Starting phenix.real_space_refine on Fri Jul 3 18:38:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vnq_32045/07_2026/7vnq_32045_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vnq_32045/07_2026/7vnq_32045.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vnq_32045/07_2026/7vnq_32045.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vnq_32045/07_2026/7vnq_32045.map" model { file = "/net/cci-nas-00/data/ceres_data/7vnq_32045/07_2026/7vnq_32045_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vnq_32045/07_2026/7vnq_32045_trim.cif" } resolution = 2.96 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= -0.000 sd= 0.012 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 K 3 8.98 5 S 88 5.16 5 C 9984 2.51 5 N 2656 2.21 5 O 2776 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15507 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2747 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 6, 'TRANS': 332} Chain breaks: 2 Chain: "B" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1110 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 2, 'TRANS': 138} Chain: "C" Number of atoms: 2747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2747 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 6, 'TRANS': 332} Chain breaks: 2 Chain: "D" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1110 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 2, 'TRANS': 138} Chain: "E" Number of atoms: 2747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2747 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 6, 'TRANS': 332} Chain breaks: 2 Chain: "F" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1110 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 2, 'TRANS': 138} Chain: "G" Number of atoms: 2747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2747 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 6, 'TRANS': 332} Chain breaks: 2 Chain: "H" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1110 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 2, 'TRANS': 138} Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 19 Ad-hoc single atom residues: {' K': 3} Unusual residues: {'7YV': 1} Classifications: {'undetermined': 1} Chain breaks: 3 Chain: "C" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'7YV': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'7YV': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'7YV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.43, per 1000 atoms: 0.22 Number of scatterers: 15507 At special positions: 0 Unit cell: (120.54, 120.54, 121.36, 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) K 3 19.00 S 88 16.00 O 2776 8.00 N 2656 7.00 C 9984 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.35 Conformation dependent library (CDL) restraints added in 734.9 milliseconds 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3576 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 8 sheets defined 78.8% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 74 through 96 removed outlier: 3.828A pdb=" N ARG A 93 " --> pdb=" O ASN A 89 " (cutoff:3.500A) Proline residue: A 94 - end of helix Processing helix chain 'A' and resid 98 through 121 Processing helix chain 'A' and resid 125 through 154 removed outlier: 3.627A pdb=" N ILE A 148 " --> pdb=" O GLY A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 169 Processing helix chain 'A' and resid 173 through 191 Processing helix chain 'A' and resid 200 through 216 Processing helix chain 'A' and resid 222 through 234 Processing helix chain 'A' and resid 234 through 261 Processing helix chain 'A' and resid 269 through 282 removed outlier: 3.802A pdb=" N THR A 282 " --> pdb=" O THR A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 308 removed outlier: 3.614A pdb=" N VAL A 298 " --> pdb=" O TRP A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 311 No H-bonds generated for 'chain 'A' and resid 309 through 311' Processing helix chain 'A' and resid 312 through 335 removed outlier: 3.574A pdb=" N GLY A 316 " --> pdb=" O ALA A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 355 Processing helix chain 'A' and resid 533 through 551 Processing helix chain 'A' and resid 559 through 587 Processing helix chain 'B' and resid 8 through 20 removed outlier: 3.604A pdb=" N PHE B 19 " --> pdb=" O ALA B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 39 Processing helix chain 'B' and resid 44 through 54 Processing helix chain 'B' and resid 65 through 75 Processing helix chain 'B' and resid 78 through 92 removed outlier: 4.072A pdb=" N PHE B 92 " --> pdb=" O ALA B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 112 Processing helix chain 'B' and resid 117 through 128 Processing helix chain 'B' and resid 138 through 146 Processing helix chain 'C' and resid 75 through 96 removed outlier: 3.828A pdb=" N ARG C 93 " --> pdb=" O ASN C 89 " (cutoff:3.500A) Proline residue: C 94 - end of helix Processing helix chain 'C' and resid 98 through 121 Processing helix chain 'C' and resid 125 through 154 removed outlier: 3.627A pdb=" N ILE C 148 " --> pdb=" O GLY C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 169 Processing helix chain 'C' and resid 173 through 191 Processing helix chain 'C' and resid 200 through 216 Processing helix chain 'C' and resid 222 through 234 Processing helix chain 'C' and resid 234 through 261 Processing helix chain 'C' and resid 269 through 282 removed outlier: 3.803A pdb=" N THR C 282 " --> pdb=" O THR C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 308 removed outlier: 3.613A pdb=" N VAL C 298 " --> pdb=" O TRP C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 311 No H-bonds generated for 'chain 'C' and resid 309 through 311' Processing helix chain 'C' and resid 312 through 335 removed outlier: 3.574A pdb=" N GLY C 316 " --> pdb=" O ALA C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 355 Processing helix chain 'C' and resid 533 through 551 Processing helix chain 'C' and resid 559 through 587 Processing helix chain 'D' and resid 8 through 20 removed outlier: 3.605A pdb=" N PHE D 19 " --> pdb=" O ALA D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 39 Processing helix chain 'D' and resid 44 through 54 Processing helix chain 'D' and resid 65 through 75 Processing helix chain 'D' and resid 78 through 92 removed outlier: 4.072A pdb=" N PHE D 92 " --> pdb=" O ALA D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 112 Processing helix chain 'D' and resid 117 through 128 Processing helix chain 'D' and resid 138 through 146 Processing helix chain 'E' and resid 75 through 96 removed outlier: 3.828A pdb=" N ARG E 93 " --> pdb=" O ASN E 89 " (cutoff:3.500A) Proline residue: E 94 - end of helix Processing helix chain 'E' and resid 98 through 121 Processing helix chain 'E' and resid 125 through 154 removed outlier: 3.626A pdb=" N ILE E 148 " --> pdb=" O GLY E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 169 Processing helix chain 'E' and resid 173 through 191 Processing helix chain 'E' and resid 200 through 216 Processing helix chain 'E' and resid 222 through 234 Processing helix chain 'E' and resid 234 through 261 Processing helix chain 'E' and resid 269 through 282 removed outlier: 3.802A pdb=" N THR E 282 " --> pdb=" O THR E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 308 removed outlier: 3.613A pdb=" N VAL E 298 " --> pdb=" O TRP E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 311 No H-bonds generated for 'chain 'E' and resid 309 through 311' Processing helix chain 'E' and resid 312 through 335 removed outlier: 3.575A pdb=" N GLY E 316 " --> pdb=" O ALA E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 355 Processing helix chain 'E' and resid 533 through 551 Processing helix chain 'E' and resid 559 through 587 Processing helix chain 'F' and resid 8 through 20 removed outlier: 3.604A pdb=" N PHE F 19 " --> pdb=" O ALA F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 39 Processing helix chain 'F' and resid 44 through 54 Processing helix chain 'F' and resid 65 through 75 Processing helix chain 'F' and resid 78 through 92 removed outlier: 4.073A pdb=" N PHE F 92 " --> pdb=" O ALA F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 112 Processing helix chain 'F' and resid 117 through 128 Processing helix chain 'F' and resid 138 through 146 Processing helix chain 'G' and resid 75 through 96 removed outlier: 3.829A pdb=" N ARG G 93 " --> pdb=" O ASN G 89 " (cutoff:3.500A) Proline residue: G 94 - end of helix Processing helix chain 'G' and resid 98 through 121 Processing helix chain 'G' and resid 125 through 154 removed outlier: 3.627A pdb=" N ILE G 148 " --> pdb=" O GLY G 144 " (cutoff:3.500A) Processing helix chain 'G' and resid 162 through 169 Processing helix chain 'G' and resid 173 through 191 Processing helix chain 'G' and resid 200 through 216 Processing helix chain 'G' and resid 222 through 234 Processing helix chain 'G' and resid 234 through 261 Processing helix chain 'G' and resid 269 through 282 removed outlier: 3.803A pdb=" N THR G 282 " --> pdb=" O