.032 5.00e-02 4.00e+02 4.73e-02 3.58e+00 pdb=" N PRO A 254 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 254 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 254 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET A 260 " -0.009 2.00e-02 2.50e+03 1.76e-02 3.08e+00 pdb=" C MET A 260 " 0.030 2.00e-02 2.50e+03 pdb=" O MET A 260 " -0.011 2.00e-02 2.50e+03 pdb=" N CYS A 261 " -0.010 2.00e-02 2.50e+03 ... (remaining 946 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 288 2.73 - 3.27: 6249 3.27 - 3.81: 9332 3.81 - 4.36: 10261 4.36 - 4.90: 17713 Nonbonded interactions: 43843 Sorted by model distance: nonbonded pdb=" O THR A 237 " pdb=" OG1 THR A 240 " model vdw 2.182 3.040 nonbonded pdb=" O ILE A 256 " pdb=" OG SER A 259 " model vdw 2.239 3.040 nonbonded pdb=" O LYS B 216 " pdb=" OG1 THR B 219 " model vdw 2.250 3.040 nonbonded pdb=" O ARG C 476 " pdb=" OG SER C 480 " model vdw 2.317 3.040 nonbonded pdb=" O THR A 445 " pdb=" OG1 THR A 449 " model vdw 2.320 3.040 ... (remaining 43838 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 188 through 189 or (resid 190 and (name N or name CA or na \ me C or name O or name CB )) or resid 191 through 193 or (resid 194 and (name N \ or name CA or name C or name O or name CB )) or resid 195 through 197 or (resid \ 198 through 199 and (name N or name CA or name C or name O or name CB )) or resi \ d 200 or resid 205 or (resid 206 through 208 and (name N or name CA or name C or \ name O or name CB )) or resid 209 or (resid 210 and (name N or name CA or name \ C or name O or name CB )) or resid 211 through 277 or (resid 278 through 279 and \ (name N or name CA or name C or name O or name CB )) or resid 280 through 293 o \ r (resid 294 through 295 and (name N or name CA or name C or name O or name CB ) \ ) or resid 296 through 333 or (resid 334 and (name N or name CA or name C or nam \ e O or name CB )) or resid 335 through 371 or (resid 372 and (name N or name CA \ or name C or name O or name CB )) or resid 373 through 409 or (resid 410 and (na \ me N or name CA or name C or name O or name CB )) or resid 411 through 412 or (r \ esid 413 through 414 and (name N or name CA or name C or name O or name CB )) or \ resid 415 or (resid 416 through 417 and (name N or name CA or name C or name O \ or name CB )) or resid 418 through 421 or (resid 430 through 432 and (name N or \ name CA or name C or name O or name CB )) or resid 433 through 466 or (resid 467 \ and (name N or name CA or name C or name O or name CB )) or resid 468 through 4 \ 69 or (resid 470 and (name N or name CA or name C or name O or name CB )) or res \ id 471 through 493 or (resid 494 and (name N or name CA or name C or name O or n \ ame CB )) or resid 495 through 501 or (resid 502 and (name N or name CA or name \ C or name O or name CB )) or resid 503 through 510 or (resid 511 and (name N or \ name CA or name C or name O or name CB )) or resid 512 through 513 or resid 601 \ through 605)) selection = (chain 'B' and (resid 188 through 195 or (resid 196 and (name N or name CA or na \ me C or name O or name CB )) or resid 197 through 198 or (resid 199 and (name N \ or name CA or name C or name O or name CB )) or resid 204 through 278 or (resid \ 279 and (name N or name CA or name C or name O or name CB )) or resid 280 throug \ h 282 or (resid 289 and (name N or name CA or name C or name O or name CB )) or \ resid 290 or (resid 291 through 292 and (name N or name CA or name C or name O o \ r name CB )) or resid 293 through 507 or (resid 508 and (name N or name CA or na \ me C or name O or name CB )) or resid 509 or (resid 510 through 511 and (name N \ or name CA or name C or name O or name CB )) or resid 512 through 513 or resid 6 \ 01 through 605)) } 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 group one per residue 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: 1.060 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.870 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 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 : 0.006 0.057 6055 Z= 0.300 Angle : 0.915 8.508 8311 Z= 0.423 Chirality : 0.063 0.321 989 Planarity : 0.005 0.047 949 Dihedral : 12.827 87.412 2587 