Starting phenix.real_space_refine on Fri Oct 10 13:18:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wm9_37646/10_2025/8wm9_37646_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wm9_37646/10_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 { model { file = "/net/cci-nas-00/data/ceres_data/8wm9_37646/10_2025/8wm9_37646_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wm9_37646/10_2025/8wm9_37646_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wm9_37646/10_2025/8wm9_37646.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wm9_37646/10_2025/8wm9_37646.map" } resolution = 3.53 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: {'ARG:plan': 3, 'ASN:plan1': 1, 'GLU:plan': 3, 'PHE:plan': 1, 'GLN:plan1': 1, 'TYR:plan': 1} 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, 'TYR:plan': 2, 'ASP:plan': 2, 'GLU:plan': 5, 'PHE:plan': 1, 'ARG:plan': 2, 'TRP:plan': 1, 'HIS:plan': 1} 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: {'HIS:plan': 1, 'GLU:plan': 2, 'PHE:plan': 1, 'ARG:plan': 2, 'TYR: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: 1.36, per 1000 atoms: 0.23 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: 0.54 Conformation dependent library (CDL) restraints added in 328.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.18 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: 0.81 Time building geometry restraints manager: 0.72 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 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 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: 1.170 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: 0.090 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 6.990 Find NCS groups from input model: 0.100 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.720 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG B 247 TYR 0.023 0.002 TYR B 262 PHE 0.020 0.002 PHE B 482 TRP 0.029 0.002 TRP A 222 HIS 0.005 0.001 HIS B 348 Details of bonding type rmsd covalent geometry : bond 0.00633 ( 6051) covalent geometry : angle 0.91196 ( 8303) SS BOND : bond 0.00512 ( 4) SS BOND : angle 2.53765 ( 8) hydrogen bonds : bond 0.13591 ( 367) hydrogen bonds : angle 5.80218 ( 1083) *********************** 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 : 0.211 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: 0.0668 time to fit residues: 11.7942 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 : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 20.0000 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.0770 chunk 61 optimal weight: 0.0070 chunk 45 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 overall best weight: 0.4156 ------------------------------------------------------------------------------- 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 = 0.4156 r_free = 0.4156 target = 0.169354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.135953 restraints weight = 8880.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.139594 restraints weight = 5248.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.142022 restraints weight = 3801.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.143222 restraints weight = 3103.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.144390 restraints weight = 2770.609| |-----------------------------------------------------------------------------| r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6886 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6055 Z= 0.154 Angle : 0.582 7.608 8311 Z= 0.299 Chirality : 0.042 0.283 989 Planarity : 0.004 0.042 949 Dihedral : 8.607 59.639 1477 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.61 % Allowed : 7.32 % Favored : 91.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.31), residues: 705 helix: 1.41 (0.23), residues: 474 sheet: -3.95 (1.70), residues: 10 loop : -2.27 (0.36), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 272 TYR 0.020 0.001 TYR B 262 PHE 0.020 0.002 PHE B 236 TRP 0.022 0.001 TRP A 222 HIS 0.003 0.001 HIS C 490 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 6051) covalent geometry : angle 0.58080 ( 8303) SS BOND : bond 0.00098 ( 4) SS BOND : angle 1.27258 ( 8) hydrogen bonds : bond 0.06461 ( 367) hydrogen bonds : angle 4.43919 ( 1083) *********************** 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 138 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 129 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 349 ILE cc_start: 0.8214 (mt) cc_final: 0.7881 (mt) REVERT: B 222 TRP cc_start: 0.6684 (t-100) cc_final: 0.6372 (t-100) REVERT: B 262 TYR cc_start: 0.7539 (m-80) cc_final: 0.7207 (m-80) REVERT: B 298 LYS cc_start: 0.7713 (mttp) cc_final: 0.7303 (mttp) REVERT: B 314 MET cc_start: 0.7131 (mmm) cc_final: 0.6861 (mmm) REVERT: B 436 LYS cc_start: 0.8123 (ttmm) cc_final: 0.7711 (tmmt) REVERT: C 463 TYR cc_start: 0.6944 (t80) cc_final: 0.6484 (t80) outliers start: 9 outliers final: 7 residues processed: 130 average time/residue: 0.0713 time to fit residues: 12.4284 Evaluate side-chains 131 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 124 time to evaluate : 0.202 ------------------------------------------------------------------------------- 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 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 12 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 45 optimal weight: 0.0470 chunk 32 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 overall best weight: 0.6878 ------------------------------------------------------------------------------- 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 = 0.168619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.137706 restraints weight = 8865.