Starting phenix.real_space_refine on Sat May 10 09:54:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wm9_37646/05_2025/8wm9_37646_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wm9_37646/05_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_37646/05_2025/8wm9_37646.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wm9_37646/05_2025/8wm9_37646.map" model { file = "/net/cci-nas-00/data/ceres_data/8wm9_37646/05_2025/8wm9_37646_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wm9_37646/05_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 4.57, per 1000 atoms: 0.78 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: 1.57 Conformation dependent library (CDL) restraints added in 786.6 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: 0.56 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: 1.48 Time building geometry restraints manager: 1.82 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: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 17.670 Find NCS groups from input model: 0.230 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: 0.010 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.250 ------------------------------------------------------------------------------- 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 : 0.658 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: 0.1626 time to fit residues: 28.1430 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 : 0.571 ------------------------------------------------------------------------------- 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 = 0.133997 restraints weight = 8863.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.137639 restraints weight = 5279.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.139458 restraints weight = 3820.061| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 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 : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 349 ILE cc_start: 0.8282 (mt) cc_final: 0.7964 (mt) REVERT: B 222 TRP cc_start: 0.6813 (t-100) cc_final: 0.6392 (t-100) REVERT: B 262 TYR cc_start: 0.7582 (m-80) cc_final: 0.7258 (m-80) REVERT: B 298 LYS cc_start: 0.7779 (mttp) cc_final: 0.7324 (mttp) REVERT: B 314 MET cc_start: 0.7153 (mmm) cc_final: 0.6867 (mmm) REVERT: B 436 LYS cc_start: 0.8144 (ttmm) cc_final: 0.7671 (tmmt) REVERT: C 463 TYR cc_start: 0.6956 (t80) cc_final: 0.6522 (t80) REVERT: C 493 ASN cc_start: 0.8210 (m-40) cc_final: 0.8002 (m-40) outliers start: 10 outliers final: 8 residues processed: 125 average time/residue: 0.1615 time to fit residues: 26.8748 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 : 0.565 ------------------------------------------------------------------------------- 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: 0.7980 chunk 41 optimal weight: 10.0000 chunk 45 optimal weight: 0.0270 chunk 20 optimal weight: 0.7980 chunk 39 optimal weight: 0.2980 chunk 38 optimal weight: 0.0050 chunk 18 optimal weight: 0.5980 chunk 46 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 overall best weight: 0.3452 ------------------------------------------------------------------------------- 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 = 0.167457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.134399 restraints weight = 8831.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.137918 restraints weight = 5301.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.140165 restraints weight = 3853.456| |-----------------------------------------------------------------------------| r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6932 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6055 Z= 0.140 Angle : 0.556 8.239 8311 Z= 0.283 Chirality : 0.040 0.268 989 Planarity : 0.003 0.042 949 Dihedral : 8.417 59.843 1477 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.79 % Allowed : 10.36 % Favored : 87.86 % 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: 0.54 (0.31), residues: 705 helix: 1.53 (0.23), residues: 475 sheet: -4.08 (1.64), residues: 10 loop : -2.13 (0.37), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 327 HIS 0.002 0.001 HIS B 348 PHE 0.019 