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.29), residues: 705 helix: 0.62 (0.22), residues: 463 sheet: -4.29 (1.48), residues: 10 loop : -2.39 (0.34), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 222 HIS 0.005 0.001 HIS B 348 PHE 0.020 0.002 PHE B 482 TYR 0.023 0.002 TYR B 262 ARG 0.003 0.000 ARG B 247 Details of bonding type rmsd hydrogen bonds : bond 0.13591 ( 367) hydrogen bonds : angle 5.80218 ( 1083) SS BOND : bond 0.00512 ( 4) SS BOND : angle 2.53765 ( 8) covalent geometry : bond 0.00633 ( 6051) covalent geometry : angle 0.91196 ( 8303) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.534 Fit side-chains revert: symmetry clash REVERT: A 349 ILE cc_start: 0.8149 (mt) cc_final: 0.7894 (mt) REVERT: A 434 MET cc_start: 0.5923 (mtm) cc_final: 0.5673 (mtm) REVERT: A 444 TYR cc_start: 0.8248 (t80) cc_final: 0.7688 (t80) REVERT: B 222 TRP cc_start: 0.6859 (t-100) cc_final: 0.6477 (t-100) REVERT: B 382 GLN cc_start: 0.7703 (mm110) cc_final: 0.7311 (mp10) REVERT: B 436 LYS cc_start: 0.8068 (ttmm) cc_final: 0.7647 (tmmt) REVERT: C 493 ASN cc_start: 0.8227 (m-40) cc_final: 0.8024 (m-40) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.1516 time to fit residues: 26.3099 Evaluate side-chains 120 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 59 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 0.2980 chunk 36 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 33 optimal weight: 20.0000 chunk 41 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.167610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.133996 restraints weight = 8863.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.137644 restraints weight = 5279.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.139467 restraints weight = 3819.372| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 6055 Z= 0.199 Angle : 0.619 7.446 8311 Z= 0.318 Chirality : 0.043 0.277 989 Planarity : 0.004 0.048 949 Dihedral : 8.820 59.892 1477 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.79 % Allowed : 7.32 % Favored : 90.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.30), residues: 705 helix: 1.16 (0.23), residues: 474 sheet: -3.93 (1.72), residues: 10 loop : -2.29 (0.36), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 222 HIS 0.005 0.001 HIS B 348 PHE 0.018 0.002 PHE B 236 TYR 0.020 0.002 TYR B 265 ARG 0.004 0.001 ARG A 272 Details of bonding type rmsd hydrogen bonds : bond 0.07250 ( 367) hydrogen bonds : angle 4.61294 ( 1083) SS BOND : bond 0.00333 ( 4) SS BOND : angle 1.70406 ( 8) covalent geometry : bond 0.00443 ( 6051) covalent geometry : angle 0.61750 ( 8303) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 349 ILE cc_start: 0.8281 (mt) cc_final: 0.7963 (mt) REVERT: B 222 TRP cc_start: 0.6813 (t-100) cc_final: 0.6392 (t-100) REVERT: B 262 TYR cc_start: 0.7581 (m-80) cc_final: 0.7258 (m-80) REVERT: B 298 LYS cc_start: 0.7781 (mttp) cc_final: 0.7325 (mttp) REVERT: B 314 MET cc_start: 0.7156 (mmm) cc_final: 0.6869 (mmm) REVERT: B 436 LYS cc_start: 0.8144 (ttmm) cc_final: 0.7669 (tmmt) REVERT: C 463 TYR cc_start: 0.6956 (t80) cc_final: 0.6522 (t80) REVERT: C 493 ASN cc_start: 0.8212 (m-40) cc_final: 0.8003 (m-40) outliers start: 10 outliers final: 8 residues processed: 125 average time/residue: 0.1934 time to fit residues: 31.8808 Evaluate side-chains 127 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 119 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain C residue 464 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 28 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 41 optimal weight: 10.0000 chunk 45 optimal weight: 0.0270 chunk 20 optimal weight: 0.8980 chunk 39 optimal weight: 0.2980 chunk 38 optimal weight: 0.4980 chunk 18 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 overall best weight: 0.5038 ------------------------------------------------------------------------------- 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 = 0.4149 r_free = 0.4149 target = 0.168766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.135092 restraints weight = 8859.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.138676 restraints weight = 5312.