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.140129 restraints weight = 5498.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.141458 restraints weight = 4414.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.141321 restraints weight = 3299.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.141792 restraints weight = 3210.375| |-----------------------------------------------------------------------------| r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.1475 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= 0.186 Angle : 0.592 7.938 8311 Z= 0.301 Chirality : 0.042 0.270 989 Planarity : 0.004 0.046 949 Dihedral : 8.511 58.565 1477 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.96 % Allowed : 10.18 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.31), residues: 705 helix: 1.39 (0.23), residues: 474 sheet: -4.20 (1.54), residues: 10 loop : -2.18 (0.37), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 432 TYR 0.022 0.001 TYR B 265 PHE 0.019 0.002 PHE B 236 TRP 0.020 0.002 TRP B 327 HIS 0.005 0.001 HIS B 348 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 6051) covalent geometry : angle 0.58963 ( 8303) SS BOND : bond 0.00309 ( 4) SS BOND : angle 1.76108 ( 8) hydrogen bonds : bond 0.06719 ( 367) hydrogen bonds : angle 4.45164 ( 1083) *********************** 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 : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 349 ILE cc_start: 0.8098 (mt) cc_final: 0.7757 (mt) REVERT: A 404 LEU cc_start: 0.8052 (mm) cc_final: 0.7821 (mm) REVERT: A 444 TYR cc_start: 0.8272 (t80) cc_final: 0.7609 (t80) REVERT: B 222 TRP cc_start: 0.6775 (t-100) cc_final: 0.6394 (t-100) REVERT: B 262 TYR cc_start: 0.7535 (m-80) cc_final: 0.7329 (m-80) REVERT: B 298 LYS cc_start: 0.7758 (mttp) cc_final: 0.7400 (mttp) REVERT: B 314 MET cc_start: 0.7114 (mmm) cc_final: 0.6790 (mmm) REVERT: B 358 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7932 (mttp) REVERT: B 436 LYS cc_start: 0.8127 (ttmm) cc_final: 0.7665 (tmmt) REVERT: C 463 TYR cc_start: 0.6967 (t80) cc_final: 0.6593 (t80) outliers start: 11 outliers final: 8 residues processed: 128 average time/residue: 0.0777 time to fit residues: 13.2756 Evaluate side-chains 133 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 124 time to evaluate : 0.205 ------------------------------------------------------------------------------- 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 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 7 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 20 optimal weight: 0.2980 chunk 62 optimal weight: 1.9990 chunk 69 optimal weight: 0.3980 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 = 0.4150 r_free = 0.4150 target = 0.169407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.138375 restraints weight = 8953.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.139854 restraints weight = 5475.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.141736 restraints weight = 4480.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.141605 restraints weight = 3450.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.141786 restraints weight = 3548.789| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6055 Z= 0.164 Angle : 0.568 8.132 8311 Z= 0.290 Chirality : 0.041 0.267 989 Planarity : 0.003 0.045 949 Dihedral : 8.319 59.791 1477 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.86 % Allowed : 11.96 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.31), residues: 705 helix: 1.50 (0.23), residues: 474 sheet: -4.30 (1.48), residues: 10 loop : -2.14 (0.37), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 417 TYR 0.019 0.001 TYR B 265 PHE 0.017 0.001 PHE A 312 TRP 0.034 0.002 TRP B 327 HIS 0.003 0.001 HIS B 348 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 6051) covalent geometry : angle 0.56466 ( 8303) SS BOND : bond 0.00252 ( 4) SS BOND : angle 1.91510 ( 8) hydrogen bonds : bond 0.06442 ( 367) hydrogen bonds : angle 4.36263 ( 1083) *********************** 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 146 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.7046 (OUTLIER) cc_final: 0.6614 (mm) REVERT: A 349 ILE cc_start: 0.8165 (mt) cc_final: 0.7849 (mt) REVERT: A 404 LEU cc_start: 0.8057 (mm) cc_final: 0.7810 (mm) REVERT: B 218 PHE cc_start: 0.8430 (t80) cc_final: 0.7289 (t80) REVERT: B 222 TRP cc_start: 0.6812 (t-100) cc_final: 0.6385 (t-100) REVERT: B 262 TYR cc_start: 0.7504 (m-80) cc_final: 