0.001 PHE A 236 TYR 0.016 0.001 TYR B 262 ARG 0.005 0.000 ARG A 432 Details of bonding type rmsd hydrogen bonds : bond 0.06147 ( 367) hydrogen bonds : angle 4.34426 ( 1083) SS BOND : bond 0.00284 ( 4) SS BOND : angle 1.55805 ( 8) covalent geometry : bond 0.00296 ( 6051) covalent geometry : angle 0.55386 ( 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 136 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 126 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 349 ILE cc_start: 0.8266 (mt) cc_final: 0.7997 (mt) REVERT: A 404 LEU cc_start: 0.8078 (mm) cc_final: 0.7867 (mm) REVERT: B 218 PHE cc_start: 0.8352 (t80) cc_final: 0.7208 (t80) REVERT: B 222 TRP cc_start: 0.6723 (t-100) cc_final: 0.6297 (t-100) REVERT: B 236 PHE cc_start: 0.8007 (t80) cc_final: 0.7683 (t80) REVERT: B 262 TYR cc_start: 0.7519 (m-80) cc_final: 0.7290 (m-80) REVERT: B 298 LYS cc_start: 0.7711 (mttp) cc_final: 0.7306 (mttp) REVERT: B 358 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7925 (mttp) REVERT: B 436 LYS cc_start: 0.8136 (ttmm) cc_final: 0.7754 (tmmt) REVERT: C 463 TYR cc_start: 0.6920 (t80) cc_final: 0.6541 (t80) outliers start: 10 outliers final: 8 residues processed: 128 average time/residue: 0.1685 time to fit residues: 28.4255 Evaluate side-chains 130 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 121 time to evaluate : 0.565 ------------------------------------------------------------------------------- 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 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 B residue 474 MET 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: 0.0270 chunk 8 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 chunk 20 optimal weight: 0.4980 chunk 53 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- 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 = 0.4141 r_free = 0.4141 target = 0.166349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.133248 restraints weight = 9078.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.136794 restraints weight = 5392.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.139106 restraints weight = 3914.254| |-----------------------------------------------------------------------------| r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6055 Z= 0.156 Angle : 0.559 8.182 8311 Z= 0.285 Chirality : 0.041 0.259 989 Planarity : 0.003 0.044 949 Dihedral : 8.272 57.709 1477 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.68 % Allowed : 12.32 % Favored : 85.00 % 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: 0.58 (0.31), residues: 705 helix: 1.57 (0.23), residues: 474 sheet: -4.33 (1.47), residues: 10 loop : -2.10 (0.37), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 327 HIS 0.004 0.001 HIS B 348 PHE 0.018 0.001 PHE A 312 TYR 0.018 0.001 TYR B 265 ARG 0.002 0.000 ARG A 417 Details of bonding type rmsd hydrogen bonds : bond 0.06248 ( 367) hydrogen bonds : angle 4.31641 ( 1083) SS BOND : bond 0.00195 ( 4) SS BOND : angle 1.53951 ( 8) covalent geometry : bond 0.00342 ( 6051) covalent geometry : angle 0.55709 ( 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 139 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.7063 (OUTLIER) cc_final: 0.6637 (mm) REVERT: A 349 ILE cc_start: 0.8336 (mt) cc_final: 0.8050 (mt) REVERT: A 404 LEU cc_start: 0.8081 (mm) cc_final: 0.7841 (mm) REVERT: B 222 TRP cc_start: 0.6763 (t-100) cc_final: 0.6415 (t-100) REVERT: B 298 LYS cc_start: 0.7718 (mttp) cc_final: 0.7386 (mttp) REVERT: B 358 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7943 (mttp) REVERT: C 463 TYR cc_start: 0.7138 (t80) cc_final: 0.6791 (t80) outliers start: 15 outliers final: 7 residues processed: 128 average time/residue: 0.1692 time to fit residues: 28.6550 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 : 0.592 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 58 optimal weight: 0.0170 chunk 62 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- 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 = 0.4140 r_free = 0.4140 target = 0.166216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.133023 restraints weight = 8899.