Starting phenix.real_space_refine on Thu Sep 18 11:39:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jlb_61582/09_2025/9jlb_61582_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jlb_61582/09_2025/9jlb_61582.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jlb_61582/09_2025/9jlb_61582.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jlb_61582/09_2025/9jlb_61582.map" model { file = "/net/cci-nas-00/data/ceres_data/9jlb_61582/09_2025/9jlb_61582_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jlb_61582/09_2025/9jlb_61582_trim.cif" } resolution = 3.0 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= 0.150 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 63 5.16 5 C 5260 2.51 5 N 1427 2.21 5 O 1539 1.98 5 H 8173 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16462 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8271 Classifications: {'peptide': 533} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 511} Chain breaks: 3 Chain: "B" Number of atoms: 712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 712 Classifications: {'peptide': 43} Link IDs: {'TRANS': 42} Chain breaks: 1 Chain: "C" Number of atoms: 7393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 7393 Classifications: {'peptide': 476} Link IDs: {'PTRANS': 20, 'TRANS': 455} Chain breaks: 3 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'O6E': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'O6E': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.22, per 1000 atoms: 0.20 Number of scatterers: 16462 At special positions: 0 Unit cell: (66.744, 112.888, 117.008, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 63 16.00 O 1539 8.00 N 1427 7.00 C 5260 6.00 H 8173 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.42 Conformation dependent library (CDL) restraints added in 526.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1964 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 8 sheets defined 48.6% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 56 through 78 removed outlier: 3.554A pdb=" N TYR A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N THR A 62 " --> pdb=" O ILE A 58 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL A 63 " --> pdb=" O GLN A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 90 Processing helix chain 'A' and resid 97 through 110 removed outlier: 3.530A pdb=" N ILE A 101 " --> pdb=" O PRO A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 141 Processing helix chain 'A' and resid 162 through 167 removed outlier: 3.853A pdb=" N PHE A 167 " --> pdb=" O ARG A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 180 Processing helix chain 'A' and resid 223 through 247 Processing helix chain 'A' and resid 252 through 269 Processing helix chain 'A' and resid 304 through 308 Processing helix chain 'A' and resid 309 through 319 Processing helix chain 'A' and resid 355 through 366 Processing helix chain 'A' and resid 411 through 457 Processing helix chain 'A' and resid 461 through 466 removed outlier: 3.723A pdb=" N GLN A 466 " --> pdb=" O GLY A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 473 Processing helix chain 'A' and resid 495 through 510 Processing helix chain 'A' and resid 528 through 533 Processing helix chain 'A' and resid 556 through 561 Processing helix chain 'A' and resid 580 through 592 Processing helix chain 'A' and resid 600 through 620 removed outlier: 3.675A pdb=" N GLU A 620 " --> pdb=" O ASP A 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 54 Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'C' and resid 136 through 141 Processing helix chain 'C' and resid 162 through 167 removed outlier: 3.554A pdb=" N PHE C 167 " --> pdb=" O ARG C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 181 Processing helix chain 'C' and resid 183 through 187 Processing helix chain 'C' and resid 223 through 247 removed outlier: 3.935A pdb=" N GLN C 235 " --> pdb=" O ALA C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 269 Processing helix chain 'C' and resid 304 through 308 Processing helix chain 'C' and resid 309 through 319 Processing helix chain 'C' and resid 355 through 366 Processing helix chain 'C' and resid 411 through 458 Processing helix chain 'C' and resid 459 through 465 Processing helix chain 'C' and resid 469 through 473 Processing helix chain 'C' and resid 495 through 510 Processing helix chain 'C' and resid 520 through 525 Processing helix chain 'C' and resid 528 through 533 Processing helix chain 'C' and resid 534 through 536 No H-bonds generated for 'chain 'C' and resid 534 through 536' Processing helix chain 'C' and resid 556 through 561 removed outlier: 3.591A pdb=" N ILE C 561 " --> pdb=" O ALA C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 592 Processing helix chain 'C' and resid 600 through 621 Processing sheet with id=AA1, first strand: chain 'A' and resid 113 through 114 removed outlier: 6.522A pdb=" N ALA A 122 " --> pdb=" O ILE A 131 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N TYR A 133 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N MET A 120 " --> pdb=" O TYR A 133 