0.7303 (m-80) REVERT: B 298 LYS cc_start: 0.7781 (mttp) cc_final: 0.7421 (mttp) REVERT: B 358 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7944 (mttp) REVERT: C 463 TYR cc_start: 0.7160 (t80) cc_final: 0.6803 (t80) outliers start: 16 outliers final: 8 residues processed: 135 average time/residue: 0.0788 time to fit residues: 14.0324 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 : 0.198 ------------------------------------------------------------------------------- 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 437 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 16 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 41 optimal weight: 0.0040 chunk 14 optimal weight: 0.0980 chunk 42 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 10 optimal weight: 0.3980 chunk 22 optimal weight: 0.0980 chunk 45 optimal weight: 1.9990 overall best weight: 0.2392 ------------------------------------------------------------------------------- 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 = 0.4168 r_free = 0.4168 target = 0.168698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.135790 restraints weight = 9050.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.139315 restraints weight = 5389.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.141623 restraints weight = 3907.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.142896 restraints weight = 3205.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.143911 restraints weight = 2854.025| |-----------------------------------------------------------------------------| r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 6055 Z= 0.135 Angle : 0.546 8.288 8311 Z= 0.279 Chirality : 0.040 0.249 989 Planarity : 0.003 0.038 949 Dihedral : 8.012 58.794 1477 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.50 % Allowed : 14.64 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.31), residues: 705 helix: 1.65 (0.23), residues: 473 sheet: -4.23 (1.48), residues: 10 loop : -1.91 (0.37), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 440 TYR 0.015 0.001 TYR A 444 PHE 0.016 0.001 PHE A 312 TRP 0.032 0.001 TRP B 327 HIS 0.002 0.001 HIS B 348 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 6051) covalent geometry : angle 0.54349 ( 8303) SS BOND : bond 0.00118 ( 4) SS BOND : angle 1.89085 ( 8) hydrogen bonds : bond 0.05660 ( 367) hydrogen bonds : angle 4.28160 ( 1083) *********************** 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 143 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.7024 (OUTLIER) cc_final: 0.6562 (mm) REVERT: A 272 ARG cc_start: 0.7201 (tmm-80) cc_final: 0.6929 (tmt170) REVERT: A 349 ILE cc_start: 0.8269 (mt) cc_final: 0.7965 (mt) REVERT: A 404 LEU cc_start: 0.8103 (mm) cc_final: 0.7859 (mm) REVERT: B 218 PHE cc_start: 0.8319 (t80) cc_final: 0.7431 (t80) REVERT: B 222 TRP cc_start: 0.6616 (t-100) cc_final: 0.6256 (t-100) REVERT: B 298 LYS cc_start: 0.7655 (mttp) cc_final: 0.7283 (mttp) REVERT: B 358 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7862 (mttp) REVERT: C 440 ARG cc_start: 0.7029 (mmp80) cc_final: 0.6709 (mmp80) REVERT: C 463 TYR cc_start: 0.7238 (t80) cc_final: 0.6961 (t80) outliers start: 14 outliers final: 9 residues processed: 134 average time/residue: 0.0733 time to fit residues: 13.1826 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 : 0.153 ------------------------------------------------------------------------------- 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 363 LEU Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain B residue 219 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 24 optimal weight: 0.8980 chunk 44 optimal weight: 0.3980 chunk 46 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 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 = 0.4157 r_free = 0.4157 target = 0.166835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.131778 restraints weight = 8838.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.135557 restraints weight = 5176.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.138001 restraints weight = 3739.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.139392 restraints weight = 3071.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.140349 restraints weight = 2737.769| |-----------------------------------------------------------------------------| r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6055 Z= 0.193 Angle : 0.596 9.007 8311 Z= 0.300 Chirality : 0.042 0.254 989 Planarity : 0.003 0.045 949 Dihedral : 8.098 57.026 1477 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.50 % Allowed : 16.61 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.31), residues: 705 helix: 1.58 (0.23), residues: 473 sheet: -4.20 (1.51), residues: 10 loop : -1.94 (0.37), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 440 TYR 0.024 0.002 TYR B 265 PHE 0.019 0.002 PHE A 312 TRP 0.016 0.002 TRP A 222 HIS 0.004 0.001 HIS B 348 Details of bonding type rmsd covalent geometry : bond 0.00440 ( 6051) covalent geometry : angle 0.59407 ( 8303) SS BOND : bond 0.00255 ( 4) SS BOND : angle 