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.136454 restraints weight = 5360.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.138706 restraints weight = 3917.560| |-----------------------------------------------------------------------------| r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6055 Z= 0.172 Angle : 0.574 7.905 8311 Z= 0.292 Chirality : 0.041 0.257 989 Planarity : 0.003 0.044 949 Dihedral : 8.187 57.215 1477 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.50 % Allowed : 15.36 % Favored : 82.14 % 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: 0.57 (0.31), residues: 705 helix: 1.54 (0.23), residues: 473 sheet: -4.32 (1.49), residues: 10 loop : -2.01 (0.37), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 327 HIS 0.004 0.001 HIS B 348 PHE 0.018 0.002 PHE A 312 TYR 0.021 0.001 TYR B 262 ARG 0.002 0.000 ARG A 417 Details of bonding type rmsd hydrogen bonds : bond 0.06408 ( 367) hydrogen bonds : angle 4.41158 ( 1083) SS BOND : bond 0.00488 ( 4) SS BOND : angle 1.88307 ( 8) covalent geometry : bond 0.00386 ( 6051) covalent geometry : angle 0.57117 ( 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 139 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.7067 (OUTLIER) cc_final: 0.6613 (mm) REVERT: A 272 ARG cc_start: 0.7291 (tmm-80) cc_final: 0.6878 (tmt170) REVERT: A 349 ILE cc_start: 0.8347 (mt) cc_final: 0.8057 (mt) REVERT: A 404 LEU cc_start: 0.8109 (mm) cc_final: 0.7866 (mm) REVERT: B 222 TRP cc_start: 0.6801 (t-100) cc_final: 0.6445 (t-100) REVERT: B 298 LYS cc_start: 0.7716 (mttp) cc_final: 0.7372 (mttp) REVERT: B 358 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.7957 (mttp) REVERT: B 486 LEU cc_start: 0.8001 (tp) cc_final: 0.7793 (tp) REVERT: C 463 TYR cc_start: 0.7249 (t80) cc_final: 0.6952 (t80) outliers start: 14 outliers final: 8 residues processed: 130 average time/residue: 0.1836 time to fit residues: 31.1384 Evaluate side-chains 130 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 120 time to evaluate : 0.592 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 9 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 50 optimal weight: 0.0870 chunk 51 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 = 0.166329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.132933 restraints weight = 8832.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.136378 restraints weight = 5311.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.138618 restraints weight = 3888.870| |-----------------------------------------------------------------------------| r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6055 Z= 0.171 Angle : 0.577 7.700 8311 Z= 0.293 Chirality : 0.041 0.256 989 Planarity : 0.003 0.044 949 Dihedral : 8.091 56.823 1477 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.50 % Allowed : 16.79 % 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: 0.67 (0.31), residues: 705 helix: 1.60 (0.23), residues: 473 sheet: -4.26 (1.50), residues: 10 loop : -1.94 (0.37), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 327 HIS 0.004 0.001 HIS B 348 PHE 0.018 0.001 PHE A 312 TYR 0.021 0.001 TYR B 262 ARG 0.007 0.000 ARG C 440 Details of bonding type rmsd hydrogen bonds : bond 0.06397 ( 367) hydrogen bonds : angle 4.36389 ( 1083) SS BOND : bond 0.00210 ( 4) SS BOND : angle 2.07744 ( 8) covalent geometry : bond 0.00384 ( 6051) covalent geometry : angle 0.57331 ( 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 135 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.7054 (OUTLIER) cc_final: 0.6640 (mm) REVERT: A 272 ARG cc_start: 0.7341 (tmm-80) cc_final: 0.6876 (tmt170) REVERT: A 349 ILE cc_start: 0.8366 (mt) cc_final: 0.8073 (mt) REVERT: A 404 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7866 (mm) REVERT: B 222 TRP cc_start: 0.6790 (t-100) cc_final: 0.6442 (t-100) REVERT: B 298 LYS cc_start: 0.7699 (mttp) cc_final: 0.7383 (mttp) REVERT: B 358 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7942 (mttp) REVERT: B 486 LEU cc_start: 0.8014 (tp) cc_final: 0.7803 (tp) REVERT: C 463 TYR cc_start: 0.7282 (t80) cc_final: 0.7063 (t80) outliers start: 14 outliers final: 8 residues processed: 125 average time/residue: 0.1714 time to fit residues: 