THR G 278 " (cutoff:3.500A) Processing helix chain 'G' and resid 293 through 308 removed outlier: 3.612A pdb=" N VAL G 298 " --> pdb=" O TRP G 294 " (cutoff:3.500A) Processing helix chain 'G' and resid 309 through 311 No H-bonds generated for 'chain 'G' and resid 309 through 311' Processing helix chain 'G' and resid 312 through 335 removed outlier: 3.575A pdb=" N GLY G 316 " --> pdb=" O ALA G 312 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 355 Processing helix chain 'G' and resid 533 through 551 Processing helix chain 'G' and resid 559 through 587 Processing helix chain 'H' and resid 8 through 20 removed outlier: 3.605A pdb=" N PHE H 19 " --> pdb=" O ALA H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 39 Processing helix chain 'H' and resid 44 through 54 Processing helix chain 'H' and resid 65 through 75 Processing helix chain 'H' and resid 78 through 92 removed outlier: 4.072A pdb=" N PHE H 92 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 112 Processing helix chain 'H' and resid 117 through 128 Processing helix chain 'H' and resid 138 through 146 Processing sheet with id=AA1, first strand: chain 'B' and resid 26 through 27 Processing sheet with id=AA2, first strand: chain 'B' and resid 99 through 101 Processing sheet with id=AA3, first strand: chain 'D' and resid 26 through 27 Processing sheet with id=AA4, first strand: chain 'D' and resid 99 through 101 Processing sheet with id=AA5, first strand: chain 'F' and resid 26 through 27 Processing sheet with id=AA6, first strand: chain 'F' and resid 99 through 101 Processing sheet with id=AA7, first strand: chain 'H' and resid 26 through 27 Processing sheet with id=AA8, first strand: chain 'H' and resid 99 through 101 1125 hydrogen bonds defined for protein. 3363 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.60 Time building geometry restraints manager: 1.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2512 1.31 - 1.44: 4436 1.44 - 1.57: 8708 1.57 - 1.70: 20 1.70 - 1.82: 152 Bond restraints: 15828 Sorted by residual: bond pdb=" C04 7YV C1101 " pdb=" C05 7YV C1101 " ideal model delta sigma weight residual 1.531 1.336 0.195 2.00e-02 2.50e+03 9.53e+01 bond pdb=" C04 7YV A1101 " pdb=" C05 7YV A1101 " ideal model delta sigma weight residual 1.531 1.336 0.195 2.00e-02 2.50e+03 9.51e+01 bond pdb=" C04 7YV E1101 " pdb=" C05 7YV E1101 " ideal model delta sigma weight residual 1.531 1.336 0.195 2.00e-02 2.50e+03 9.50e+01 bond pdb=" C04 7YV G1101 " pdb=" C05 7YV G1101 " ideal model delta sigma weight residual 1.531 1.336 0.195 2.00e-02 2.50e+03 9.46e+01 bond pdb=" C03 7YV E1101 " pdb=" C05 7YV E1101 " ideal model delta sigma weight residual 1.531 1.347 0.184 2.00e-02 2.50e+03 8.46e+01 ... (remaining 15823 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 20039 1.89 - 3.77: 1106 3.77 - 5.66: 146 5.66 - 7.54: 45 7.54 - 9.43: 24 Bond angle restraints: 21360 Sorted by residual: angle pdb=" N LEU A 553 " pdb=" CA LEU A 553 " pdb=" C LEU A 553 " ideal model delta sigma weight residual 113.72 104.62 9.10 1.30e+00 5.92e-01 4.90e+01 angle pdb=" N LEU C 553 " pdb=" CA LEU C 553 " pdb=" C LEU C 553 " ideal model delta sigma weight residual 113.72 104.65 9.07 1.30e+00 5.92e-01 4.87e+01 angle pdb=" N LEU G 553 " pdb=" CA LEU G 553 " pdb=" C LEU G 553 " ideal model delta sigma weight residual 113.72 104.66 9.06 1.30e+00 5.92e-01 4.86e+01 angle pdb=" N LEU E 553 " pdb=" CA LEU E 553 " pdb=" C LEU E 553 " ideal model delta sigma weight residual 113.72 104.66 9.06 1.30e+00 5.92e-01 4.85e+01 angle pdb=" N CYS A 175 " pdb=" CA CYS A 175 " pdb=" C CYS A 175 " ideal model delta sigma weight residual 111.36 104.74 6.62 1.09e+00 8.42e-01 3.69e+01 ... (remaining 21355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 8285 17.62 - 35.23: 766 35.23 - 52.85: 255 52.85 - 70.47: 66 70.47 - 88.08: 8 Dihedral angle restraints: 9380 sinusoidal: 3840 harmonic: 5540 Sorted by residual: dihedral pdb=" CA LEU G 553 " pdb=" C LEU G 553 " pdb=" N ARG G 554 " pdb=" CA ARG G 554 " ideal model delta harmonic sigma weight residual 180.00 152.72 27.28 0 5.00e+00 4.00e-02 2.98e+01 dihedral pdb=" CA LEU C 553 " pdb=" C LEU C 553 " pdb=" N ARG C 554 " pdb=" CA ARG C 554 " ideal model delta harmonic sigma weight residual 180.00 152.74 27.26 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA LEU E 553 " pdb=" C LEU E 553 " pdb=" N ARG E 554 " pdb=" CA ARG E 554 " ideal model delta harmonic sigma weight residual 180.00 152.75 27.25 0 5.00e+00 4.00e-02 2.97e+01 ... (remaining 9377 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 2209 0.111 - 0.222: 143 0.222 - 0.334: 4 0.334 - 0.445: 0 0.445 - 0.556: 8 Chirality restraints: 2364 Sorted by residual: chirality pdb=" C03 7YV A1101 " pdb=" C05 7YV A1101 " pdb=" C06 7YV A1101 " pdb=" C08 7YV A1101 " both_signs ideal model delta sigma weight residual False -3.26 -2.71 -0.56 2.00e-01 2.50e+01 7.72e+00 chirality pdb=" C03 7YV G1101 " pdb=" C05 7YV G1101 " pdb=" C06 7YV G1101 " pdb=" C08 7YV G1101 " both_signs ideal model delta sigma weight residual False -3.26 -2.71 -0.55 2.00e-01 2.50e+01 7.66e+00 chirality pdb=" C03 7YV E1101 " pdb=" C05 7YV E1101 " pdb=" C06 7YV E1101 " pdb=" C08 7YV E1101 " both_signs ideal model delta sigma weight residual False -3.26 -2.71 -0.55 2.00e-01 2.50e+01 7.64e+00 ... (remaining 2361 not shown) Planarity restraints: 2692 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS E 172 " 0.069 5.00e-02 4.00e+02 1.04e-01 1.73e+01 pdb=" N PRO E 173 " -0.180 5.00e-02 4.00e+02 pdb=" CA PRO E 173 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO E 173 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS G 172 " -0.069 5.00e-02 4.00e+02 1.04e-01 1.73e+01 pdb=" N PRO G 173 " 0.180 5.00e-02 4.00e+02 pdb=" CA PRO G 173 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO G 173 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 172 " -0.069 5.00e-02 4.00e+02 1.04e-01 1.73e+01 pdb=" N PRO A 173 " 0.180 5.00e-02 4.00e+02 pdb=" CA PRO A 173 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 173 " -0.057 5.00e-02 4.00e+02 ... (remaining 2689 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.79: 4099 2.79 - 3.38: 18740 3.38 - 3.97: 30076 3.97 - 4.55: 42253 4.55 - 5.14: 59282 Nonbonded interactions: 154450 Sorted by model distance: nonbonded pdb=" O THR G 282 " pdb=" OG1 THR G 283 " model vdw 2.207 3.040 nonbonded pdb=" O THR E 282 " pdb=" OG1 THR E 283 " model vdw 2.208 3.040 nonbonded pdb=" O THR C 282 " pdb=" OG1 THR C 283 " model vdw 2.208 3.040 nonbonded pdb=" O THR A 282 " pdb=" OG1 THR A 283 " model vdw 2.208 3.040 nonbonded pdb=" OG1 THR H 28 " pdb=" OE1 GLU H 31 " model vdw 2.217 3.040 ... (remaining 154445 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 74 through 1101) selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } 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=0.00 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: 3.030 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: 0.340 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.600 Find NCS groups from input model: 0.350 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: 0.010 Load rotamer database and sin/cos tables:6.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4486 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 : 0.010 0.195 15828 Z= 0.494 Angle : 1.024 9.425 21360 Z= 0.645 Chirality : 0.064 0.556 2364 Planarity : 0.007 0.104 2692 Dihedral : 15.831 88.083 5804 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.72 % Favored : 93.86 % Rotamer: Outliers : 6.90 % Allowed : 7.27 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.00 (0.18), residues: 1888 helix: -0.48 (0.12), residues: 1536 sheet: None (None), residues: 0 loop : -0.69 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 351 TYR 0.016 0.002 TYR G 101 PHE 0.030 0.003 PHE A 169 TRP 0.030 0.003 TRP E 86 HIS 0.006 0.002 HIS G 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00985 / 0.49 (15828) covalent geometry : angle 1.02425 / 0.65 (21360) hydrogen bonds : bond 0.15372 / 10.29 ( 1125) hydrogen bonds : angle 6.33381 / 4.68 ( 3363) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 420 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 TRP cc_start: 0.8392 (m100) cc_final: 0.7992 (m-90) REVERT: A 104 PHE cc_start: 0.8742 (OUTLIER) cc_final: 0.8327 (t80) REVERT: A 146 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8596 (mm-30) REVERT: C 104 PHE cc_start: 0.8715 (OUTLIER) cc_final: 0.8353 (t80) REVERT: C 329 GLN cc_start: 0.8811 (pt0) cc_final: 0.8361 (pp30) REVERT: C 330 HIS cc_start: 0.8497 (m90) cc_final: 0.8257 (m90) REVERT: C 333 LYS cc_start: 0.9606 (pptt) cc_final: 0.9328 (pptt) REVERT: E 104 PHE cc_start: 0.8731 (OUTLIER) cc_final: 0.8394 (t80) REVERT: E 146 GLU cc_start: 0.8833 (mm-30) cc_final: 0.8450 (mm-30) REVERT: E 207 ARG cc_start: 0.8216 (mtt-85) cc_final: 0.7933 (mtp-110) REVERT: E 333 LYS cc_start: 0.9629 (pptt) cc_final: 0.9423 (pptt) REVERT: G 86 TRP cc_start: 0.8449 (m100) cc_final: 0.7863 (m-90) REVERT: G 104 PHE cc_start: 0.8717 (OUTLIER) cc_final: 0.8258 (t80) REVERT: G 118 LEU cc_start: 0.9445 (tt) cc_final: 0.9244 (tm) REVERT: G 146 GLU cc_start: 0.8754 (mm-30) cc_final: 0.8547 (mm-30) outliers start: 112 outliers final: 16 residues processed: 483 average time/residue: 0.6851 time to fit residues: 358.7354 Evaluate side-chains 260 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 240 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 559 LYS Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 104 PHE Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 554 ARG Chi-restraints excluded: chain C residue 559 LYS Chi-restraints excluded: chain C residue 577 LYS Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 554 ARG Chi-restraints excluded: chain E residue 559 LYS Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 104 PHE Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain G residue 559 LYS Chi-restraints excluded: chain G residue 575 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.2980 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 20.0000 chunk 77 optimal weight: 0.2980 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 9.9990 overall best weight: 2.