1.55369 ( 8) hydrogen bonds : bond 0.06480 ( 367) hydrogen bonds : angle 4.37818 ( 1083) *********************** 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 136 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 0.154 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.7020 (OUTLIER) cc_final: 0.6592 (mm) REVERT: A 272 ARG cc_start: 0.7338 (tmm-80) cc_final: 0.6894 (tmt170) REVERT: A 349 ILE cc_start: 0.8309 (mt) cc_final: 0.7995 (mt) REVERT: A 404 LEU cc_start: 0.8004 (mm) cc_final: 0.7763 (mm) REVERT: B 218 PHE cc_start: 0.8438 (t80) cc_final: 0.7544 (t80) REVERT: B 222 TRP cc_start: 0.6657 (t-100) cc_final: 0.6131 (t-100) REVERT: B 298 LYS cc_start: 0.7718 (mttp) cc_final: 0.7391 (mttp) REVERT: B 358 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7869 (mttp) REVERT: B 486 LEU cc_start: 0.7986 (tp) cc_final: 0.7751 (tp) REVERT: C 463 TYR cc_start: 0.7317 (t80) cc_final: 0.7068 (t80) outliers start: 14 outliers final: 10 residues processed: 126 average time/residue: 0.0682 time to fit residues: 11.4949 Evaluate side-chains 134 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.149 ------------------------------------------------------------------------------- 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 B residue 318 ILE Chi-restraints excluded: chain B residue 358 LYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 14 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 68 optimal weight: 0.0070 chunk 32 optimal weight: 8.9990 chunk 42 optimal weight: 0.0970 chunk 43 optimal weight: 0.0870 overall best weight: 0.2774 ------------------------------------------------------------------------------- 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 = 0.4196 r_free = 0.4196 target = 0.170202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.135697 restraints weight = 8876.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.139402 restraints weight = 5240.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.141805 restraints weight = 3801.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.143211 restraints weight = 3133.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.143924 restraints weight = 2792.772| |-----------------------------------------------------------------------------| r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.2363 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= 0.127 Angle : 0.546 10.783 8311 Z= 0.275 Chirality : 0.039 0.242 989 Planarity : 0.003 0.040 949 Dihedral : 7.814 59.436 1477 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.50 % Allowed : 17.32 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.31), residues: 705 helix: 1.78 (0.23), residues: 473 sheet: -4.06 (1.54), residues: 10 loop : -1.79 (0.38), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 440 TYR 0.019 0.001 TYR B 262 PHE 0.016 0.001 PHE A 312 TRP 0.021 0.001 TRP A 222 HIS 0.001 0.000 HIS B 348 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 6051) covalent geometry : angle 0.54559 ( 8303) SS BOND : bond 0.00090 ( 4) SS BOND : angle 0.81781 ( 8) hydrogen bonds : bond 0.05458 ( 367) hydrogen bonds : angle 4.18099 ( 1083) *********************** 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 142 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.6996 (OUTLIER) cc_final: 0.6536 (mm) REVERT: A 272 ARG cc_start: 0.7286 (tmm-80) cc_final: 0.6909 (tmt170) REVERT: A 349 ILE cc_start: 0.8270 (mt) cc_final: 0.7985 (mt) REVERT: A 404 LEU cc_start: 0.7991 (mm) cc_final: 0.7757 (mm) REVERT: B 218 PHE cc_start: 0.8346 (t80) cc_final: 0.7811 (t80) REVERT: B 222 TRP cc_start: 0.6315 (t-100) cc_final: 0.5858 (t-100) REVERT: B 298 LYS cc_start: 0.7649 (mttp) cc_final: 0.7307 (mttp) REVERT: B 327 TRP cc_start: 0.7504 (t60) cc_final: 0.7173 (t60) REVERT: B 358 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7836 (mttp) REVERT: C 463 TYR cc_start: 0.7267 (t80) cc_final: 0.7048 (t80) REVERT: C 500 GLN cc_start: 0.7768 (mp10) cc_final: 0.7547 (mp10) outliers start: 14 outliers final: 4 residues processed: 132 average time/residue: 0.0674 time to fit residues: 11.9359 Evaluate side-chains 130 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 124 time to evaluate : 0.148 ------------------------------------------------------------------------------- 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 385 ASP 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 31 optimal weight: 0.0770 chunk 66 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 chunk 17 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 68 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 11 optimal weight: 0.1980 chunk 13 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 overall best weight: 0.4338 ------------------------------------------------------------------------------- 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 = 0.4178 r_free = 0.4178 target = 0.168795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.134323 restraints weight = 8836.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.137940 restraints weight = 5203.