28.1321 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 : 0.547 ------------------------------------------------------------------------------- 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 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 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: 0.8980 chunk 50 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 41 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 11 optimal weight: 0.0970 chunk 26 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4129 r_free = 0.4129 target = 0.165151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.132005 restraints weight = 8947.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.135433 restraints weight = 5371.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.137698 restraints weight = 3924.298| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6055 Z= 0.193 Angle : 0.596 7.728 8311 Z= 0.304 Chirality : 0.042 0.261 989 Planarity : 0.003 0.046 949 Dihedral : 8.066 56.682 1477 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.68 % Allowed : 17.14 % Favored : 80.18 % 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: 0.58 (0.31), residues: 705 helix: 1.52 (0.23), residues: 473 sheet: -4.19 (1.53), residues: 10 loop : -1.97 (0.37), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 327 HIS 0.005 0.001 HIS B 348 PHE 0.019 0.002 PHE A 312 TYR 0.023 0.002 TYR B 262 ARG 0.005 0.001 ARG C 440 Details of bonding type rmsd hydrogen bonds : bond 0.06674 ( 367) hydrogen bonds : angle 4.40563 ( 1083) SS BOND : bond 0.00310 ( 4) SS BOND : angle 1.74257 ( 8) covalent geometry : bond 0.00438 ( 6051) covalent geometry : angle 0.59384 ( 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: 15 poor density : 124 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.7068 (OUTLIER) cc_final: 0.6608 (mm) REVERT: A 272 ARG cc_start: 0.7438 (tmm-80) cc_final: 0.6845 (tmt170) REVERT: A 349 ILE cc_start: 0.8414 (mt) cc_final: 0.8096 (mt) REVERT: A 404 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7840 (mm) REVERT: A 444 TYR cc_start: 0.8125 (t80) cc_final: 0.7493 (t80) REVERT: B 218 PHE cc_start: 0.8379 (t80) cc_final: 0.7270 (t80) REVERT: B 222 TRP cc_start: 0.6845 (t-100) cc_final: 0.6290 (t-100) REVERT: B 298 LYS cc_start: 0.7679 (mttp) cc_final: 0.7388 (mttp) REVERT: B 327 TRP cc_start: 0.7593 (t60) cc_final: 0.7183 (t60) REVERT: B 358 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.7927 (mttp) REVERT: B 486 LEU cc_start: 0.8050 (tp) cc_final: 0.7828 (tp) outliers start: 15 outliers final: 8 residues processed: 130 average time/residue: 0.1760 time to fit residues: 29.9676 Evaluate side-chains 135 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 124 time to evaluate : 0.580 ------------------------------------------------------------------------------- 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 404 LEU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 504 TRP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 4 optimal weight: 0.3980 chunk 18 optimal weight: 0.8980 chunk 42 optimal weight: 0.0870 chunk 39 optimal weight: 0.6980 chunk 20 optimal weight: 0.3980 chunk 10 optimal weight: 0.5980 chunk 67 optimal weight: 0.7980 chunk 66 optimal weight: 0.1980 chunk 29 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 32 optimal weight: 0.0970 overall best weight: 0.2356 ------------------------------------------------------------------------------- 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 = 0.4177 r_free = 0.4177 target = 0.170258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.139299 restraints weight = 8904.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.142617 restraints weight = 5428.