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.141126 restraints weight = 3840.336| |-----------------------------------------------------------------------------| r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6055 Z= 0.156 Angle : 0.569 8.098 8311 Z= 0.290 Chirality : 0.041 0.271 989 Planarity : 0.003 0.044 949 Dihedral : 8.437 59.233 1477 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.96 % Allowed : 10.54 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.31), residues: 705 helix: 1.47 (0.23), residues: 475 sheet: -4.10 (1.64), residues: 10 loop : -2.15 (0.37), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 327 HIS 0.003 0.001 HIS B 348 PHE 0.020 0.001 PHE A 236 TYR 0.017 0.001 TYR B 265 ARG 0.004 0.000 ARG A 432 Details of bonding type rmsd hydrogen bonds : bond 0.06409 ( 367) hydrogen bonds : angle 4.38092 ( 1083) SS BOND : bond 0.00213 ( 4) SS BOND : angle 1.41486 ( 8) covalent geometry : bond 0.00339 ( 6051) covalent geometry : angle 0.56788 ( 8303) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 349 ILE cc_start: 0.8279 (mt) cc_final: 0.8021 (mt) REVERT: B 218 PHE cc_start: 0.8417 (t80) cc_final: 0.7276 (t80) REVERT: B 222 TRP cc_start: 0.6799 (t-100) cc_final: 0.6342 (t-100) REVERT: B 236 PHE cc_start: 0.7945 (t80) cc_final: 0.7620 (t80) REVERT: B 262 TYR cc_start: 0.7530 (m-80) cc_final: 0.7320 (m-80) REVERT: B 298 LYS cc_start: 0.7763 (mttp) cc_final: 0.7343 (mttp) REVERT: B 358 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7920 (mttp) REVERT: B 436 LYS cc_start: 0.8147 (ttmm) cc_final: 0.7712 (tmmt) REVERT: C 463 TYR cc_start: 0.6952 (t80) cc_final: 0.6618 (t80) outliers start: 11 outliers final: 8 residues processed: 128 average time/residue: 0.1618 time to fit residues: 27.4737 Evaluate side-chains 131 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 122 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 358 LYS Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain C residue 464 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 45 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 39 optimal weight: 0.2980 chunk 6 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 20 optimal weight: 0.4980 chunk 53 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 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 = 0.4117 r_free = 0.4117 target = 0.165973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.132091 restraints weight = 9087.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.135695 restraints weight = 5390.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.138107 restraints weight = 3900.560| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 6055 Z= 0.234 Angle : 0.633 7.820 8311 Z= 0.321 Chirality : 0.044 0.270 989 Planarity : 0.004 0.052 949 Dihedral : 8.465 55.162 1477 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.04 % Allowed : 13.04 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.31), residues: 705 helix: 1.32 (0.23), residues: 473 sheet: -4.35 (1.49), residues: 10 loop : -2.20 (0.36), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 327 HIS 0.004 0.002 HIS B 348 PHE 0.020 0.002 PHE A 312 TYR 0.026 0.002 TYR B 265 ARG 0.003 0.000 ARG A 417 Details of bonding type rmsd hydrogen bonds : bond 0.07344 ( 367) hydrogen bonds : angle 4.57625 ( 1083) SS BOND : bond 0.00296 ( 4) SS BOND : angle 1.60986 ( 8) covalent geometry : bond 0.00535 ( 6051) covalent geometry : angle 0.63172 ( 8303) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.7042 (OUTLIER) cc_final: 0.6593 (mm) REVERT: A 349 ILE cc_start: 0.8359 (mt) cc_final: 0.8052 (mt) REVERT: A 444 TYR cc_start: 0.8294 (t80) cc_final: 0.7750 (t80) REVERT: A 477 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7368 (mm-30) REVERT: B 298 LYS cc_start: 0.7798 (mttp) cc_final: 0.7428 (mttp) REVERT: B 358 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.7950 (mttp) REVERT: B 486 LEU cc_start: 0.8024 (tp) cc_final: 0.7791 (tp) REVERT: C 463 TYR cc_start: 0.7154 (t80) cc_final: 0.6888 (t80) outliers start: 17 outliers final: 9 residues processed: 130 average time/residue: 0.1659 time to fit residues: 28.5710 Evaluate side-chains 134 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 123 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 337 HIS Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain B residue 358 LYS Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain C residue 464 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 58 optimal weight: 0.0070 chunk 62 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 46 optimal weight: 0.4980 chunk 45 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- 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 = 0.4142 r_free = 0.4142 target = 0.168918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.135338 restraints weight = 8851.