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 210 GLN A 344 ASN ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 HIS C 210 GLN C 344 ASN ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 GLN E 344 ASN ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 210 GLN G 344 ASN ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4832 r_free = 0.4832 target = 0.197185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.118181 restraints weight = 36337.724| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 6.17 r_work: 0.3220 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3195 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3194 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.4140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 15828 Z= 0.213 Angle : 0.772 12.088 21360 Z= 0.395 Chirality : 0.043 0.170 2364 Planarity : 0.006 0.111 2692 Dihedral : 7.024 57.776 2240 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 6.40 % Allowed : 16.38 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.78 (0.19), residues: 1888 helix: 0.77 (0.13), residues: 1536 sheet: None (None), residues: 0 loop : -0.17 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 575 TYR 0.019 0.002 TYR C 147 PHE 0.026 0.002 PHE E 169 TRP 0.013 0.001 TRP E 294 HIS 0.006 0.001 HIS E 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.21 (15828) covalent geometry : angle 0.77170 / 0.39 (21360) hydrogen bonds : bond 0.04910 / 3.30 ( 1125) hydrogen bonds : angle 4.91010 / 3.62 ( 3363) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 282 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 MET cc_start: 0.7317 (OUTLIER) cc_final: 0.6979 (tmm) REVERT: A 217 MET cc_start: 0.5839 (ppp) cc_final: 0.5397 (ppp) REVERT: A 220 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.7976 (pmt-80) REVERT: A 328 GLU cc_start: 0.9267 (tm-30) cc_final: 0.8986 (tm-30) REVERT: A 340 MET cc_start: 0.9302 (mmm) cc_final: 0.9046 (tmm) REVERT: A 559 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8723 (pttt) REVERT: B 12 PHE cc_start: 0.6846 (m-10) cc_final: 0.6374 (m-10) REVERT: B 18 LEU cc_start: -0.0345 (OUTLIER) cc_final: -0.0673 (tm) REVERT: B 76 MET cc_start: 0.0163 (ptm) cc_final: -0.0482 (ptm) REVERT: B 124 MET cc_start: 0.6157 (tmm) cc_final: 0.5950 (ppp) REVERT: B 126 ARG cc_start: 0.8768 (mtm-85) cc_final: 0.8511 (ppt170) REVERT: B 145 MET cc_start: 0.4094 (ttm) cc_final: 0.3796 (mmm) REVERT: C 139 MET cc_start: 0.7107 (OUTLIER) cc_final: 0.6818 (tmm) REVERT: C 220 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.7722 (pmm150) REVERT: C 328 GLU cc_start: 0.9236 (tm-30) cc_final: 0.8972 (tm-30) REVERT: C 335 PHE cc_start: 0.8275 (t80) cc_final: 0.7838 (t80) REVERT: C 340 MET cc_start: 0.9400 (mmm) cc_final: 0.9141 (tpp) REVERT: C 563 GLU cc_start: 0.9581 (tm-30) cc_final: 0.9367 (pp20) REVERT: D 18 LEU cc_start: 0.0108 (OUTLIER) cc_final: -0.0226 (tm) REVERT: D 24 ASP cc_start: 0.5593 (t0) cc_final: 0.5310 (p0) REVERT: D 126 ARG cc_start: 0.8586 (mtm-85) cc_final: 0.8213 (ptt90) REVERT: D 144 MET cc_start: 0.7850 (ptp) cc_final: 0.7094 (pp-130) REVERT: D 145 MET cc_start: 0.3939 (ttm) cc_final: 0.3630 (ttp) REVERT: E 139 MET cc_start: 0.7358 (OUTLIER) cc_final: 0.7004 (tmm) REVERT: E 182 PHE cc_start: 0.7967 (OUTLIER) cc_final: 0.7640 (t80) REVERT: E 214 MET cc_start: 0.8165 (tpt) cc_final: 0.7962 (tpt) REVERT: E 220 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7560 (pmm150) REVERT: E 328 GLU cc_start: 0.9237 (tm-30) cc_final: 0.8943 (tm-30) REVERT: E 335 PHE cc_start: 0.8290 (t80) cc_final: 0.7816 (t80) REVERT: E 340 MET cc_start: 0.9398 (mmm) cc_final: 0.9168 (tpp) REVERT: E 542 PHE cc_start: 0.7781 (t80) cc_final: 0.7101 (t80) REVERT: F 18 LEU cc_start: 0.0397 (OUTLIER) cc_final: 0.0017 (tm) REVERT: F 142 VAL cc_start: 0.8302 (p) cc_final: 0.8044 (m) REVERT: F 145 MET cc_start: 0.3703 (ttm) cc_final: 0.2958 (ttp) REVERT: G 220 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7911 (pmm150) REVERT: G 328 GLU cc_start: 0.9330 (tm-30) cc_final: 0.9129 (tm-30) REVERT: G 563 GLU cc_start: 0.9564 (tm-30) cc_final: 0.9357 (pp20) REVERT: H 18 LEU cc_start: -0.0208 (OUTLIER) cc_final: -0.0520 (tm) REVERT: H 69 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.7379 (mt) REVERT: H 76 MET cc_start: 0.1041 (ptm) cc_final: 0.0014 (ptm) REVERT: H 145 MET cc_start: 0.4208 (ttm) cc_final: 0.3769 (mmm) outliers start: 104 outliers final: 41 residues processed: 354 average time/residue: 0.5323 time to fit residues: 207.4748 Evaluate side-chains 269 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 214 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 550 LYS Chi-restraints excluded: chain A residue 559 LYS Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 569 HIS Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 107 HIS Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 139 MET Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain C residue 559 LYS Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 107 HIS Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 139 MET Chi-restraints excluded: chain E residue 182 PHE Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 220 ARG Chi-restraints excluded: chain E residue 559 LYS Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 95 ASP Chi-restraints excluded: chain F residue 107 HIS Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain G residue 220 ARG Chi-restraints excluded: chain G residue 550 LYS Chi-restraints excluded: chain G residue 559 LYS Chi-restraints excluded: chain G residue 575 ARG Chi-restraints excluded: chain G residue 587 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 95 ASP Chi-restraints excluded: chain H residue 107 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 15 optimal weight: 0.9990 chunk 185 optimal weight: 0.3980 chunk 155 optimal weight: 0.8980 chunk 154 optimal weight: 0.5980 chunk 103 optimal weight: 8.9990 chunk 104 optimal weight: 10.0000 chunk 83 optimal weight: 0.0970 chunk 66 optimal weight: 0.6980 chunk 160 optimal weight: 0.7980 chunk 172 optimal weight: 2.9990 chunk 173 optimal weight: 6.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 124 HIS ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 HIS ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 ASN ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 111 ASN G 124 HIS ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4847 r_free = 0.4847 target = 0.198554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.120509 restraints weight = 37117.082| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 3.78 r_work: 0.3281 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3286 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3286 r_free = 0.3286 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3286 r_free = 0.3286 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3286 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.5017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15828 Z= 0.141 Angle : 0.710 13.128 21360 Z= 0.355 Chirality : 0.040 0.177 2364 Planarity : 0.006 0.112 2692 Dihedral : 6.443 54.387 2222 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 5.30 % Allowed : 19.46 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.34 (0.20), residues: 1888 helix: 1.19 (0.13), residues: 1536 sheet: None (None), residues: 0 loop : -0.11 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 106 TYR 0.021 0.001 TYR E 556 PHE 0.024 0.001 PHE G 169 TRP 0.011 0.001 TRP E 350 HIS 0.004 0.001 HIS A 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (15828) covalent geometry : angle 0.71012 / 0.35 (21360) hydrogen bonds : bond 0.04275 / 2.90 ( 1125) hydrogen bonds : angle 4.68937 / 3.46 ( 3363) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 276 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 THR cc_start: 0.7783 (OUTLIER) cc_final: 