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.144674 restraints weight = 3969.013| |-----------------------------------------------------------------------------| r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.2358 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= 0.129 Angle : 0.553 8.413 8311 Z= 0.283 Chirality : 0.039 0.246 989 Planarity : 0.003 0.040 949 Dihedral : 7.766 58.887 1477 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.14 % Allowed : 17.32 % Favored : 80.54 % 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: 0.92 (0.32), residues: 705 helix: 1.80 (0.24), residues: 471 sheet: -3.33 (1.00), residues: 20 loop : -1.74 (0.39), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 222 HIS 0.002 0.001 HIS C 464 PHE 0.016 0.001 PHE A 312 TYR 0.026 0.001 TYR C 463 ARG 0.006 0.000 ARG C 440 Details of bonding type rmsd hydrogen bonds : bond 0.05504 ( 367) hydrogen bonds : angle 4.21388 ( 1083) SS BOND : bond 0.00166 ( 4) SS BOND : angle 1.40743 ( 8) covalent geometry : bond 0.00267 ( 6051) covalent geometry : angle 0.55161 ( 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: 12 poor density : 124 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.7010 (OUTLIER) cc_final: 0.6573 (mm) REVERT: A 234 THR cc_start: 0.8115 (OUTLIER) cc_final: 0.7762 (p) REVERT: A 272 ARG cc_start: 0.7331 (tmm-80) cc_final: 0.6870 (tmt170) REVERT: A 349 ILE cc_start: 0.8301 (mt) cc_final: 0.8035 (mt) REVERT: A 404 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7860 (mm) REVERT: B 218 PHE cc_start: 0.8285 (t80) cc_final: 0.7398 (t80) REVERT: B 222 TRP cc_start: 0.6630 (t-100) cc_final: 0.6298 (t-100) REVERT: B 298 LYS cc_start: 0.7650 (mttp) cc_final: 0.7306 (mttp) REVERT: B 358 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7879 (mttp) REVERT: C 463 TYR cc_start: 0.6678 (t80) cc_final: 0.6306 (t80) outliers start: 12 outliers final: 5 residues processed: 129 average time/residue: 0.1934 time to fit residues: 32.9950 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 : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain B residue 219 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 15 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 33 optimal weight: 0.0050 chunk 51 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 48 optimal weight: 0.0980 chunk 28 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.168067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.133219 restraints weight = 8843.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.137055 restraints weight = 5133.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.139535 restraints weight = 3683.116| |-----------------------------------------------------------------------------| r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6055 Z= 0.157 Angle : 0.587 10.510 8311 Z= 0.297 Chirality : 0.041 0.244 989 Planarity : 0.003 0.043 949 Dihedral : 7.840 59.390 1477 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.79 % Allowed : 18.93 % Favored : 79.29 % 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: 0.82 (0.31), residues: 705 helix: 1.69 (0.23), residues: 472 sheet: -4.01 (1.57), residues: 10 loop : -1.79 (0.38), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 327 HIS 0.004 0.001 HIS B 348 PHE 0.029 0.001 PHE B 236 TYR 0.020 0.001 TYR C 463 ARG 0.004 0.000 ARG C 440 Details of bonding type rmsd hydrogen bonds : bond 0.05996 ( 367) hydrogen bonds : angle 4.25760 ( 1083) SS BOND : bond 0.00217 ( 4) SS BOND : angle 1.51199 ( 8) covalent geometry : bond 0.00352 ( 6051) covalent geometry : angle 0.58540 ( 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 129 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 119 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.7001 (OUTLIER) cc_final: 0.6575 (mm) REVERT: A 234 THR cc_start: 0.8046 (OUTLIER) cc_final: 0.7694 (p) REVERT: A 272 ARG cc_start: 0.7430 (tmm-80) cc_final: 0.6877 (tmt170) REVERT: A 349 ILE cc_start: 0.8312 (mt) cc_final: 0.7998 (mt) REVERT: A 404 LEU cc_start: 0.7986 (mm) cc_final: 0.7742 (mm) REVERT: B 218 PHE cc_start: 0.8433 (t80) cc_final: 0.7703 (t80) REVERT: B 222 TRP cc_start: 0.6560 (t-100) cc_final: 0.6110 (t-100) REVERT: B 358 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7826 (mttp) REVERT: C 463 TYR cc_start: 0.6817 (t80) cc_final: 0.6468 (t80) outliers start: 10 outliers final: 6 residues processed: 124 average time/residue: 0.1627 time to fit residues: 26.6179 Evaluate side-chains 127 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 504 TRP Chi-restraints excluded: chain B residue 358 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 55 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 40 optimal weight: 0.3980 chunk 15 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.165787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.131154 restraints weight = 8931.