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.138945 restraints weight = 5234.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.141294 restraints weight = 3791.027| |-----------------------------------------------------------------------------| r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6055 Z= 0.165 Angle : 0.583 7.960 8311 Z= 0.297 Chirality : 0.041 0.266 989 Planarity : 0.003 0.047 949 Dihedral : 8.220 56.178 1477 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.50 % Allowed : 14.46 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.31), residues: 705 helix: 1.49 (0.23), residues: 473 sheet: -4.22 (1.51), residues: 10 loop : -2.12 (0.37), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP B 327 HIS 0.003 0.001 HIS A 337 PHE 0.017 0.002 PHE A 312 TYR 0.022 0.001 TYR B 262 ARG 0.006 0.000 ARG C 440 Details of bonding type rmsd hydrogen bonds : bond 0.06536 ( 367) hydrogen bonds : angle 4.40090 ( 1083) SS BOND : bond 0.00167 ( 4) SS BOND : angle 2.35598 ( 8) covalent geometry : bond 0.00361 ( 6051) covalent geometry : angle 0.57847 ( 8303) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.7030 (OUTLIER) cc_final: 0.6559 (mm) REVERT: A 272 ARG cc_start: 0.7309 (tmm-80) cc_final: 0.6841 (tmt170) REVERT: A 349 ILE cc_start: 0.8352 (mt) cc_final: 0.8052 (mt) REVERT: A 404 LEU cc_start: 0.8093 (mm) cc_final: 0.7838 (mm) REVERT: A 477 GLU cc_start: 0.7560 (mm-30) cc_final: 0.7226 (mm-30) REVERT: B 298 LYS cc_start: 0.7789 (mttp) cc_final: 0.7403 (mttp) REVERT: B 327 TRP cc_start: 0.7644 (t60) cc_final: 0.7308 (t60) REVERT: B 358 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7934 (mttp) REVERT: B 486 LEU cc_start: 0.7983 (tp) cc_final: 0.7782 (tp) REVERT: C 463 TYR cc_start: 0.7159 (t80) cc_final: 0.6887 (t80) outliers start: 14 outliers final: 9 residues processed: 134 average time/residue: 0.1677 time to fit residues: 29.7302 Evaluate side-chains 137 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 358 LYS Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain C residue 464 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 37 optimal weight: 0.5980 chunk 60 optimal weight: 0.5980 chunk 9 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 68 optimal weight: 0.0970 chunk 59 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 = 0.4144 r_free = 0.4144 target = 0.166380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.133480 restraints weight = 8834.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.136822 restraints weight = 5315.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.139096 restraints weight = 3910.603| |-----------------------------------------------------------------------------| r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6055 Z= 0.160 Angle : 0.563 7.362 8311 Z= 0.288 Chirality : 0.041 0.258 989 Planarity : 0.003 0.046 949 Dihedral : 8.105 59.790 1477 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.86 % Allowed : 16.43 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.31), residues: 705 helix: 1.66 (0.23), residues: 473 sheet: -4.11 (1.53), residues: 10 loop : -2.08 (0.37), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 327 HIS 0.003 0.001 HIS A 337 PHE 0.018 0.001 PHE A 312 TYR 0.021 0.001 TYR B 262 ARG 0.004 0.000 ARG C 440 Details of bonding type rmsd hydrogen bonds : bond 0.06282 ( 367) hydrogen bonds : angle 4.26328 ( 1083) SS BOND : bond 0.00211 ( 4) SS BOND : angle 1.61915 ( 8) covalent geometry : bond 0.00353 ( 6051) covalent geometry : angle 0.56137 ( 8303) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.7049 (OUTLIER) cc_final: 0.6610 (mm) REVERT: A 272 ARG cc_start: 0.7373 (tmm-80) cc_final: 0.6914 (tmt170) REVERT: A 349 ILE cc_start: 0.8363 (mt) cc_final: 0.8068 (mt) REVERT: A 404 LEU cc_start: 0.8102 (mm) cc_final: 0.7846 (mm) REVERT: A 444 TYR cc_start: 0.8134 (t80) cc_final: 0.7464 (t80) REVERT: A 477 GLU cc_start: 0.7447 (mm-30) cc_final: 0.7149 (mm-30) REVERT: B 218 PHE cc_start: 0.8222 (t80) cc_final: 0.7868 (t80) REVERT: B 298 LYS cc_start: 0.7681 (mttp) cc_final: 0.7365 (mttp) REVERT: B 358 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7958 (mttp) REVERT: B 486 LEU cc_start: 0.8031 (tp) cc_final: 0.7820 (tp) outliers start: 16 outliers final: 11 residues processed: 128 average time/residue: 0.1552 time to fit residues: 26.6158 Evaluate side-chains 137 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 504 TRP Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 358 LYS Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain C residue 464 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 64 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 41 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 11 optimal weight: 0.0980 chunk 26 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 5 optimal weight: 0.0980 chunk 57 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.4149 r_free = 0.4149 target = 0.167808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.136325 restraints weight = 8967.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.139599 restraints weight = 5379.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.141739 restraints weight = 3920.940| |-----------------------------------------------------------------------------| r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6055 Z= 0.158 Angle : 0.570 7.644 8311 Z= 0.291 Chirality : 0.041 0.254 989 Planarity : 0.003 0.045 949 Dihedral : 8.020 57.470 1477 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.86 % Allowed : 17.32 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.32), residues: 705 helix: 1.68 (0.23), residues: 473 sheet: -4.04 (1.54), residues: 10 loop : -2.00 (0.38), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 327 HIS 0.003 0.001 HIS B 348 PHE 0.018 0.001 PHE B 236 TYR 0.025 0.002 TYR C 463 ARG 0.005 0.000 ARG C 440 Details of bonding type rmsd hydrogen bonds : bond 0.06250 ( 367) hydrogen bonds : angle 4.31745 ( 1083) SS BOND : bond 0.00172 ( 4) SS BOND : angle 1.25297 ( 8) covalent geometry : bond 0.00346 ( 6051) covalent geometry : angle 0.56857 ( 8303) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.7071 (OUTLIER) cc_final: 0.6580 (mm) REVERT: A 272 ARG cc_start: 0.7384 (tmm-80) cc_final: 0.6900 (tmt170) REVERT: A 349 ILE cc_start: 0.8355 (mt) cc_final: 0.8068 (mt) REVERT: A 404 LEU cc_start: 0.8109 (mm) cc_final: 0.7880 (mm) REVERT: B 298 LYS cc_start: 0.7650 (mttp) cc_final: 0.7314 (mttp) REVERT: B 327 TRP cc_start: 0.7530 (t60) cc_final: 0.7292 (t60) REVERT: B 358 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.7968 (mttp) REVERT: B 486 LEU cc_start: 0.8040 (tp) cc_final: 0.7840 (tp) outliers start: 16 outliers final: 9 residues processed: 128 average time/residue: 0.1707 time to fit residues: 29.0524 Evaluate side-chains 129 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 504 TRP Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 358 LYS Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain C residue 464 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 4 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 20 optimal weight: 0.3980 chunk 10 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 32 optimal weight: 0.0030 overall best weight: 0.4790 ------------------------------------------------------------------------------- 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 = 0.4156 r_free = 0.4156 target = 0.168310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.137170 restraints weight = 8918.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.140338 restraints weight = 5447.