0.7554 (t) REVERT: A 182 PHE cc_start: 0.7737 (t80) cc_final: 0.7428 (t80) REVERT: A 207 ARG cc_start: 0.8295 (mtt180) cc_final: 0.7991 (mtp180) REVERT: A 220 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7669 (pmm150) REVERT: A 563 GLU cc_start: 0.9546 (pp20) cc_final: 0.9341 (pp20) REVERT: A 575 ARG cc_start: 0.6779 (ptt-90) cc_final: 0.6568 (ptt180) REVERT: B 18 LEU cc_start: -0.0573 (OUTLIER) cc_final: -0.0897 (tm) REVERT: B 76 MET cc_start: -0.0145 (ptm) cc_final: -0.0507 (ptm) REVERT: C 120 THR cc_start: 0.7770 (OUTLIER) cc_final: 0.7529 (t) REVERT: C 220 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7685 (pmm150) REVERT: C 328 GLU cc_start: 0.9256 (tm-30) cc_final: 0.8913 (tm-30) REVERT: D 18 LEU cc_start: 0.0345 (OUTLIER) cc_final: 0.0065 (tm) REVERT: D 24 ASP cc_start: 0.5624 (t0) cc_final: 0.5363 (p0) REVERT: D 41 GLN cc_start: 0.6925 (tp-100) cc_final: 0.6517 (pt0) REVERT: D 126 ARG cc_start: 0.8535 (mtm-85) cc_final: 0.8224 (ppt170) REVERT: D 144 MET cc_start: 0.8082 (ptp) cc_final: 0.7329 (pp-130) REVERT: E 120 THR cc_start: 0.7834 (OUTLIER) cc_final: 0.7602 (t) REVERT: E 139 MET cc_start: 0.7188 (OUTLIER) cc_final: 0.6956 (tmm) REVERT: E 220 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7648 (pmm150) REVERT: E 328 GLU cc_start: 0.9210 (tm-30) cc_final: 0.8866 (tm-30) REVERT: E 357 MET cc_start: 0.4838 (ppp) cc_final: 0.4515 (ppp) REVERT: F 18 LEU cc_start: 0.0649 (OUTLIER) cc_final: 0.0330 (tm) REVERT: F 106 ARG cc_start: 0.9232 (mmm-85) cc_final: 0.8983 (mpt180) REVERT: G 139 MET cc_start: 0.7182 (OUTLIER) cc_final: 0.6684 (tmm) REVERT: G 220 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7742 (pmm150) REVERT: G 328 GLU cc_start: 0.9316 (tm-30) cc_final: 0.9015 (tm-30) REVERT: G 563 GLU cc_start: 0.9591 (tm-30) cc_final: 0.9237 (pp20) REVERT: H 18 LEU cc_start: -0.0077 (OUTLIER) cc_final: -0.0437 (tm) outliers start: 86 outliers final: 29 residues processed: 336 average time/residue: 0.6180 time to fit residues: 226.8935 Evaluate side-chains 249 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 207 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 569 HIS Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 107 HIS Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain C residue 569 HIS Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 107 HIS Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 139 MET Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 220 ARG Chi-restraints excluded: chain E residue 569 HIS Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 95 ASP Chi-restraints excluded: chain F residue 107 HIS Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 137 PHE Chi-restraints excluded: chain G residue 139 MET Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain G residue 220 ARG Chi-restraints excluded: chain G residue 330 HIS Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 95 ASP Chi-restraints excluded: chain H residue 107 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 3 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 127 optimal weight: 20.0000 chunk 104 optimal weight: 5.9990 chunk 163 optimal weight: 0.9980 chunk 62 optimal weight: 0.3980 chunk 103 optimal weight: 8.9990 chunk 37 optimal weight: 8.9990 chunk 33 optimal weight: 30.0000 chunk 36 optimal weight: 50.0000 chunk 29 optimal weight: 5.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 344 ASN ** B 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 HIS ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 143 GLN ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 143 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4810 r_free = 0.4810 target = 0.194587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.119913 restraints weight = 36440.061| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 6.84 r_work: 0.3115 rms_B_bonded: 5.45 restraints_weight: 2.0000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3107 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3107 r_free = 0.3107 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3107 r_free = 0.3107 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3107 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.5511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 15828 Z= 0.231 Angle : 0.775 11.101 21360 Z= 0.387 Chirality : 0.043 0.185 2364 Planarity : 0.006 0.110 2692 Dihedral : 5.312 54.414 2200 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 5.85 % Allowed : 21.49 % Favored : 72.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.44 (0.20), residues: 1888 helix: 1.24 (0.13), residues: 1544 sheet: None (None), residues: 0 loop : -0.03 (0.36), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 547 TYR 0.020 0.002 TYR A 147 PHE 0.026 0.002 PHE E 169 TRP 0.014 0.001 TRP E 350 HIS 0.011 0.001 HIS B 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.23 (15828) covalent geometry : angle 0.77478 / 0.39 (21360) hydrogen bonds : bond 0.04521 / 3.07 ( 1125) hydrogen bonds : angle 4.70090 / 3.47 ( 3363) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 235 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 ARG cc_start: 0.8259 (mpp-170) cc_final: 0.8042 (mtt90) REVERT: A 220 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.8153 (pmm150) REVERT: B 18 LEU cc_start: -0.0398 (OUTLIER) cc_final: -0.0608 (tm) REVERT: B 72 MET cc_start: 0.3572 (tmm) cc_final: 0.3266 (pp-130) REVERT: B 84 GLU cc_start: 0.7081 (mm-30) cc_final: 0.6211 (tt0) REVERT: B 85 ILE cc_start: 0.5114 (mm) cc_final: 0.4832 (mt) REVERT: B 124 MET cc_start: 0.6860 (tmm) cc_final: 0.5977 (ppp) REVERT: C 207 ARG cc_start: 0.8526 (mtt180) cc_final: 0.8225 (mtp180) REVERT: C 219 ARG cc_start: 0.8312 (mpp-170) cc_final: 0.7709 (ttm110) REVERT: C 220 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.8213 (pmm150) REVERT: C 262 ASP cc_start: 0.9288 (p0) cc_final: 0.9056 (p0) REVERT: C 328 GLU cc_start: 0.9334 (tm-30) cc_final: 0.9031 (tm-30) REVERT: C 572 MET cc_start: 0.9130 (tpt) cc_final: 0.8805 (ptp) REVERT: D 18 LEU cc_start: 0.0302 (OUTLIER) cc_final: 0.0037 (tm) REVERT: D 76 MET cc_start: 0.1602 (ptt) cc_final: 0.1208 (ptt) REVERT: D 84 GLU cc_start: 0.6883 (mm-30) cc_final: 0.6560 (mm-30) REVERT: D 115 LYS cc_start: 0.9530 (OUTLIER) cc_final: 0.9327 (tmmt) REVERT: D 126 ARG cc_start: 0.8488 (mtm-85) cc_final: 0.8074 (ppt170) REVERT: D 144 MET cc_start: 0.8252 (ptp) cc_final: 0.7439 (pp-130) REVERT: E 139 MET cc_start: 0.7348 (OUTLIER) cc_final: 0.7103 (tmm) REVERT: E 217 MET cc_start: 0.6110 (ppp) cc_final: 0.4664 (ppp) REVERT: E 219 ARG cc_start: 0.8593 (mpp-170) cc_final: 0.7689 (ttm110) REVERT: E 220 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.8164 (pmm150) REVERT: E 262 ASP cc_start: 0.9276 (p0) cc_final: 0.9039 (p0) REVERT: E 328 GLU cc_start: 0.9313 (tm-30) cc_final: 0.8999 (tm-30) REVERT: F 18 LEU cc_start: 0.0868 (OUTLIER) cc_final: 0.0611 (tm) REVERT: F 84 GLU cc_start: 0.7006 (mm-30) cc_final: 0.6544 (mm-30) REVERT: G 139 MET cc_start: 0.7373 (OUTLIER) cc_final: 0.6814 (tmm) REVERT: G 220 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.8251 (pmm150) REVERT: G 328 GLU cc_start: 0.9384 (tm-30) cc_final: 0.9071 (tm-30) REVERT: H 18 LEU cc_start: 0.0227 (OUTLIER) cc_final: -0.0087 (tm) REVERT: H 84 GLU cc_start: 0.7171 (mm-30) cc_final: 0.6402 (tt0) outliers start: 95 outliers final: 40 residues processed: 303 average time/residue: 0.5602 time to fit residues: 186.8576 Evaluate side-chains 259 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 208 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 330 HIS Chi-restraints excluded: chain A residue 550 LYS Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 569 HIS Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 107 HIS Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 124 HIS Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 569 HIS Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 107 HIS Chi-restraints excluded: chain D residue 115 LYS Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 139 MET Chi-restraints excluded: chain E residue 220 ARG Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 95 ASP Chi-restraints excluded: chain F residue 107 HIS Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 137 PHE Chi-restraints excluded: chain G residue 139 MET Chi-restraints excluded: chain G residue 146 GLU Chi-restraints excluded: chain G residue 220 ARG Chi-restraints excluded: chain G residue 550 LYS Chi-restraints excluded: chain G residue 569 HIS Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 95 ASP Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain H residue 107 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 64 optimal weight: 0.9990 chunk 160 optimal weight: 0.1980 chunk 47 optimal weight: 50.0000 chunk 106 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 166 optimal weight: 8.9990 chunk 162 optimal weight: 0.9980 chunk 78 optimal weight: 7.9990 chunk 152 optimal weight: 0.3980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 102 HIS ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 HIS ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 569 HIS F 41 GLN ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 HIS ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4805 r_free = 0.4805 target = 0.197042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.117446 restraints weight = 36847.280| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 4.32 r_work: 0.3174 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3185 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 49 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3185 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.6113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15828 Z= 0.140 Angle : 0.736 11.617 21360 Z= 0.366 Chirality : 0.041 0.162 2364 Planarity : 0.006 0.110 2692 Dihedral : 5.061 52.836 2192 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 4.50 % Allowed : 24.51 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.20), residues: 1888 helix: 1.26 (0.13), residues: 1536 sheet: None (None), residues: 0 loop : -0.39 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 554 TYR 0.018 0.001 TYR A 147 PHE 0.024 0.001 PHE G 169 TRP 0.014 0.001 TRP E 350 HIS 0.004 0.001 HIS C 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (15828) covalent geometry : angle 0.73600 / 0.37 (21360) hydrogen bonds : bond 0.03962 / 2.71 ( 1125) hydrogen bonds : angle 4.58374 / 3.37 ( 3363) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 247 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 THR cc_start: 0.7723 (OUTLIER) cc_final: 0.7493 (t) REVERT: A 220 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.8116 (pmm150) REVERT: A 340 MET cc_start: 0.9467 (pp-130) cc_final: 0.8960 (mmm) REVERT: A 351 ARG cc_start: 0.6229 (mtt90) cc_final: 0.5948 (tpt170) REVERT: A 357 MET cc_start: 0.5048 (ppp) cc_final: 0.3957 (ptm) REVERT: B 84 GLU cc_start: 0.6995 (mm-30) cc_final: 0.6122 (tt0) REVERT: B 85 ILE cc_start: 0.5384 (mm) cc_final: 0.5170 (mt) REVERT: C 120 THR cc_start: 0.7731 (OUTLIER) cc_final: 0.7493 (t) REVERT: C 219 ARG cc_start: 0.8177 (mpp-170) cc_final: 0.7833 (ttm110) REVERT: C 220 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.8124 (pmm150) REVERT: C 260 GLU cc_start: 0.8552 (pt0) cc_final: 0.8247 (mt-10) REVERT: C 328 GLU cc_start: 0.9254 (tm-30) cc_final: 0.8952 (tm-30) REVERT: C 340 MET cc_start: 0.9563 (pp-130) cc_final: 0.9122 (mmm) REVERT: C 572 MET cc_start: 0.9145 (tpt) cc_final: 0.8812 (mtt) REVERT: D 18 LEU cc_start: 0.0285 (OUTLIER) cc_final: 0.0040 (tm) REVERT: D 72 MET cc_start: 0.4703 (tpt) cc_final: 0.4370 (pp-130) REVERT: D 84 GLU cc_start: 0.6794 (mm-30) cc_final: 0.6452 (mm-30) REVERT: D 122 ASP cc_start: 0.8704 (m-30) cc_final: 0.8434 (m-30) REVERT: D 126 ARG cc_start: 0.8483 (mtm-85) cc_final: 0.8104 (ppt170) REVERT: D 144 MET cc_start: 0.8171 (ptp) cc_final: 0.7497 (pp-130) REVERT: D 145 MET cc_start: 0.3783 (OUTLIER) cc_final: 0.3481 (tpt) REVERT: E 120 THR cc_start: 0.7765 (OUTLIER) cc_final: 0.7527 (t) REVERT: E 139 MET cc_start: 0.7386 (mtp) cc_final: 0.7168 (tmm) REVERT: E 217 MET cc_start: 0.5688 (ppp) cc_final: 0.4629 (ppp) REVERT: E 219 ARG cc_start: 0.8404 (mpp-170) cc_final: 0.7726 (ttm110) REVERT: E 220 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.8059 (pmm150) REVERT: E 262 ASP cc_start: 0.9225 (p0) cc_final: 0.9021 (p0) REVERT: E 328 GLU cc_start: 0.9231 (tm-30) cc_final: 0.8934 (tm-30) REVERT: E 335 PHE cc_start: 0.8662 (t80) cc_final: 0.8281 (t80) REVERT: F 18 LEU cc_start: 0.0458 (OUTLIER) cc_final: 0.0225 (tm) REVERT: F 72 MET cc_start: 0.4714 (tpt) cc_final: 0.4260 (pp-130) REVERT: F 84 GLU cc_start: 0.6901 (mm-30) cc_final: 0.6442 (mm-30) REVERT: F 123 GLU cc_start: 0.6592 (OUTLIER) cc_final: 0.6242 (pt0) REVERT: G 139 MET cc_start: 0.7441 (OUTLIER) cc_final: 0.6903 (tmm) REVERT: G 219 ARG cc_start: 0.8348 (mtm-85) cc_final: 0.7927 (ttm110) REVERT: G 220 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.8240 (pmm150) REVERT: G 328 GLU cc_start: 0.9314 (tm-30) cc_final: 0.9047 (tm-30) REVERT: G 340 MET cc_start: 0.9558 (pp-130) cc_final: 0.9276 (tmm) REVERT: G 556 TYR cc_start: 0.4961 (OUTLIER) cc_final: 0.4664 (p90) REVERT: H 18 LEU cc_start: 0.0050 (OUTLIER) cc_final: -0.0254 (tm) outliers start: 73 outliers final: 30 residues processed: 299 average time/residue: 0.6075 time to fit residues: 198.8884 Evaluate side-chains 258 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 214 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 569 HIS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 42 ASN Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 99 TYR Chi-restraints excluded: chain B residue 107 HIS Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain C residue 330 HIS Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 107 HIS Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 137 PHE Chi-restraints excluded: chain E residue 220 ARG Chi-restraints excluded: chain E residue 569 HIS Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 95 ASP Chi-restraints excluded: chain F residue 107 HIS Chi-restraints excluded: chain F residue 123 GLU Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 137 PHE Chi-restraints excluded: chain G residue 139 MET Chi-restraints excluded: chain G residue 220 ARG Chi-restraints excluded: chain G residue 330 HIS Chi-restraints excluded: chain G residue 550 LYS Chi-restraints excluded: chain G residue 556 TYR Chi-restraints excluded: chain G residue 569 HIS Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 95 ASP Chi-restraints excluded: chain H residue 107 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 12 optimal weight: 6.9990 chunk 172 optimal weight: 7.9990 chunk 153 optimal weight: 30.0000 chunk 61 optimal weight: 0.7980 chunk 104 optimal weight: 20.0000 chunk 0 optimal weight: 50.0000 chunk 68 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 41 GLN ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 569 HIS ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 330 HIS ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4769 r_free = 0.4769 target = 0.193481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.111668 restraints weight = 36509.948| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 4.23 r_work: 0.3083 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3089 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 49 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 50 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3089 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.6425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 15828 Z= 0.227 Angle : 0.791 11.846 21360 Z= 0.397 Chirality : 0.044 0.185 2364 Planarity : 0.006 0.106 2692 Dihedral : 5.173 54.075 2192 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 5.11 % Allowed : 24.26 % Favored : 70.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.20 (0.20), residues: 1888 helix: 1.09 (0.13), residues: 1548 sheet: None (None), residues: 0 loop : -0.22 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 547 TYR 0.016 0.002 TYR A 147 PHE 0.025 0.002 PHE E 169 TRP 0.015 0.001 TRP E 350 HIS 0.012 0.001 HIS E 569 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.23 (15828) covalent geometry : angle 0.79108 / 0.40 (21360) hydrogen bonds : bond 0.04436 / 3.02 ( 1125) hydrogen bonds : angle 4.69756 / 3.46 ( 3363) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 224 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 ARG cc_start: 0.9075 (ttp80) cc_final: 0.8620 (tmm-80) REVERT: A 340 MET cc_start: 0.9458 (pp-130) cc_final: 0.9011 (mmm) REVERT: A 351 ARG cc_start: 0.6134 (mtt90) cc_final: 0.5910 (tpt170) REVERT: B 41 GLN cc_start: 0.5876 (OUTLIER) cc_final: 0.5603 (pp30) REVERT: B 71 MET cc_start: 0.4716 (mmm) cc_final: 0.4414 (mtt) REVERT: B 84 GLU cc_start: 0.6951 (mm-30) cc_final: 0.6273 (tt0) REVERT: C 207 ARG cc_start: 0.8493 (mtt180) cc_final: 0.8277 (mtp180) REVERT: C 214 MET cc_start: 0.7623 (tpt) cc_final: 0.7036 (tmm) REVERT: C 218 ASP cc_start: 0.7392 (OUTLIER) cc_final: 0.6396 (t0) REVERT: C 220 ARG cc_start: 0.8824 (OUTLIER) cc_final: 0.8321 (pmm150) REVERT: C 328 GLU cc_start: 0.9282 (tm-30) cc_final: 0.9005 (tm-30) REVERT: C 340 MET cc_start: 0.9577 (pp-130) cc_final: 0.9100 (mmm) REVERT: C 351 ARG cc_start: 0.6469 (mtt90) cc_final: 0.5807 (tpt170) REVERT: C 572 MET cc_start: 0.9175 (OUTLIER) cc_final: 0.8814 (mtt) REVERT: D 12 PHE cc_start: 0.6593 (m-80) cc_final: 0.6328 (m-80) REVERT: D 18 LEU cc_start: 0.0146 (OUTLIER) cc_final: -0.0098 (tm) REVERT: D 69 LEU cc_start: 0.6433 (tt) cc_final: 0.6155 (pp) REVERT: D 109 MET cc_start: 0.6760 (ppp) cc_final: 0.6527 (ppp) REVERT: D 115 LYS cc_start: 0.9104 (mppt) cc_final: 0.8742 (mppt) REVERT: D 126 ARG cc_start: 0.8401 (mtm-85) cc_final: 0.8102 (ptm-80) REVERT: D 144 MET cc_start: 0.8222 (ptp) cc_final: 0.7389 (pp-130) REVERT: D 145 MET cc_start: 0.3993 (OUTLIER) cc_final: 0.3724 (tpt) REVERT: E 214 MET cc_start: 0.7590 (tpt) cc_final: 0.7360 (tpt) REVERT: E 218 ASP cc_start: 0.7284 (OUTLIER) cc_final: 0.6760 (m-30) REVERT: E 220 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.8299 (pmm150) REVERT: E 262 ASP cc_start: 0.9255 (p0) cc_final: 0.9000 (p0) REVERT: E 328 GLU cc_start: 0.9268 (tm-30) cc_final: 0.8995 (tm-30) REVERT: F 18 LEU cc_start: 0.0544 (OUTLIER) cc_final: 0.0314 (tm) REVERT: F 72 MET cc_start: 0.4829 (tpt) cc_final: 0.4533 (pp-130) REVERT: F 84 GLU cc_start: 0.6976 (mm-30) cc_final: 0.6486 (mm-30) REVERT: G 139 MET cc_start: 0.7532 (OUTLIER) cc_final: 0.6945 (tmm) REVERT: G 182 PHE cc_start: 0.7969 (t80) cc_final: 0.7742 (t80) REVERT: G 328 GLU cc_start: 0.9337 (tm-30) cc_final: 0.9103 (tm-30) REVERT: G 340 MET cc_start: 0.9563 (pp-130) cc_final: 0.9287 (tmm) REVERT: G 556 TYR cc_start: 0.4835 (OUTLIER) cc_final: 0.4512 (p90) REVERT: H 18 LEU cc_start: -0.0196 (OUTLIER) cc_final: -0.0474 (tm) REVERT: H 84 GLU cc_start: 0.7046 (mm-30) cc_final: 0.6316 (tt0) REVERT: H 85 ILE cc_start: 0.5501 (mm) cc_final: 0.5112 (tt) outliers start: 83 outliers final: 39 residues processed: 281 average time/residue: 0.5155 time to fit residues: 159.2944 Evaluate side-chains 258 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 207 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 569 HIS Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 41 GLN Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 99 TYR Chi-restraints excluded: chain B residue 107 HIS Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 124 HIS Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain C residue 569 HIS Chi-restraints excluded: chain C residue 572 MET Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain D residue 107 HIS Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 124 HIS Chi-restraints excluded: chain E residue 137 PHE Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 220 ARG Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 95 ASP Chi-restraints excluded: chain F residue 99 TYR Chi-restraints excluded: chain F residue 107 HIS Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 137 PHE Chi-restraints excluded: chain G residue 139 MET Chi-restraints excluded: chain G residue 146 GLU Chi-restraints excluded: chain G residue 330 HIS Chi-restraints excluded: chain G residue 550 LYS Chi-restraints excluded: chain G residue 556 TYR Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 95 ASP Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain H residue 107 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 120 optimal weight: 5.9990 chunk 148 optimal weight: 9.9990 chunk 23 optimal weight: 0.9990 chunk 180 optimal weight: 8.9990 chunk 58 optimal weight: 30.0000 chunk 170 optimal weight: 6.9990 chunk 56 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 172 optimal weight: 9.9990 chunk 42 optimal weight: 30.0000 chunk 40 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 102 HIS B 42 ASN ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 HIS D 42 ASN ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 143 GLN E 569 HIS F 42 ASN ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 HIS ** G 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4729 r_free = 0.4729 target = 0.189634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.105643 restraints weight = 36568.416| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 3.46 r_work: 0.3049 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3049 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3049 r_free = 0.3049 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 50 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3049 r_free = 0.3049 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 50 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3049 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.6892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.062 15828 Z= 0.351 Angle : 0.884 12.387 21360 Z= 0.447 Chirality : 0.049 0.299 2364 Planarity : 0.006 0.104 2692 Dihedral : 5.534 53.918 2192 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 20.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.34 % Favored : 95.60 % Rotamer: Outliers : 4.93 % Allowed : 25.55 % Favored : 69.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.78 (0.19), residues: 1888 helix: 0.85 (0.13), residues: 1532 sheet: None (None), residues: 0 loop : -0.56 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 547 TYR 0.016 0.002 TYR B 99 PHE 0.027 0.002 PHE E 169 TRP 0.012 0.002 TRP G 350 HIS 0.014 0.002 HIS C 569 Details of bonding type rmsd/Z covalent geometry : bond 0.00800 / 0.35 (15828) covalent geometry : angle 0.88418 / 0.45 (21360) hydrogen bonds : bond 0.05059 / 3.40 ( 1125) hydrogen bonds : angle 5.03379 / 3.71 ( 3363) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 239 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 MET cc_start: 0.7949 (tpt) cc_final: 0.7694 (tpt) REVERT: A 219 ARG cc_start: 0.9006 (ttp80) cc_final: 0.8032 (tmm160) REVERT: A 220 ARG cc_start: 0.9339 (pmt170) cc_final: 0.8340 (tpm170) REVERT: A 340 MET cc_start: 0.9488 (pp-130) cc_final: 0.8991 (mmm) REVERT: A 351 ARG cc_start: 0.6161 (mtt90) cc_final: 0.5889 (mmt180) REVERT: A 547 ARG cc_start: 0.9252 (mmm160) cc_final: 0.8967 (tpp-160) REVERT: B 51 MET cc_start: 0.8773 (ppp) cc_final: 0.8058 (pmm) REVERT: B 84 GLU cc_start: 0.7004 (mm-30) cc_final: 0.6287 (pt0) REVERT: B 85 ILE cc_start: 0.5927 (mt) cc_final: 0.5521 (tt) REVERT: C 219 ARG cc_start: 0.9245 (ttm110) cc_final: 0.8336 (ttt180) REVERT: C 220 ARG cc_start: 0.9230 (OUTLIER) cc_final: 0.7960 (tpm170) REVERT: C 328 GLU cc_start: 0.9321 (tm-30) cc_final: 0.9080 (tm-30) REVERT: D 18 LEU cc_start: 0.0164 (OUTLIER) cc_final: -0.0049 (tm) REVERT: D 69 LEU cc_start: 0.6492 (tt) cc_final: 0.6182 (pp) REVERT: D 84 GLU cc_start: 0.7028 (mm-30) cc_final: 0.6608 (mm-30) REVERT: D 145 MET cc_start: 0.4681 (OUTLIER) cc_final: 0.4264 (mmm) REVERT: E 262 ASP cc_start: 0.9199 (p0) cc_final: 0.8913 (p0) REVERT: E 328 GLU cc_start: 0.9313 (tm-30) cc_final: 0.9048 (tm-30) REVERT: F 18 LEU cc_start: 0.0524 (OUTLIER) cc_final: 0.0306 (tm) REVERT: F 84 GLU cc_start: 0.6978 (mm-30) cc_final: 0.6437 (mm-30) REVERT: G 139 MET cc_start: 0.7534 (OUTLIER) cc_final: 0.6856 (tmm) REVERT: G 218 ASP cc_start: 0.7764 (OUTLIER) cc_final: 0.7553 (m-30) REVERT: G 219 ARG cc_start: 0.9200 (mtt90) cc_final: 0.8897 (mpt180) REVERT: G 328 GLU cc_start: 0.9377 (tm-30) cc_final: 0.9167 (tm-30) REVERT: G 335 PHE cc_start: 0.8764 (t80) cc_final: 0.8340 (t80) REVERT: G 340 MET cc_start: 0.9561 (pp-130) cc_final: 0.9061 (mmm) REVERT: G 556 TYR cc_start: 0.4683 (OUTLIER) cc_final: 0.4420 (p90) REVERT: H 84 GLU cc_start: 0.7094 (mm-30) cc_final: 0.6342 (tt0) REVERT: H 85 ILE cc_start: 0.5719 (mm) cc_final: 0.5362 (tt) outliers start: 80 outliers final: 39 residues processed: 295 average time/residue: 0.5170 time to fit residues: 168.8046 Evaluate side-chains 248 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 202 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 124 HIS Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 569 HIS Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 107 HIS Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 124 HIS Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 572 MET Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain D residue 107 HIS Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 124 HIS Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 95 ASP Chi-restraints excluded: chain F residue 99 TYR Chi-restraints excluded: chain F residue 107 HIS Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 124 HIS Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain G residue 137 PHE Chi-restraints excluded: chain G residue 139 MET Chi-restraints excluded: chain G residue 218 ASP Chi-restraints excluded: chain G residue 550 LYS Chi-restraints excluded: chain G residue 556 TYR Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 95 ASP Chi-restraints excluded: chain H residue 107 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 125 optimal weight: 2.9990 chunk 92 optimal weight: 0.4980 chunk 39 optimal weight: 7.9990 chunk 75 optimal weight: 7.9990 chunk 68 optimal weight: 0.2980 chunk 89 optimal weight: 8.9990 chunk 140 optimal weight: 8.9990 chunk 22 optimal weight: 0.9990 chunk 165 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 123 optimal weight: 7.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 102 HIS C 102 HIS D 143 GLN ** E 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 569 HIS ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4772 r_free = 0.4772 target = 0.194844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.115572 restraints weight = 36632.727| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 3.82 r_work: 0.3158 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3159 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3159 r_free = 0.3159 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 50 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3159 r_free = 0.3159 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 50 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3159 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.7232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 15828 Z= 0.150 Angle : 0.826 13.214 21360 Z= 0.406 Chirality : 0.043 0.276 2364 Planarity : 0.006 0.106 2692 Dihedral : 5.282 56.513 2192 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.26 % Allowed : 27.71 % Favored : 69.