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 302 through 303 removed outlier: 5.645A pdb=" N VAL A 286 " --> pdb=" O LYS A 277 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LYS A 277 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA A 288 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N TRP A 397 " --> pdb=" O PHE A 278 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL A 375 " --> pdb=" O TRP A 397 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N LEU A 399 " --> pdb=" O MET A 373 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N MET A 373 " --> pdb=" O LEU A 399 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N VAL A 401 " --> pdb=" O LEU A 371 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEU A 371 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N HIS A 403 " --> pdb=" O ALA A 369 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA A 369 " --> pdb=" O HIS A 403 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 486 through 491 Processing sheet with id=AA4, first strand: chain 'A' and resid 486 through 491 Processing sheet with id=AA5, first strand: chain 'B' and resid 18 through 23 Processing sheet with id=AA6, first strand: chain 'C' and resid 113 through 114 removed outlier: 6.557A pdb=" N ALA C 122 " --> pdb=" O ILE C 131 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N TYR C 133 " --> pdb=" O MET C 120 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N MET C 120 " --> pdb=" O TYR C 133 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 302 through 303 removed outlier: 6.480A pdb=" N VAL C 275 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLU C 289 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL C 273 " --> pdb=" O GLU C 289 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N TRP C 397 " --> pdb=" O PHE C 278 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL C 375 " --> pdb=" O TRP C 397 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LEU C 399 " --> pdb=" O MET C 373 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N MET C 373 " --> pdb=" O LEU C 399 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N VAL C 401 " --> pdb=" O LEU C 371 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LEU C 371 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N HIS C 403 " --> pdb=" O ALA C 369 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ALA C 369 " --> pdb=" O HIS C 403 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 486 through 491 491 hydrogen bonds defined for protein. 1320 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: 3.85 Time building geometry restraints manager: 1.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8152 1.03 - 1.23: 37 1.23 - 1.42: 3525 1.42 - 1.62: 4808 1.62 - 1.81: 105 Bond restraints: 16627 Sorted by residual: bond pdb=" CAP O6E A1201 " pdb=" CBL O6E A1201 " ideal model delta sigma weight residual 1.448 1.324 0.124 2.00e-02 2.50e+03 3.83e+01 bond pdb=" CAC O6E A1201 " pdb=" CAH O6E A1201 " ideal model delta sigma weight residual 1.522 1.636 -0.114 2.00e-02 2.50e+03 3.27e+01 bond pdb=" CAP O6E C1201 " pdb=" CBL O6E C1201 " ideal model delta sigma weight residual 1.448 1.339 0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" CAQ O6E A1201 " pdb=" CAY O6E A1201 " ideal model delta sigma weight residual 1.436 1.358 0.078 2.00e-02 2.50e+03 1.52e+01 bond pdb=" CAB O6E A1201 " pdb=" CBI O6E A1201 " ideal model delta sigma weight residual 1.449 1.372 0.077 2.00e-02 2.50e+03 1.49e+01 ... (remaining 16622 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.26: 29966 4.26 - 8.52: 15 8.52 - 12.78: 0 12.78 - 17.04: 1 17.04 - 21.30: 1 Bond angle restraints: 29983 Sorted by residual: angle pdb=" CAH O6E C1201 " pdb=" CAC O6E C1201 " pdb=" CBJ O6E C1201 " ideal model delta sigma weight residual 112.38 133.68 -21.30 3.00e+00 1.11e-01 5.04e+01 angle pdb=" CAC O6E A1201 " pdb=" CBJ O6E A1201 " pdb=" CBN O6E A1201 " ideal model delta sigma weight residual 111.76 126.50 -14.74 3.00e+00 1.11e-01 2.42e+01 angle pdb=" CAS O6E A1201 " pdb=" CBC O6E A1201 " pdb=" CAW O6E A1201 " ideal model delta sigma weight residual 122.75 130.23 -7.48 3.00e+00 1.11e-01 6.22e+00 angle pdb=" CAP O6E A1201 " pdb=" CAW O6E A1201 " pdb=" NAJ O6E A1201 " ideal model delta sigma weight residual 127.94 121.07 6.87 3.00e+00 1.11e-01 5.25e+00 angle pdb=" CAP O6E A1201 " pdb=" CAW O6E A1201 " pdb=" CBC O6E A1201 " ideal model delta sigma weight residual 125.85 132.63 -6.78 3.00e+00 1.11e-01 5.10e+00 ... (remaining 29978 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.27: 7539 29.27 - 58.55: 298 58.55 - 87.82: 18 87.82 - 117.10: 0 117.10 - 146.37: 1 Dihedral angle restraints: 7856 sinusoidal: 4315 harmonic: 3541 Sorted by residual: dihedral pdb=" CAG O6E C1201 " pdb=" CAB O6E C1201 " pdb=" CBI O6E C1201 " pdb=" CBC O6E C1201 " ideal model delta sinusoidal sigma weight residual -179.89 -33.52 -146.37 1 3.00e+01 1.11e-03 1.95e+01 dihedral pdb=" CG ARG C 446 " pdb=" CD ARG C 446 " pdb=" NE ARG C 446 " pdb=" CZ ARG C 446 " ideal model delta sinusoidal sigma weight residual 90.00 41.35 48.65 2 1.50e+01 4.44e-03 1.20e+01 