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.142423 restraints weight = 4012.081| |-----------------------------------------------------------------------------| r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 6055 Z= 0.152 Angle : 0.560 7.993 8311 Z= 0.287 Chirality : 0.041 0.251 989 Planarity : 0.003 0.044 949 Dihedral : 7.893 58.835 1477 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.68 % Allowed : 17.86 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.32), residues: 705 helix: 1.72 (0.23), residues: 473 sheet: -3.51 (0.97), residues: 20 loop : -1.90 (0.39), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 222 HIS 0.003 0.001 HIS B 348 PHE 0.017 0.001 PHE A 312 TYR 0.020 0.001 TYR C 463 ARG 0.003 0.000 ARG C 440 Details of bonding type rmsd hydrogen bonds : bond 0.06079 ( 367) hydrogen bonds : angle 4.29318 ( 1083) SS BOND : bond 0.00173 ( 4) SS BOND : angle 1.30882 ( 8) covalent geometry : bond 0.00337 ( 6051) covalent geometry : angle 0.55917 ( 8303) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.7053 (OUTLIER) cc_final: 0.6592 (mm) REVERT: A 272 ARG cc_start: 0.7410 (tmm-80) cc_final: 0.6900 (tmt170) REVERT: A 349 ILE cc_start: 0.8340 (mt) cc_final: 0.8048 (mt) REVERT: A 404 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7852 (mm) REVERT: A 444 TYR cc_start: 0.8103 (t80) cc_final: 0.7446 (t80) REVERT: A 477 GLU cc_start: 0.7252 (mm-30) cc_final: 0.7027 (mm-30) REVERT: B 327 TRP cc_start: 0.7499 (t60) cc_final: 0.7207 (t60) REVERT: B 358 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.7957 (mttp) REVERT: B 486 LEU cc_start: 0.8039 (tp) cc_final: 0.7823 (tp) outliers start: 15 outliers final: 9 residues processed: 127 average time/residue: 0.1706 time to fit residues: 28.6349 Evaluate side-chains 131 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 504 TRP Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 358 LYS Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 461 ASN Chi-restraints excluded: chain C residue 464 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 15 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 33 optimal weight: 0.1980 chunk 51 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4143 r_free = 0.4143 target = 0.168698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.134911 restraints weight = 8927.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.138551 restraints weight = 5284.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.141008 restraints weight = 3815.947| |-----------------------------------------------------------------------------| r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6055 Z= 0.178 Angle : 0.587 7.887 8311 Z= 0.298 Chirality : 0.041 0.254 989 Planarity : 0.003 0.046 949 Dihedral : 7.909 59.096 1477 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.86 % Allowed : 18.04 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.31), residues: 705 helix: 1.63 (0.23), residues: 473 sheet: -3.52 (0.97), residues: 20 loop : -1.88 (0.39), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 327 HIS 0.003 0.001 HIS B 348 PHE 0.018 0.001 PHE A 312 TYR 0.021 0.002 TYR B 265 ARG 0.003 0.000 ARG C 440 Details of bonding type rmsd hydrogen bonds : bond 0.06433 ( 367) hydrogen bonds : angle 4.34779 ( 1083) SS BOND : bond 0.00219 ( 4) SS BOND : angle 1.72236 ( 8) covalent geometry : bond 0.00403 ( 6051) covalent geometry : angle 0.58494 ( 8303) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.7018 (OUTLIER) cc_final: 0.6569 (mm) REVERT: A 272 ARG cc_start: 0.7453 (tmm-80) cc_final: 0.6866 (tmt170) REVERT: A 349 ILE cc_start: 0.8375 (mt) cc_final: 0.8046 (mt) REVERT: A 404 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7746 (mm) REVERT: A 444 TYR cc_start: 0.8156 (t80) cc_final: 0.7588 (t80) REVERT: B 305 ILE cc_start: 0.7271 (OUTLIER) cc_final: 0.7042 (mt) REVERT: B 314 MET cc_start: 0.7317 (mmm) cc_final: 0.7097 (mmm) REVERT: B 358 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7533 (mtmm) REVERT: B 486 LEU cc_start: 0.8031 (tp) cc_final: 0.7810 (tp) outliers start: 16 outliers final: 9 residues processed: 134 average time/residue: 0.1836 time to fit residues: 32.5079 Evaluate side-chains 137 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 504 TRP Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 358 LYS Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 461 ASN Chi-restraints excluded: chain C residue 464 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 55 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 62 optimal weight: 0.4980 chunk 29 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 40 optimal weight: 0.1980 chunk 15 optimal weight: 0.0870 chunk 4 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 343 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.167117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.133647 restraints weight = 9022.