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.140315 restraints weight = 3791.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.141723 restraints weight = 3125.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.142536 restraints weight = 2790.884| |-----------------------------------------------------------------------------| r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 6055 Z= 0.146 Angle : 0.571 11.552 8311 Z= 0.288 Chirality : 0.040 0.241 989 Planarity : 0.003 0.041 949 Dihedral : 7.828 59.295 1477 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.50 % Allowed : 18.57 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.31), residues: 705 helix: 1.71 (0.23), residues: 473 sheet: -4.02 (1.57), residues: 10 loop : -1.79 (0.38), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 440 TYR 0.020 0.001 TYR B 262 PHE 0.018 0.001 PHE A 312 TRP 0.018 0.001 TRP A 222 HIS 0.003 0.001 HIS B 348 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 6051) covalent geometry : angle 0.57032 ( 8303) SS BOND : bond 0.00205 ( 4) SS BOND : angle 0.99711 ( 8) hydrogen bonds : bond 0.05765 ( 367) hydrogen bonds : angle 4.23959 ( 1083) *********************** 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 135 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.7031 (OUTLIER) cc_final: 0.6581 (mm) REVERT: A 272 ARG cc_start: 0.7345 (tmm-80) cc_final: 0.6925 (tmt170) REVERT: A 349 ILE cc_start: 0.8311 (mt) cc_final: 0.7992 (mt) REVERT: A 404 LEU cc_start: 0.8030 (mm) cc_final: 0.7784 (mm) REVERT: B 222 TRP cc_start: 0.6412 (t-100) cc_final: 0.5974 (t-100) REVERT: B 358 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7827 (mttp) REVERT: C 500 GLN cc_start: 0.7739 (mp10) cc_final: 0.7519 (mp10) outliers start: 14 outliers final: 6 residues processed: 128 average time/residue: 0.0701 time to fit residues: 11.9558 Evaluate side-chains 129 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 121 time to evaluate : 0.206 ------------------------------------------------------------------------------- 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 385 ASP 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 C residue 464 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 40 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 0 optimal weight: 10.9990 chunk 5 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.4152 r_free = 0.4152 target = 0.166530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.132020 restraints weight = 8911.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.135546 restraints weight = 5309.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.137905 restraints weight = 3895.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.139154 restraints weight = 3229.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.140114 restraints weight = 2892.519| |-----------------------------------------------------------------------------| r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6941 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 6055 Z= 0.207 Angle : 0.636 12.057 8311 Z= 0.321 Chirality : 0.043 0.255 989 Planarity : 0.003 0.046 949 Dihedral : 7.963 58.708 1477 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.32 % Allowed : 18.57 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.31), residues: 705 helix: 1.49 (0.23), residues: 474 sheet: -3.45 (0.98), residues: 20 loop : -1.77 (0.39), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 417 TYR 0.025 0.002 TYR B 265 PHE 0.020 0.002 PHE A 312 TRP 0.015 0.002 TRP B 504 HIS 0.005 0.001 HIS B 348 Details of bonding type rmsd covalent geometry : bond 0.00472 ( 6051) covalent geometry : angle 0.62863 ( 8303) SS BOND : bond 0.00336 ( 4) SS BOND : angle 3.14356 ( 8) hydrogen bonds : bond 0.06677 ( 367) hydrogen bonds : angle 4.38969 ( 1083) *********************** 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 134 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.149 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.7060 (OUTLIER) cc_final: 0.6618 (mm) REVERT: A 272 ARG cc_start: 0.7477 (tmm-80) cc_final: 0.6916 (tmt170) REVERT: A 280 ILE cc_start: 0.7943 (mt) cc_final: 0.7741 (mm) REVERT: A 349 ILE cc_start: 0.8380 (mt) cc_final: 0.8052 (mt) REVERT: A 404 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7765 (mm) REVERT: A 444 TYR cc_start: 0.8102 (t80) cc_final: 0.7473 (t80) REVERT: A 477 GLU cc_start: 0.7405 (mm-30) cc_final: 0.7186 (mm-30) REVERT: B 218 PHE cc_start: 0.8386 (t80) cc_final: 0.7869 (t80) REVERT: B 222 TRP cc_start: 0.6607 (t-100) cc_final: 0.6092 (t-100) REVERT: B 358 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7911 (mttp) REVERT: C 463 TYR cc_start: 0.6694 (t80) cc_final: 0.6313 (t80) outliers start: 13 outliers final: 7 residues processed: 126 average time/residue: 0.0701 time to fit residues: 11.9753 Evaluate side-chains 131 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 121 time to evaluate : 0.202 ------------------------------------------------------------------------------- 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 385 ASP Chi-restraints excluded: chain A residue 404 LEU 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 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 27 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 63 optimal weight: 0.0970 chunk 33 optimal weight: 0.0170 chunk 37 optimal weight: 2.9990 chunk 69 optimal weight: 0.4980 chunk 0 optimal weight: 7.9990 chunk 5 optimal weight: 0.0570 chunk 21 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 overall best weight: 0.2734 ------------------------------------------------------------------------------- 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 = 0.4195 r_free = 0.4195 target = 0.170061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.135267 restraints weight = 8967.