dihedral pdb=" CA PHE A 201 " pdb=" C PHE A 201 " pdb=" N TYR A 202 " pdb=" CA TYR A 202 " ideal model delta harmonic sigma weight residual 180.00 162.73 17.27 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 7853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.180: 1277 0.180 - 0.360: 2 0.360 - 0.540: 0 0.540 - 0.720: 0 0.720 - 0.900: 1 Chirality restraints: 1280 Sorted by residual: chirality pdb=" CBJ O6E A1201 " pdb=" CAC O6E A1201 " pdb=" CBD O6E A1201 " pdb=" CBN O6E A1201 " both_signs ideal model delta sigma weight residual False 2.70 1.80 0.90 2.00e-01 2.50e+01 2.03e+01 chirality pdb=" CBD O6E C1201 " pdb=" CAT O6E C1201 " pdb=" CAX O6E C1201 " pdb=" CBJ O6E C1201 " both_signs ideal model delta sigma weight residual False -2.69 -2.47 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CBD O6E A1201 " pdb=" CAT O6E A1201 " pdb=" CAX O6E A1201 " pdb=" CBJ O6E A1201 " both_signs ideal model delta sigma weight residual False -2.69 -2.50 -0.19 2.00e-01 2.50e+01 9.19e-01 ... (remaining 1277 not shown) Planarity restraints: 2465 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAB O6E A1201 " -0.606 2.00e-02 2.50e+03 3.26e-01 2.66e+03 pdb=" CAP O6E A1201 " -0.253 2.00e-02 2.50e+03 pdb=" CAS O6E A1201 " 0.598 2.00e-02 2.50e+03 pdb=" CAW O6E A1201 " 0.041 2.00e-02 2.50e+03 pdb=" CBC O6E A1201 " 0.162 2.00e-02 2.50e+03 pdb=" CBI O6E A1201 " -0.129 2.00e-02 2.50e+03 pdb=" CBL O6E A1201 " -0.325 2.00e-02 2.50e+03 pdb=" CBM O6E A1201 " 0.101 2.00e-02 2.50e+03 pdb=" NAJ O6E A1201 " 0.330 2.00e-02 2.50e+03 pdb=" OAK O6E A1201 " 0.081 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAA O6E C1201 " -0.483 2.00e-02 2.50e+03 2.87e-01 2.06e+03 pdb=" CAO O6E C1201 " 0.114 2.00e-02 2.50e+03 pdb=" CAP O6E C1201 " -0.413 2.00e-02 2.50e+03 pdb=" CAR O6E C1201 " 0.576 2.00e-02 2.50e+03 pdb=" CAV O6E C1201 " 0.008 2.00e-02 2.50e+03 pdb=" CBB O6E C1201 " -0.129 2.00e-02 2.50e+03 pdb=" CBH O6E C1201 " 0.139 2.00e-02 2.50e+03 pdb=" CBL O6E C1201 " -0.056 2.00e-02 2.50e+03 pdb=" CBO O6E C1201 " 0.178 2.00e-02 2.50e+03 pdb=" NAE O6E C1201 " 0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAB O6E C1201 " 0.014 2.00e-02 2.50e+03 1.56e-01 6.10e+02 pdb=" CAP O6E C1201 " -0.387 2.00e-02 2.50e+03 pdb=" CAS O6E C1201 " 0.011 2.00e-02 2.50e+03 pdb=" CAW O6E C1201 " -0.045 2.00e-02 2.50e+03 pdb=" CBC O6E C1201 " 0.001 2.00e-02 2.50e+03 pdb=" CBI O6E C1201 " 0.001 2.00e-02 2.50e+03 pdb=" CBL O6E C1201 " 0.259 2.00e-02 2.50e+03 pdb=" CBM O6E C1201 " 0.021 2.00e-02 2.50e+03 pdb=" NAJ O6E C1201 " 0.153 2.00e-02 2.50e+03 pdb=" OAK O6E C1201 " -0.030 2.00e-02 2.50e+03 ... (remaining 2462 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.14: 489 2.14 - 2.76: 31151 2.76 - 3.37: 47240 3.37 - 3.99: 61780 3.99 - 4.60: 98517 Nonbonded interactions: 239177 Sorted by model distance: nonbonded pdb=" OE1 GLU C 560 " pdb=" H GLU C 560 " model vdw 1.530 2.450 nonbonded pdb="HH12 ARG A 272 " pdb=" O GLU A 296 " model vdw 1.602 2.450 nonbonded pdb=" OE2 GLU C 560 " pdb="HE21 GLN C 597 " model vdw 1.616 2.450 nonbonded pdb=" O THR C 514 " pdb="HE22 GLN C 611 " model vdw 1.621 2.450 nonbonded pdb=" O LYS C 475 " pdb="HH21 ARG C 554 " model vdw 1.631 2.450 ... (remaining 239172 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 111 and (name N or name CA or name C or name O or name HA \ 2 or name HA3)) or resid 112 through 356 or (resid 357 and (name N or name CA or \ name C or name O or name CB or name SG or name H or name HA or name HB2 or name \ HB3)) or resid 358 through 565 or (resid 577 and (name N or name CA or name C o \ r name O or name CB or name CG or name CD or name OE1 or name NE2 or name HA or \ name HB2 or name HB3 or name HG2 or name HG3 or name HE21 or name HE22)) or resi \ d 578 through 1201)) selection = (chain 'C' and (resid 111 through 143 or resid 156 through 192 or (resid 193 and \ (name N or name CA or name C or name O or name CB or name CG or name ND1 or nam \ e CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or na \ me HD1 or name HD2 or name HE1)) or resid 194 through 321 or (resid 322 and (nam \ e N or name CA or name C or name O or name CB or name CG or name CD or name NE o \ r name CZ or name NH1 or name NH2 or name H or name HA or name HB2 or name HB3 o \ r name HG2 or name HG3 or name HD2 or name HD3 or name HE or name HH11 or name H \ H21)) or resid 323 through 1201)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.500 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: 0.060 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 16.820 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 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 : 0.004 0.124 8456 Z= 0.235 Angle : 0.584 21.302 11440 Z= 0.284 Chirality : 0.047 0.900 1280 Planarity : 0.014 0.326 1464 Dihedral : 14.318 146.372 3162 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.78 % Allowed : 9.53 % Favored : 89.