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.07 (0.20), residues: 1888 helix: 1.07 (0.14), residues: 1508 sheet: None (None), residues: 0 loop : -0.45 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG G 547 TYR 0.016 0.001 TYR A 556 PHE 0.029 0.002 PHE F 12 TRP 0.014 0.001 TRP G 350 HIS 0.020 0.001 HIS G 569 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (15828) covalent geometry : angle 0.82630 / 0.41 (21360) hydrogen bonds : bond 0.04122 / 2.82 ( 1125) hydrogen bonds : angle 4.76855 / 3.52 ( 3363) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 235 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 THR cc_start: 0.7791 (OUTLIER) cc_final: 0.7551 (t) REVERT: A 219 ARG cc_start: 0.8933 (ttp80) cc_final: 0.8494 (tmm-80) REVERT: A 262 ASP cc_start: 0.9245 (p0) cc_final: 0.8983 (p0) REVERT: A 340 MET cc_start: 0.9467 (pp-130) cc_final: 0.8991 (mmm) REVERT: A 357 MET cc_start: 0.5499 (ppp) cc_final: 0.4102 (ptp) REVERT: B 84 GLU cc_start: 0.6910 (mm-30) cc_final: 0.6211 (pt0) REVERT: B 85 ILE cc_start: 0.5678 (mt) cc_final: 0.5069 (tt) REVERT: B 145 MET cc_start: 0.3601 (tpt) cc_final: 0.3250 (mmp) REVERT: C 120 THR cc_start: 0.7743 (OUTLIER) cc_final: 0.7495 (t) REVERT: C 139 MET cc_start: 0.7660 (ppp) cc_final: 0.7440 (ptt) REVERT: C 219 ARG cc_start: 0.9215 (ttm110) cc_final: 0.8618 (tmm-80) REVERT: C 220 ARG cc_start: 0.9259 (pmt170) cc_final: 0.8788 (pmm150) REVERT: C 260 GLU cc_start: 0.8633 (pt0) cc_final: 0.8194 (mt-10) REVERT: C 262 ASP cc_start: 0.9246 (p0) cc_final: 0.8999 (p0) REVERT: C 328 GLU cc_start: 0.9327 (tm-30) cc_final: 0.9075 (tm-30) REVERT: C 351 ARG cc_start: 0.6629 (mtt90) cc_final: 0.6375 (mmt180) REVERT: D 18 LEU cc_start: 0.0261 (OUTLIER) cc_final: 0.0059 (tm) REVERT: D 72 MET cc_start: 0.5001 (tpt) cc_final: 0.4409 (pp-130) REVERT: D 84 GLU cc_start: 0.7006 (mm-30) cc_final: 0.6463 (mm-30) REVERT: D 85 ILE cc_start: 0.5327 (tt) cc_final: 0.4927 (mt) REVERT: D 145 MET cc_start: 0.5116 (OUTLIER) cc_final: 0.4573 (mmp) REVERT: E 104 PHE cc_start: 0.9323 (t80) cc_final: 0.9089 (t80) REVERT: E 120 THR cc_start: 0.7796 (OUTLIER) cc_final: 0.7556 (t) REVERT: E 219 ARG cc_start: 0.8648 (mtm-85) cc_final: 0.8346 (ttt90) REVERT: E 262 ASP cc_start: 0.9229 (p0) cc_final: 0.9004 (p0) REVERT: E 328 GLU cc_start: 0.9290 (tm-30) cc_final: 0.9011 (tm-30) REVERT: F 72 MET cc_start: 0.5089 (tpt) cc_final: 0.4539 (pp-130) REVERT: F 84 GLU cc_start: 0.6884 (mm-30) cc_final: 0.6532 (tt0) REVERT: F 105 LEU cc_start: 0.7542 (OUTLIER) cc_final: 0.7246 (pt) REVERT: F 145 MET cc_start: 0.4795 (mmm) cc_final: 0.4191 (mmm) REVERT: G 139 MET cc_start: 0.7512 (OUTLIER) cc_final: 0.6869 (tmm) REVERT: G 218 ASP cc_start: 0.7814 (OUTLIER) cc_final: 0.7486 (m-30) REVERT: G 262 ASP cc_start: 0.9271 (p0) cc_final: 0.9019 (p0) REVERT: G 328 GLU cc_start: 0.9356 (tm-30) cc_final: 0.9101 (tm-30) REVERT: G 340 MET cc_start: 0.9549 (pp-130) cc_final: 0.9282 (tmm) REVERT: G 350 TRP cc_start: 0.6987 (t-100) cc_final: 0.6614 (t-100) REVERT: G 563 GLU cc_start: 0.9458 (tm-30) cc_final: 0.9241 (pp20) REVERT: H 72 MET cc_start: 0.2462 (pp-130) cc_final: 0.2006 (pp-130) REVERT: H 84 GLU cc_start: 0.7117 (mm-30) cc_final: 0.6404 (pt0) REVERT: H 85 ILE cc_start: 0.5681 (mm) cc_final: 0.5053 (tt) outliers start: 53 outliers final: 18 residues processed: 270 average time/residue: 0.5545 time to fit residues: 164.8547 Evaluate side-chains 231 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 205 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 569 HIS Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 107 HIS Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 330 HIS Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 572 MET Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 107 HIS Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 107 HIS Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 139 MET Chi-restraints excluded: chain G residue 218 ASP Chi-restraints excluded: chain G residue 330 HIS Chi-restraints excluded: chain G residue 550 LYS Chi-restraints excluded: chain H residue 107 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 159 optimal weight: 0.6980 chunk 37 optimal weight: 10.0000 chunk 129 optimal weight: 30.0000 chunk 101 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 chunk 167 optimal weight: 0.9990 chunk 125 optimal weight: 7.9990 chunk 161 optimal weight: 0.8980 chunk 176 optimal weight: 0.9990 chunk 59 optimal weight: 20.0000 chunk 153 optimal weight: 0.0040 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 HIS ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 143 GLN ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4808 r_free = 0.4808 target = 0.195780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.118411 restraints weight = 35334.100| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 4.07 r_work: 0.3258 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3254 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 50 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 50 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3254 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.7540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 15828 Z= 0.150 Angle : 0.848 13.554 21360 Z= 0.418 Chirality : 0.044 0.263 2364 Planarity : 0.006 0.106 2692 Dihedral : 5.310 56.667 2192 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.02 % Allowed : 28.88 % Favored : 68.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.03 (0.20), residues: 1888 helix: 1.02 (0.14), residues: 1508 sheet: None (None), residues: 0 loop : -0.39 (0.34), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG G 547 TYR 0.020 0.001 TYR H 99 PHE 0.026 0.002 PHE E 169 TRP 0.017 0.001 TRP E 350 HIS 0.011 0.001 HIS G 569 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (15828) covalent geometry : angle 0.84807 / 0.42 (21360) hydrogen bonds : bond 0.04111 / 2.81 ( 1125) hydrogen bonds : angle 4.76068 / 3.51 ( 3363) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 228 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 THR cc_start: 0.7892 (OUTLIER) cc_final: 0.7670 (t) REVERT: A 139 MET cc_start: 0.7276 (ptt) cc_final: 0.7041 (pp-130) REVERT: A 217 MET cc_start: 0.8084 (tpp) cc_final: 0.7770 (tpt) REVERT: A 219 ARG cc_start: 0.8969 (ttp80) cc_final: 0.8626 (tmm-80) REVERT: A 262 ASP cc_start: 0.9264 (p0) cc_final: 0.9033 (p0) REVERT: A 340 MET cc_start: 0.9455 (pp-130) cc_final: 0.8983 (mmm) REVERT: A 357 MET cc_start: 0.5303 (ppp) cc_final: 0.3917 (ptp) REVERT: B 84 GLU cc_start: 0.6933 (mm-30) cc_final: 0.6259 (pt0) REVERT: B 85 ILE cc_start: 0.5713 (mt) cc_final: 0.5218 (tp) REVERT: B 145 MET cc_start: 0.4077 (tpt) cc_final: 0.3649 (mmp) REVERT: C 120 THR cc_start: 0.7870 (OUTLIER) cc_final: 0.7646 (t) REVERT: C 219 ARG cc_start: 0.9214 (ttm110) cc_final: 0.8623 (tmm-80) REVERT: C 262 ASP cc_start: 0.9252 (p0) cc_final: 0.9031 (p0) REVERT: C 328 GLU cc_start: 0.9317 (tm-30) cc_final: 0.9035 (tm-30) REVERT: D 18 LEU cc_start: 0.0218 (OUTLIER) cc_final: -0.0010 (tm) REVERT: D 36 MET cc_start: 0.5554 (pp-130) cc_final: 0.5263 (tmm) REVERT: D 51 MET cc_start: 0.8765 (ppp) cc_final: 0.8230 (pmm) REVERT: D 72 MET cc_start: 0.5026 (tpt) cc_final: 0.4512 (pp-130) REVERT: D 84 GLU cc_start: 0.6914 (mm-30) cc_final: 0.6452 (mm-30) REVERT: D 144 MET cc_start: 0.6798 (ptt) cc_final: 0.6051 (ppp) REVERT: E 104 PHE cc_start: 0.9283 (t80) cc_final: 0.9074 (t80) REVERT: E 120 THR cc_start: 0.7920 (OUTLIER) cc_final: 0.7693 (t) REVERT: E 139 MET cc_start: 0.7490 (OUTLIER) cc_final: 0.7080 (pp-130) REVERT: E 182 PHE cc_start: 0.7838 (t80) cc_final: 0.7571 (t80) REVERT: E 219 ARG cc_start: 0.8621 (mtm-85) cc_final: 0.8264 (ttm-80) REVERT: E 220 ARG cc_start: 0.9018 (pmt-80) cc_final: 0.8653 (pmm-80) REVERT: E 262 ASP cc_start: 0.9234 (p0) cc_final: 0.9031 (p0) REVERT: E 328 GLU cc_start: 0.9282 (tm-30) cc_final: 0.8977 (tm-30) REVERT: F 72 MET cc_start: 0.5289 (tpt) cc_final: 0.4746 (pp-130) REVERT: F 76 MET cc_start: 0.1225 (ptt) cc_final: -0.0806 (ptt) REVERT: F 84 GLU cc_start: 0.7185 (mm-30) cc_final: 0.6539 (tt0) REVERT: F 105 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.7091 (pt) REVERT: F 145 MET cc_start: 0.4892 (OUTLIER) cc_final: 0.4213 (mmm) REVERT: G 139 MET cc_start: 0.7598 (OUTLIER) cc_final: 0.7033 (tmm) REVERT: G 140 ILE cc_start: 0.7808 (OUTLIER) cc_final: 0.7592 (tp) REVERT: G 262 ASP cc_start: 0.9268 (p0) cc_final: 0.9043 (p0) REVERT: G 328 GLU cc_start: 0.9343 (tm-30) cc_final: 0.9056 (tm-30) REVERT: G 340 MET cc_start: 0.9545 (pp-130) cc_final: 0.9298 (tmm) REVERT: G 556 TYR cc_start: 0.4644 (OUTLIER) cc_final: 0.4377 (p90) REVERT: H 71 MET cc_start: 0.4289 (mmt) cc_final: 0.4086 (mtt) REVERT: H 84 GLU cc_start: 0.7175 (mm-30) cc_final: 0.6475 (pt0) REVERT: H 85 ILE cc_start: 0.5709 (mm) cc_final: 0.5084 (tt) outliers start: 49 outliers final: 22 residues processed: 258 average time/residue: 0.5612 time to fit residues: 160.3683 Evaluate side-chains 230 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 198 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 330 HIS Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 569 HIS Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 107 HIS Chi-restraints excluded: chain B residue 109 MET Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 330 HIS Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 572 MET Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 107 HIS Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 139 MET Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 107 HIS Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 145 MET Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 137 PHE Chi-restraints excluded: chain G residue 139 MET Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 330 HIS Chi-restraints excluded: chain G residue 556 TYR Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain H residue 107 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 0 optimal weight: 50.0000 chunk 19 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 138 optimal weight: 0.9990 chunk 175 optimal weight: 30.0000 chunk 30 optimal weight: 9.9990 chunk 162 optimal weight: 0.2980 chunk 153 optimal weight: 4.9990 chunk 147 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 569 HIS ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4814 r_free = 0.4814 target = 0.195956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.117477 restraints weight = 35459.479| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 3.47 r_work: 0.3333 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3282 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3282 r_free = 0.3282 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 50 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3282 r_free = 0.3282 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 52 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3282 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.7794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15828 Z= 0.150 Angle : 0.855 13.957 21360 Z= 0.423 Chirality : 0.045 0.313 2364 Planarity : 0.006 0.105 2692 Dihedral : 5.298 56.471 2192 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.91 % Allowed : 30.23 % Favored : 67.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.87 (0.20), residues: 1888 helix: 0.90 (0.13), residues: 1528 sheet: None (None), residues: 0 loop : -0.46 (0.35), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 547 TYR 0.024 0.002 TYR A 147 PHE 0.027 0.002 PHE F 12 TRP 0.022 0.001 TRP G 350 HIS 0.010 0.001 HIS G 569 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (15828) covalent geometry : angle 0.85469 / 0.42 (21360) hydrogen bonds : bond 0.04162 / 2.85 ( 1125) hydrogen bonds : angle 4.76938 / 3.52 ( 3363) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 220 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 THR cc_start: 0.7965 (OUTLIER) cc_final: 0.7741 (t) REVERT: A 139 MET cc_start: 0.7298 (ptt) cc_final: 0.7068 (pp-130) REVERT: A 214 MET cc_start: 0.7867 (tpt) cc_final: 0.7134 (tmm) REVERT: A 217 MET cc_start: 0.8135 (tpp) cc_final: 0.7801 (tpp) REVERT: A 219 ARG cc_start: 0.8912 (ttp80) cc_final: 0.8686 (tmm-80) REVERT: A 262 ASP cc_start: 0.9237 (p0) cc_final: 0.9024 (p0) REVERT: A 340 MET cc_start: 0.9415 (pp-130) cc_final: 0.8973 (mmm) REVERT: A 357 MET cc_start: 0.5079 (ppp) cc_final: 0.3529 (ptp) REVERT: B 84 GLU cc_start: 0.7075 (mm-30) cc_final: 0.6391 (pt0) REVERT: B 85 ILE cc_start: 0.5738 (mt) cc_final: 0.5246 (tp) REVERT: B 145 MET cc_start: 0.4232 (tpt) cc_final: 0.3918 (mmp) REVERT: C 120 THR cc_start: 0.7943 (OUTLIER) cc_final: 0.7728 (t) REVERT: C 139 MET cc_start: 0.7345 (ptt) cc_final: 0.7060 (pp-130) REVERT: C 182 PHE cc_start: 0.7584 (t80) cc_final: 0.7308 (m-80) REVERT: C 217 MET cc_start: 0.7792 (tpp) cc_final: 0.7461 (tpt) REVERT: C 219 ARG cc_start: 0.9230 (ttm110) cc_final: 0.8538 (tmm-80) REVERT: C 262 ASP cc_start: 0.9228 (p0) cc_final: 0.9023 (p0) REVERT: C 328 GLU cc_start: 0.9295 (tm-30) cc_final: 0.8894 (tm-30) REVERT: D 18 LEU cc_start: 0.0227 (OUTLIER) cc_final: -0.0007 (tm) REVERT: D 36 MET cc_start: 0.5620 (pp-130) cc_final: 0.5176 (tmm) REVERT: D 84 GLU cc_start: 0.6910 (mm-30) cc_final: 0.6372 (mm-30) REVERT: D 144 MET cc_start: 0.6576 (ptt) cc_final: 0.5779 (ppp) REVERT: E 120 THR cc_start: 0.7981 (OUTLIER) cc_final: 0.7769 (t) REVERT: E 139 MET cc_start: 0.7579 (OUTLIER) cc_final: 0.7153 (pp-130) REVERT: E 182 PHE cc_start: 0.7722 (t80) cc_final: 0.7456 (t80) REVERT: E 219 ARG cc_start: 0.8589 (mtm-85) cc_final: 0.8230 (ttm-80) REVERT: E 328 GLU cc_start: 0.9262 (tm-30) cc_final: 0.8934 (tm-30) REVERT: E 569 HIS cc_start: 0.9387 (p-80) cc_final: 0.9116 (p90) REVERT: F 72 MET cc_start: 0.5454 (tpt) cc_final: 0.4865 (pp-130) REVERT: F 84 GLU cc_start: 0.7196 (mm-30) cc_final: 0.6588 (tt0) REVERT: F 105 LEU cc_start: 0.7424 (OUTLIER) cc_final: 0.7009 (pt) REVERT: F 145 MET cc_start: 0.4797 (OUTLIER) cc_final: 0.4158 (mmm) REVERT: G 139 MET cc_start: 0.7632 (OUTLIER) cc_final: 0.7037 (tmm) REVERT: G 262 ASP cc_start: 0.9221 (p0) cc_final: 0.9005 (p0) REVERT: G 328 GLU cc_start: 0.9342 (tm-30) cc_final: 0.8858 (tm-30) REVERT: G 340 MET cc_start: 0.9517 (pp-130) cc_final: 0.9088 (mmp) REVERT: H 36 MET cc_start: 0.5899 (pp-130) cc_final: 0.5248 (tmm) REVERT: H 71 MET cc_start: 0.4616 (mmt) cc_final: 0.4412 (mtt) REVERT: H 84 GLU cc_start: 0.7241 (mm-30) cc_final: 0.6496 (pt0) REVERT: H 85 ILE cc_start: 0.5741 (mm) cc_final: 0.5174 (tt) REVERT: H 145 MET cc_start: 0.4839 (tpt) cc_final: 0.4348 (mmm) outliers start: 31 outliers final: 19 residues processed: 240 average time/residue: 0.5187 time to fit residues: 137.9669 Evaluate side-chains 234 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 207 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 569 HIS Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 99 TYR Chi-restraints excluded: chain B residue 107 HIS Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 330 HIS Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 572 MET Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 107 HIS Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 139 MET Chi-restraints excluded: chain E residue 330 HIS Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 145 MET Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 137 PHE Chi-restraints excluded: chain G residue 139 MET Chi-restraints excluded: chain G residue 330 HIS Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain H residue 107 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 115 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 149 optimal weight: 0.9980 chunk 110 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 chunk 79 optimal weight: 40.0000 chunk 152 optimal weight: 6.9990 chunk 72 optimal weight: 0.9990 chunk 101 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 8 GLN ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 8 GLN ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4803 r_free = 0.4803 target = 0.194676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.116170 restraints weight = 35587.866| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 3.97 r_work: 0.3232 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3207 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3207 r_free = 0.3207 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 52 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3207 r_free = 0.3207 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 52 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.3207 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.7953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 15828 Z= 0.176 Angle : 0.860 15.859 21360 Z= 0.428 Chirality : 0.046 0.292 2364 Planarity : 0.006 0.104 2692 Dihedral : 5.338 56.740 2192 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.60 % Allowed : 30.54 % Favored : 67.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.01 (0.20), residues: 1888 helix: 0.96 (0.14), residues: 1516 sheet: None (None), residues: 0 loop : -0.16 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 547 TYR 0.024 0.002 TYR B 99 PHE 0.025 0.002 PHE D 12 TRP 0.024 0.001 TRP G 350 HIS 0.010 0.001 HIS G 569 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.18 (15828) covalent geometry : angle 0.85979 / 0.43 (21360) hydrogen bonds : bond 0.04311 / 2.95 ( 1125) hydrogen bonds : angle 4.81365 / 3.56 ( 3363) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8811.40 seconds wall clock time: 149 minutes 56.61 seconds (8996.61 seconds total)