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.134749 restraints weight = 5356.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.137085 restraints weight = 3922.485| |-----------------------------------------------------------------------------| r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 6055 Z= 0.208 Angle : 0.640 12.453 8311 Z= 0.322 Chirality : 0.043 0.259 989 Planarity : 0.004 0.046 949 Dihedral : 7.954 59.746 1477 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.79 % Allowed : 18.57 % Favored : 79.64 % 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: 0.52 (0.31), residues: 705 helix: 1.43 (0.23), residues: 474 sheet: -3.98 (1.59), residues: 10 loop : -1.88 (0.37), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 327 HIS 0.004 0.001 HIS B 348 PHE 0.028 0.002 PHE B 236 TYR 0.025 0.002 TYR B 265 ARG 0.004 0.000 ARG C 440 Details of bonding type rmsd hydrogen bonds : bond 0.06840 ( 367) hydrogen bonds : angle 4.41710 ( 1083) SS BOND : bond 0.00333 ( 4) SS BOND : angle 1.66475 ( 8) covalent geometry : bond 0.00475 ( 6051) covalent geometry : angle 0.63824 ( 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 137 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 127 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.7070 (OUTLIER) cc_final: 0.6600 (mm) REVERT: A 234 THR cc_start: 0.8103 (OUTLIER) cc_final: 0.7750 (p) REVERT: A 272 ARG cc_start: 0.7496 (tmm-80) cc_final: 0.6869 (tmt170) REVERT: A 349 ILE cc_start: 0.8413 (mt) cc_final: 0.8128 (mt) REVERT: A 404 LEU cc_start: 0.8044 (mm) cc_final: 0.7794 (mm) REVERT: A 444 TYR cc_start: 0.8108 (t80) cc_final: 0.7559 (t80) REVERT: B 222 TRP cc_start: 0.6672 (t-100) cc_final: 0.6272 (t-100) REVERT: B 358 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.7908 (mttp) REVERT: B 439 VAL cc_start: 0.8550 (m) cc_final: 0.8187 (p) REVERT: C 463 TYR cc_start: 0.6758 (t80) cc_final: 0.6496 (t80) outliers start: 10 outliers final: 6 residues processed: 132 average time/residue: 0.1700 time to fit residues: 29.4212 Evaluate side-chains 135 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 126 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 504 TRP Chi-restraints excluded: chain B residue 358 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 29 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 38 optimal weight: 0.3980 chunk 49 optimal weight: 0.6980 chunk 55 optimal weight: 0.1980 chunk 53 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4169 r_free = 0.4169 target = 0.167861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.134047 restraints weight = 8755.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.137622 restraints weight = 5189.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.139870 restraints weight = 3761.838| |-----------------------------------------------------------------------------| r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.2345 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= 0.168 Angle : 0.608 12.413 8311 Z= 0.306 Chirality : 0.041 0.256 989 Planarity : 0.003 0.045 949 Dihedral : 7.817 59.522 1477 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.96 % Allowed : 18.75 % Favored : 79.29 % 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: 0.61 (0.31), residues: 705 helix: 1.53 (0.23), residues: 472 sheet: -3.30 (1.03), residues: 20 loop : -1.82 (0.39), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 327 HIS 0.004 0.001 HIS B 348 PHE 0.031 0.002 PHE B 236 TYR 0.021 0.001 TYR B 262 ARG 0.003 0.000 ARG C 440 Details of bonding type rmsd hydrogen bonds : bond 0.06320 ( 367) hydrogen bonds : angle 4.32470 ( 1083) SS BOND : bond 0.00248 ( 4) SS BOND : angle 1.85557 ( 8) covalent geometry : bond 0.00376 ( 6051) covalent geometry : angle 0.60591 ( 8303) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2112.53 seconds wall clock time: 37 minutes 37.99 seconds (2257.99 seconds total)