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 2.13 (0.27), residues: 1032 helix: 3.05 (0.24), residues: 440 sheet: -0.27 (0.38), residues: 168 loop : 0.44 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 446 TYR 0.011 0.001 TYR A 298 PHE 0.016 0.001 PHE A 420 TRP 0.004 0.001 TRP A 397 HIS 0.004 0.001 HIS A 556 Details of bonding type rmsd covalent geometry : bond 0.00440 ( 8454) covalent geometry : angle 0.58411 (11440) hydrogen bonds : bond 0.11504 ( 479) hydrogen bonds : angle 5.41381 ( 1320) Misc. bond : bond 0.05855 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 125 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 GLU cc_start: 0.8087 (tt0) cc_final: 0.7644 (mp0) REVERT: A 559 LYS cc_start: 0.8386 (tttt) cc_final: 0.7957 (ttmp) REVERT: A 597 GLN cc_start: 0.8108 (mt0) cc_final: 0.7297 (mp10) REVERT: B 16 GLU cc_start: 0.8169 (tt0) cc_final: 0.7716 (mp0) REVERT: B 59 MET cc_start: 0.8482 (mmm) cc_final: 0.8208 (mmm) REVERT: C 177 ARG cc_start: 0.7011 (mtt180) cc_final: 0.6394 (mtp180) REVERT: C 187 LEU cc_start: 0.6825 (tp) cc_final: 0.6393 (pp) REVERT: C 195 LYS cc_start: 0.8541 (tttt) cc_final: 0.7899 (ttmt) REVERT: C 199 LYS cc_start: 0.8436 (mmtt) cc_final: 0.8070 (mmtm) REVERT: C 280 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7817 (mt-10) REVERT: C 318 GLN cc_start: 0.7662 (OUTLIER) cc_final: 0.7300 (mp10) REVERT: C 335 VAL cc_start: 0.8067 (t) cc_final: 0.7850 (m) REVERT: C 360 GLN cc_start: 0.7794 (tp40) cc_final: 0.7527 (mm-40) REVERT: C 440 SER cc_start: 0.8013 (m) cc_final: 0.7626 (p) REVERT: C 475 LYS cc_start: 0.7283 (tttm) cc_final: 0.6790 (tttm) outliers start: 7 outliers final: 4 residues processed: 129 average time/residue: 1.3562 time to fit residues: 184.5920 Evaluate side-chains 125 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 120 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain A residue 416 TYR Chi-restraints excluded: chain C residue 317 LYS Chi-restraints excluded: chain C residue 318 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 428 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.141321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.103187 restraints weight = 24122.313| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 1.70 r_work: 0.2867 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.0723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8456 Z= 0.160 Angle : 0.495 9.065 11440 Z= 0.251 Chirality : 0.039 0.155 1280 Planarity : 0.005 0.051 1464 Dihedral : 6.904 75.844 1234 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.12 % Allowed : 9.53 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 2.09 (0.27), residues: 1032 helix: 2.98 (0.24), residues: 447 sheet: -0.32 (0.37), residues: 168 loop : 0.43 (0.32), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 446 TYR 0.010 0.001 TYR C 416 PHE 0.014 0.001 PHE A 420 TRP 0.005 0.001 TRP C 397 HIS 0.005 0.001 HIS C 556 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 8454) covalent geometry : angle 0.49518 (11440) hydrogen bonds : bond 0.04190 ( 479) hydrogen bonds : angle 4.70766 ( 1320) Misc. bond : bond 0.00141 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 126 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 GLU cc_start: 0.8138 (tt0) cc_final: 0.7739 (mp0) REVERT: A 559 LYS cc_start: 0.8445 (tttt) cc_final: 0.8017 (ttmp) REVERT: B 16 GLU cc_start: 0.8278 (tt0) cc_final: 0.7845 (mp0) REVERT: B 30 LYS cc_start: 0.7642 (ttmt) cc_final: 0.7426 (pttp) REVERT: B 59 MET cc_start: 0.8479 (mmm) cc_final: 0.8224 (mmm) REVERT: C 177 ARG cc_start: 0.6997 (mtt180) cc_final: 0.6416 (mtp180) REVERT: C 187 LEU cc_start: 0.6959 (tp) cc_final: 0.6510 (pp) REVERT: C 199 LYS cc_start: 0.8508 (mmtt) cc_final: 0.8178 (mmtm) REVERT: C 280 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7834 (mt-10) REVERT: C 318 GLN cc_start: 0.7874 (OUTLIER) cc_final: 0.7516 (mp10) REVERT: C 360 GLN cc_start: 0.8007 (tp40) cc_final: 0.7765 (tm-30) REVERT: C 440 SER cc_start: 0.8145 (m) cc_final: 0.7787 (p) REVERT: C 441 GLU cc_start: 0.7588 (mt-10) cc_final: 0.7304 (tt0) REVERT: C 475 LYS cc_start: 0.7617 (tttm) cc_final: 0.7074 (tttt) outliers start: 10 outliers final: 4 residues processed: 130 average time/residue: 1.5141 time to fit residues: 207.7831 Evaluate side-chains 124 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 119 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain A residue 416 TYR Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain C residue 318 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 13 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 428 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.138797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.100953 restraints weight = 24366.052| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 1.69 r_work: 0.2826 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8456 Z= 0.185 Angle : 0.510 9.297 11440 Z= 0.257 Chirality : 0.040 0.152 1280 Planarity : 0.005 0.067 1464 Dihedral : 6.823 75.209 1229 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.23 % Allowed : 10.31 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.89 (0.27), residues: 1032 helix: 2.82 (0.24), residues: 448 sheet: -0.50 (0.36), residues: 185 loop : 0.38 (0.33), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 