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.139103 restraints weight = 5139.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.141605 restraints weight = 3680.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.142862 restraints weight = 3005.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.143981 restraints weight = 2687.898| |-----------------------------------------------------------------------------| r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 moved from start: 0.2564 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= 0.134 Angle : 0.591 12.517 8311 Z= 0.294 Chirality : 0.040 0.243 989 Planarity : 0.003 0.040 949 Dihedral : 7.689 59.806 1477 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.31), residues: 705 helix: 1.70 (0.23), residues: 473 sheet: -3.47 (0.97), residues: 20 loop : -1.71 (0.40), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 440 TYR 0.020 0.001 TYR C 463 PHE 0.017 0.001 PHE A 312 TRP 0.016 0.001 TRP A 222 HIS 0.003 0.001 HIS B 343 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 6051) covalent geometry : angle 0.58792 ( 8303) SS BOND : bond 0.00169 ( 4) SS BOND : angle 2.10192 ( 8) hydrogen bonds : bond 0.05520 ( 367) hydrogen bonds : angle 4.20048 ( 1083) ********************** 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 130 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 120 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.6987 (OUTLIER) cc_final: 0.6547 (mm) REVERT: A 272 ARG cc_start: 0.7429 (tmm-80) cc_final: 0.6959 (tmt170) REVERT: A 280 ILE cc_start: 0.7884 (mt) cc_final: 0.7659 (mm) REVERT: A 349 ILE cc_start: 0.8249 (mt) cc_final: 0.7957 (mt) REVERT: A 404 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7755 (mm) REVERT: B 218 PHE cc_start: 0.8381 (t80) cc_final: 0.7487 (t80) REVERT: B 222 TRP cc_start: 0.6269 (t-100) cc_final: 0.5961 (t-100) REVERT: B 327 TRP cc_start: 0.7501 (t60) cc_final: 0.7119 (t60) REVERT: B 358 LYS cc_start: 0.8130 (OUTLIER) cc_final: 0.7788 (mttp) REVERT: C 463 TYR cc_start: 0.6755 (t80) cc_final: 0.6370 (t80) REVERT: C 500 GLN cc_start: 0.7739 (mp10) cc_final: 0.7517 (mp10) outliers start: 10 outliers final: 5 residues processed: 122 average time/residue: 0.0766 time to fit residues: 12.5658 Evaluate side-chains 125 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 117 time to evaluate : 0.215 ------------------------------------------------------------------------------- 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 385 ASP Chi-restraints excluded: chain A residue 404 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 20 optimal weight: 0.1980 chunk 45 optimal weight: 0.1980 chunk 61 optimal weight: 0.4980 chunk 9 optimal weight: 6.9990 chunk 41 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.4178 r_free = 0.4178 target = 0.168483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.134163 restraints weight = 8845.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.137772 restraints weight = 5261.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.140175 restraints weight = 3832.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.141360 restraints weight = 3152.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.142391 restraints weight = 2834.223| |-----------------------------------------------------------------------------| r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6893 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6055 Z= 0.153 Angle : 0.594 12.148 8311 Z= 0.298 Chirality : 0.041 0.242 989 Planarity : 0.003 0.042 949 Dihedral : 7.719 59.712 1477 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.61 % Allowed : 19.29 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.31), residues: 705 helix: 1.69 (0.23), residues: 473 sheet: -3.49 (0.97), residues: 20 loop : -1.71 (0.40), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 440 TYR 0.020 0.001 TYR C 463 PHE 0.018 0.001 PHE A 312 TRP 0.014 0.001 TRP A 222 HIS 0.003 0.001 HIS B 348 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 6051) covalent geometry : angle 0.58956 ( 8303) SS BOND : bond 0.00233 ( 4) SS BOND : angle 2.38494 ( 8) hydrogen bonds : bond 0.05847 ( 367) hydrogen bonds : angle 4.25040 ( 1083) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1091.41 seconds wall clock time: 19 minutes 29.20 seconds (1169.20 seconds total)