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.137139 restraints weight = 5404.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.139310 restraints weight = 3931.404| |-----------------------------------------------------------------------------| r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6055 Z= 0.145 Angle : 0.566 8.449 8311 Z= 0.289 Chirality : 0.040 0.248 989 Planarity : 0.004 0.052 949 Dihedral : 7.754 59.873 1477 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.50 % Allowed : 18.93 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.31), residues: 705 helix: 1.70 (0.23), residues: 472 sheet: -3.48 (0.97), residues: 20 loop : -1.83 (0.39), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 327 HIS 0.002 0.001 HIS A 337 PHE 0.016 0.001 PHE A 312 TYR 0.018 0.001 TYR C 463 ARG 0.006 0.000 ARG C 440 Details of bonding type rmsd hydrogen bonds : bond 0.05942 ( 367) hydrogen bonds : angle 4.26325 ( 1083) SS BOND : bond 0.00138 ( 4) SS BOND : angle 1.32927 ( 8) covalent geometry : bond 0.00314 ( 6051) covalent geometry : angle 0.56509 ( 8303) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.7034 (OUTLIER) cc_final: 0.6575 (mm) REVERT: A 272 ARG cc_start: 0.7500 (tmm-80) cc_final: 0.6938 (tmt170) REVERT: A 349 ILE cc_start: 0.8305 (mt) cc_final: 0.8039 (mt) REVERT: A 404 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7856 (mm) REVERT: B 314 MET cc_start: 0.7206 (mmm) cc_final: 0.6870 (mmm) REVERT: B 358 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7906 (mttp) REVERT: C 463 TYR cc_start: 0.6912 (t80) cc_final: 0.6612 (t80) outliers start: 14 outliers final: 8 residues processed: 126 average time/residue: 0.1720 time to fit residues: 28.4649 Evaluate side-chains 131 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 358 LYS Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 461 ASN Chi-restraints excluded: chain C residue 464 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 29 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 43 optimal weight: 0.4980 chunk 54 optimal weight: 0.0030 overall best weight: 0.5590 ------------------------------------------------------------------------------- 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 = 0.4154 r_free = 0.4154 target = 0.169933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.136186 restraints weight = 8963.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.139792 restraints weight = 5302.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.142193 restraints weight = 3816.600| |-----------------------------------------------------------------------------| r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6940 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6055 Z= 0.163 Angle : 0.582 9.067 8311 Z= 0.297 Chirality : 0.041 0.248 989 Planarity : 0.003 0.043 949 Dihedral : 7.754 59.891 1477 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.14 % Allowed : 19.29 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.31), residues: 705 helix: 1.65 (0.23), residues: 473 sheet: -3.44 (0.98), residues: 20 loop : -1.81 (0.39), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 327 HIS 0.003 0.001 HIS B 348 PHE 0.033 0.001 PHE B 236 TYR 0.020 0.001 TYR B 265 ARG 0.012 0.001 ARG C 440 Details of bonding type rmsd hydrogen bonds : bond 0.06168 ( 367) hydrogen bonds : angle 4.28649 ( 1083) SS BOND : bond 0.00176 ( 4) SS BOND : angle 1.46573 ( 8) covalent geometry : bond 0.00363 ( 6051) covalent geometry : angle 0.58095 ( 8303) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2289.16 seconds wall clock time: 40 minutes 54.54 seconds (2454.54 seconds total)