446 TYR 0.014 0.001 TYR C 416 PHE 0.013 0.001 PHE A 117 TRP 0.006 0.001 TRP C 397 HIS 0.005 0.001 HIS C 556 Details of bonding type rmsd covalent geometry : bond 0.00449 ( 8454) covalent geometry : angle 0.51049 (11440) hydrogen bonds : bond 0.04322 ( 479) hydrogen bonds : angle 4.64555 ( 1320) Misc. bond : bond 0.00144 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 GLU cc_start: 0.8036 (tt0) cc_final: 0.7621 (mp0) REVERT: A 559 LYS cc_start: 0.8415 (tttt) cc_final: 0.7807 (ttmt) REVERT: B 16 GLU cc_start: 0.8238 (tt0) cc_final: 0.7778 (mp0) REVERT: C 120 MET cc_start: 0.8893 (OUTLIER) cc_final: 0.8180 (ttp) REVERT: C 177 ARG cc_start: 0.6881 (mtt180) cc_final: 0.6229 (mtp180) REVERT: C 199 LYS cc_start: 0.8468 (mmtt) cc_final: 0.8163 (mmtm) REVERT: C 280 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7833 (mt-10) REVERT: C 318 GLN cc_start: 0.7845 (OUTLIER) cc_final: 0.7499 (mp10) REVERT: C 360 GLN cc_start: 0.7886 (tp40) cc_final: 0.7672 (mm-40) REVERT: C 440 SER cc_start: 0.8000 (m) cc_final: 0.7651 (p) REVERT: C 441 GLU cc_start: 0.7489 (mt-10) cc_final: 0.7262 (tt0) REVERT: C 475 LYS cc_start: 0.7493 (tttm) cc_final: 0.6989 (tttt) REVERT: C 489 PRO cc_start: 0.8487 (Cg_endo) cc_final: 0.7858 (Cg_exo) outliers start: 11 outliers final: 4 residues processed: 125 average time/residue: 1.5566 time to fit residues: 205.1240 Evaluate side-chains 122 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 116 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 416 TYR Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain C residue 120 MET Chi-restraints excluded: chain C residue 318 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 7 optimal weight: 0.9990 chunk 92 optimal weight: 0.0030 chunk 21 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 94 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 overall best weight: 0.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 577 GLN C 428 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.141244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.103249 restraints weight = 24167.292| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.70 r_work: 0.2865 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8456 Z= 0.118 Angle : 0.456 8.051 11440 Z= 0.229 Chirality : 0.038 0.150 1280 Planarity : 0.005 0.066 1464 Dihedral : 6.494 77.878 1229 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.23 % Allowed : 10.99 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.98 (0.27), residues: 1032 helix: 3.00 (0.24), residues: 448 sheet: -0.58 (0.37), residues: 176 loop : 0.35 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 446 TYR 0.010 0.001 TYR A 276 PHE 0.012 0.001 PHE A 420 TRP 0.004 0.001 TRP A 397 HIS 0.004 0.001 HIS A 206 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 8454) covalent geometry : angle 0.45571 (11440) hydrogen bonds : bond 0.03753 ( 479) hydrogen bonds : angle 4.43195 ( 1320) Misc. bond : bond 0.00089 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 119 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 THR cc_start: 0.7696 (m) cc_final: 0.7398 (p) REVERT: A 217 GLU cc_start: 0.8035 (tt0) cc_final: 0.7662 (mt-10) REVERT: A 559 LYS cc_start: 0.8428 (tttt) cc_final: 0.7846 (ttmt) REVERT: B 16 GLU cc_start: 0.8234 (tt0) cc_final: 0.7796 (mp0) REVERT: B 30 LYS cc_start: 0.7721 (ttmt) cc_final: 0.7505 (pttp) REVERT: C 177 ARG cc_start: 0.6985 (mtt180) cc_final: 0.6344 (mtp180) REVERT: C 199 LYS cc_start: 0.8518 (mmtt) cc_final: 0.8192 (mmtm) REVERT: C 280 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7829 (mt-10) REVERT: C 440 SER cc_start: 0.8033 (m) cc_final: 0.7686 (p) REVERT: C 441 GLU cc_start: 0.7544 (mt-10) cc_final: 0.7323 (tt0) REVERT: C 475 LYS cc_start: 0.7619 (tttm) cc_final: 0.7085 (tttm) REVERT: C 489 PRO cc_start: 0.8479 (Cg_endo) cc_final: 0.7868 (Cg_exo) outliers start: 11 outliers final: 3 residues processed: 125 average time/residue: 1.3813 time to fit residues: 182.3131 Evaluate side-chains 117 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 114 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain A residue 416 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 378 ASN A 577 GLN C 428 GLN C 597 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.140706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.101870 restraints weight = 24161.935| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 1.80 r_work: 0.2888 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8456 Z= 0.147 Angle : 0.474 8.858 11440 Z= 0.237 Chirality : 0.039 0.149 1280 Planarity : 0.005 0.074 1464 Dihedral : 6.329 77.477 1226 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.12 % Allowed : 11.32 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.95 (0.27), residues: 1032 helix: 2.98 (0.24), residues: 448 sheet: -0.51 (0.37), residues: 180 loop : 0.28 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 446 TYR 0.012 0.001 TYR C 416 PHE 0.011 0.001 PHE A 117 TRP 0.005 0.001 TRP A 397 HIS 0.004 0.001 HIS A 206 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 8454) covalent geometry : angle 0.47379 (11440) hydrogen bonds : bond 0.03879 ( 479) hydrogen bonds : angle 4.41599 ( 1320) Misc. bond : bond 0.00114 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 GLU cc_start: 0.8058 (tt0) cc_final: 0.7696 (mp0) REVERT: A 266 ASP cc_start: 0.8875 (OUTLIER) cc_final: 0.8551 (t0) REVERT: A 559 LYS cc_start: 0.8405 (tttt) cc_final: 0.7816 (ttmt) REVERT: B 16 GLU cc_start: 0.8215 (tt0) cc_final: 0.7814 (mp0) REVERT: B 30 LYS cc_start: 0.7738 (ttmt) cc_final: 0.7506 (pttp) REVERT: C 177 ARG cc_start: 0.6948 (mtt180) cc_final: 0.6303 (mtp180) REVERT: C 199 LYS cc_start: 0.8533 (mmtt) cc_final: 0.8208 (mmtm) REVERT: C 280 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7840 (mt-10) REVERT: C 440 SER cc_start: 0.8021 (m) cc_final: 0.7694 (p) REVERT: C 441 GLU cc_start: 0.7519 (mt-10) cc_final: 0.7308 (tt0) REVERT: C 454 MET cc_start: 0.6255 (mtm) cc_final: 0.5897 (mtt) REVERT: C 475 LYS cc_start: 0.7636 (tttm) cc_final: 0.7068 (tttt) REVERT: C 489 PRO cc_start: 0.8479 (Cg_endo) cc_final: 0.7885 (Cg_exo) outliers start: 10 outliers final: 4 residues processed: 124 average time/residue: 1.4819 time to fit residues: 194.0934 Evaluate side-chains 120 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 115 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 416 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 69 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 378 ASN A 577 GLN C 428 GLN C 597 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.139860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.102046 restraints weight = 24100.994| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 1.71 r_work: 0.2841 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8456 Z= 0.141 Angle : 0.470 8.700 11440 Z= 0.235 Chirality : 0.039 0.149 1280 Planarity : 0.005 0.080 1464 Dihedral : 6.326 78.182 1226 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.90 % Allowed : 12.33 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.97 (0.27), residues: 1032 helix: 3.01 (0.24), residues: 448 sheet: -0.47 (0.37), residues: 174 loop : 0.25 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 446 TYR 0.012 0.001 TYR C 416 PHE 0.010 0.001 PHE A 420 TRP 0.005 0.001 TRP A 397 HIS 0.004 0.001 HIS A 206 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 8454) covalent geometry : angle 0.47032 (11440) hydrogen bonds : bond 0.03811 ( 479) hydrogen bonds : angle 4.36189 ( 1320) Misc. bond : bond 0.00109 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 123 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 217 GLU cc_start: 0.8017 (tt0) cc_final: 0.7606 (mt-10) REVERT: A 543 TYR cc_start: 0.8431 (m-80) cc_final: 0.8165 (m-80) REVERT: A 559 LYS cc_start: 0.8386 (tttt) cc_final: 0.7787 (ttmt) REVERT: B 16 GLU cc_start: 0.8216 (tt0) cc_final: 0.7771 (mp0) REVERT: B 30 LYS cc_start: 0.7692 (ttmt) cc_final: 0.7405 (pttp) REVERT: C 177 ARG cc_start: 0.6846 (mtt180) cc_final: 0.6206 (mtp180) REVERT: C 199 LYS cc_start: 0.8523 (mmtt) cc_final: 0.8192 (mmtm) REVERT: C 360 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.7364 (tm-30) REVERT: C 439 MET cc_start: 0.7748 (mmt) cc_final: 0.7447 (mmm) REVERT: C 440 SER cc_start: 0.7936 (m) cc_final: 0.7615 (p) REVERT: C 454 MET cc_start: 0.6087 (mtm) cc_final: 0.5749 (mtt) REVERT: C 475 LYS cc_start: 0.7594 (tttm) cc_final: 0.7047 (tttt) REVERT: C 489 PRO cc_start: 0.8451 (Cg_endo) cc_final: 0.7877 (Cg_exo) outliers start: 8 outliers final: 3 residues processed: 127 average time/residue: 1.5476 time to fit residues: 207.4905 Evaluate side-chains 122 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 118 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 416 TYR Chi-restraints excluded: chain C residue 360 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 56 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 378 ASN C 428 GLN C 597 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.139969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.101858 restraints weight = 24062.653| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 1.73 r_work: 0.2837 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8456 Z= 0.142 Angle : 0.476 8.817 11440 Z= 0.237 Chirality : 0.039 0.148 1280 Planarity : 0.005 0.086 1464 Dihedral : 6.063 78.576 1223 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.23 % Allowed : 12.44 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.95 (0.27), residues: 1032 helix: 3.02 (0.24), residues: 448 sheet: -0.47 (0.36), residues: 180 loop : 0.20 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 446 TYR 0.012 0.001 TYR C 416 PHE 0.010 0.001 PHE A 420 TRP 0.005 0.001 TRP A 397 HIS 0.004 0.001 HIS A 206 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 8454) covalent geometry : angle 0.47605 (11440) hydrogen bonds : bond 0.03810 ( 479) hydrogen bonds : angle 4.34240 ( 1320) Misc. bond : bond 0.00110 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 121 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 217 GLU cc_start: 0.8031 (tt0) cc_final: 0.7622 (mt-10) REVERT: A 266 ASP cc_start: 0.8834 (OUTLIER) cc_final: 0.8511 (t0) REVERT: A 440 SER cc_start: 0.8001 (OUTLIER) cc_final: 0.7573 (p) REVERT: A 442 LYS cc_start: 0.7642 (mttm) cc_final: 0.7410 (ttmm) REVERT: A 559 LYS cc_start: 0.8366 (tttt) cc_final: 0.7759 (ttmt) REVERT: B 16 GLU cc_start: 0.8226 (tt0) cc_final: 0.7775 (mp0) REVERT: B 30 LYS cc_start: 0.7695 (ttmt) cc_final: 0.7396 (pttp) REVERT: C 177 ARG cc_start: 0.6879 (mtt180) cc_final: 0.6243 (mtp180) REVERT: C 199 LYS cc_start: 0.8519 (mmtt) cc_final: 0.8190 (mmtm) REVERT: C 360 GLN cc_start: 0.7967 (OUTLIER) cc_final: 0.7316 (tm-30) REVERT: C 439 MET cc_start: 0.7753 (mmt) cc_final: 0.7448 (mmm) REVERT: C 440 SER cc_start: 0.8000 (m) cc_final: 0.7676 (p) REVERT: C 475 LYS cc_start: 0.7589 (tttm) cc_final: 0.7065 (tttm) REVERT: C 489 PRO cc_start: 0.8465 (Cg_endo) cc_final: 0.7889 (Cg_exo) outliers start: 11 outliers final: 4 residues processed: 126 average time/residue: 1.3957 time to fit residues: 185.7993 Evaluate side-chains 124 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 117 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 416 TYR Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain C residue 360 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 1.9990 chunk 75 optimal weight: 0.0670 chunk 12 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 79 optimal weight: 0.0170 overall best weight: 0.5556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 378 ASN C 428 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.142971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.105519 restraints weight = 24069.421| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 1.71 r_work: 0.2879 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8456 Z= 0.099 Angle : 0.441 7.349 11440 Z= 0.222 Chirality : 0.038 0.145 1280 Planarity : 0.005 0.090 1464 Dihedral : 5.819 81.097 1223 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.78 % Allowed : 12.67 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 2.11 (0.27), residues: 1032 helix: 3.22 (0.24), residues: 447 sheet: -0.52 (0.37), residues: 171 loop : 0.27 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 446 TYR 0.009 0.001 TYR A 276 PHE 0.011 0.001 PHE A 420 TRP 0.004 0.001 TRP A 397 HIS 0.004 0.001 HIS A 206 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 8454) covalent geometry : angle 0.44087 (11440) hydrogen bonds : bond 0.03440 ( 479) hydrogen bonds : angle 4.20581 ( 1320) Misc. bond : bond 0.00068 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 120 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 217 GLU cc_start: 0.8007 (tt0) cc_final: 0.7639 (mt-10) REVERT: A 266 ASP cc_start: 0.8826 (OUTLIER) cc_final: 0.8485 (OUTLIER) REVERT: A 442 LYS cc_start: 0.7741 (mttm) cc_final: 0.7510 (ttmm) REVERT: A 559 LYS cc_start: 0.8398 (tttt) cc_final: 0.7790 (ttmt) REVERT: B 16 GLU cc_start: 0.8164 (tt0) cc_final: 0.7777 (mp0) REVERT: B 30 LYS cc_start: 0.7656 (ttmt) cc_final: 0.7394 (pttp) REVERT: C 159 MET cc_start: 0.8350 (mmt) cc_final: 0.8110 (mmt) REVERT: C 177 ARG cc_start: 0.6875 (mtt180) cc_final: 0.6243 (mtp180) REVERT: C 199 LYS cc_start: 0.8539 (mmtt) cc_final: 0.8220 (mmtm) REVERT: C 440 SER cc_start: 0.8008 (m) cc_final: 0.7719 (p) REVERT: C 475 LYS cc_start: 0.7573 (tttm) cc_final: 0.7068 (tttm) REVERT: C 489 PRO cc_start: 0.8469 (Cg_endo) cc_final: 0.7886 (Cg_exo) outliers start: 7 outliers final: 3 residues processed: 124 average time/residue: 1.4291 time to fit residues: 187.0114 Evaluate side-chains 119 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 116 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 416 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 20 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 33 optimal weight: 0.4980 chunk 65 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 91 optimal weight: 8.9990 chunk 5 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 378 ASN A 577 GLN C 428 GLN C 597 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.138512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.098385 restraints weight = 24207.938| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 1.86 r_work: 0.2792 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2649 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8456 Z= 0.182 Angle : 0.513 9.972 11440 Z= 0.255 Chirality : 0.040 0.148 1280 Planarity : 0.005 0.094 1464 Dihedral : 6.211 77.955 1223 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.90 % Allowed : 13.23 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.89 (0.27), residues: 1032 helix: 3.00 (0.24), residues: 448 sheet: -0.58 (0.35), residues: 190 loop : 0.22 (0.33), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 446 TYR 0.015 0.001 TYR C 416 PHE 0.014 0.001 PHE A 551 TRP 0.006 0.001 TRP C 397 HIS 0.005 0.001 HIS A 68 Details of bonding type rmsd covalent geometry : bond 0.00444 ( 8454) covalent geometry : angle 0.51344 (11440) hydrogen bonds : bond 0.04044 ( 479) hydrogen bonds : angle 4.36438 ( 1320) Misc. bond : bond 0.00141 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 119 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 217 GLU cc_start: 0.8078 (tt0) cc_final: 0.7621 (mt-10) REVERT: A 266 ASP cc_start: 0.8879 (OUTLIER) cc_final: 0.8559 (t0) REVERT: A 440 SER cc_start: 0.8062 (m) cc_final: 0.7623 (p) REVERT: A 442 LYS cc_start: 0.7703 (mttm) cc_final: 0.7460 (ttmm) REVERT: A 559 LYS cc_start: 0.8373 (tttt) cc_final: 0.7774 (ttmt) REVERT: A 586 GLN cc_start: 0.7958 (tp40) cc_final: 0.7669 (mm110) REVERT: B 16 GLU cc_start: 0.8262 (tt0) cc_final: 0.7797 (mp0) REVERT: B 30 LYS cc_start: 0.7709 (ttmt) cc_final: 0.7385 (pttp) REVERT: C 177 ARG cc_start: 0.6919 (mtt180) cc_final: 0.6256 (mtp180) REVERT: C 199 LYS cc_start: 0.8557 (mmtt) cc_final: 0.8336 (mmtm) REVERT: C 439 MET cc_start: 0.7763 (mmt) cc_final: 0.7479 (mmm) REVERT: C 440 SER cc_start: 0.8068 (m) cc_final: 0.7778 (p) REVERT: C 475 LYS cc_start: 0.7498 (tttm) cc_final: 0.7081 (tttm) REVERT: C 489 PRO cc_start: 0.8451 (Cg_endo) cc_final: 0.7863 (Cg_exo) outliers start: 8 outliers final: 5 residues processed: 124 average time/residue: 1.3884 time to fit residues: 182.1309 Evaluate side-chains 123 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 117 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 416 TYR Chi-restraints excluded: chain A residue 504 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 2 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 96 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 chunk 63 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 378 ASN C 428 GLN C 597 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.139843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.101204 restraints weight = 24002.869| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 1.80 r_work: 0.2825 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8456 Z= 0.159 Angle : 0.492 9.273 11440 Z= 0.246 Chirality : 0.039 0.148 1280 Planarity : 0.005 0.095 1464 Dihedral : 6.179 78.735 1223 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.90 % Allowed : 13.23 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.86 (0.27), residues: 1032 helix: 2.97 (0.24), residues: 448 sheet: -0.58 (0.36), residues: 184 loop : 0.18 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 446 TYR 0.015 0.001 TYR A 543 PHE 0.012 0.001 PHE A 551 TRP 0.006 0.001 TRP A 397 HIS 0.004 0.001 HIS A 206 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 8454) covalent geometry : angle 0.49220 (11440) hydrogen bonds : bond 0.03910 ( 479) hydrogen bonds : angle 4.34742 ( 1320) Misc. bond : bond 0.00123 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 114 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 217 GLU cc_start: 0.8014 (tt0) cc_final: 0.7614 (mt-10) REVERT: A 266 ASP cc_start: 0.8881 (OUTLIER) cc_final: 0.8549 (t0) REVERT: A 442 LYS cc_start: 0.7761 (mttm) cc_final: 0.7509 (ttmm) REVERT: A 559 LYS cc_start: 0.8398 (tttt) cc_final: 0.7815 (ttmt) REVERT: B 16 GLU cc_start: 0.8187 (tt0) cc_final: 0.7815 (mp0) REVERT: B 30 LYS cc_start: 0.7648 (ttmt) cc_final: 0.7401 (pttp) REVERT: C 177 ARG cc_start: 0.7011 (mtt180) cc_final: 0.6358 (mtp180) REVERT: C 199 LYS cc_start: 0.8571 (mmtt) cc_final: 0.8361 (mmtm) REVERT: C 439 MET cc_start: 0.7801 (mmt) cc_final: 0.7530 (mmm) REVERT: C 440 SER cc_start: 0.8181 (m) cc_final: 0.7905 (p) REVERT: C 475 LYS cc_start: 0.7502 (tttm) cc_final: 0.7094 (tttm) REVERT: C 489 PRO cc_start: 0.8507 (Cg_endo) cc_final: 0.7921 (Cg_exo) REVERT: C 560 GLU cc_start: 0.7609 (pm20) cc_final: 0.7326 (pm20) outliers start: 8 outliers final: 5 residues processed: 119 average time/residue: 1.4068 time to fit residues: 176.8771 Evaluate side-chains 121 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 115 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 416 TYR Chi-restraints excluded: chain A residue 504 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 6 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 79 optimal weight: 0.3980 chunk 76 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 428 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.139026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.101093 restraints weight = 24070.570| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 1.73 r_work: 0.2826 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8456 Z= 0.157 Angle : 0.491 9.217 11440 Z= 0.246 Chirality : 0.039 0.148 1280 Planarity : 0.005 0.095 1464 Dihedral : 6.168 79.053 1223 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.67 % Allowed : 13.45 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.87 (0.27), residues: 1032 helix: 2.98 (0.24), residues: 448 sheet: -0.65 (0.35), residues: 190 loop : 0.23 (0.33), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 446 TYR 0.013 0.001 TYR A 543 PHE 0.012 0.001 PHE A 551 TRP 0.006 0.001 TRP A 397 HIS 0.005 0.001 HIS A 206 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 8454) covalent geometry : angle 0.49134 (11440) hydrogen bonds : bond 0.03900 ( 479) hydrogen bonds : angle 4.34687 ( 1320) Misc. bond : bond 0.00121 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6172.01 seconds wall clock time: 104 minutes 59.50 seconds (6299.50 seconds total)