Starting phenix.real_space_refine on Thu Feb 5 05:57:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vnq_32045/02_2026/7vnq_32045_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vnq_32045/02_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_32045/02_2026/7vnq_32045.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vnq_32045/02_2026/7vnq_32045.map" model { file = "/net/cci-nas-00/data/ceres_data/7vnq_32045/02_2026/7vnq_32045_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vnq_32045/02_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/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, 22 Unusual residues: {' K': 3, '7YV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 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: 3.67, per 1000 atoms: 0.24 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: 1.61 Conformation dependent library (CDL) restraints added in 695.0 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: 0.47 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: 2.32 Time building geometry restraints manager: 1.97 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: 3.000 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.620 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 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:6.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4509 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 covalent geometry : bond 0.00985 (15828) covalent geometry : angle 1.02425 (21360) hydrogen bonds : bond 0.15372 ( 1125) hydrogen bonds : angle 6.33381 ( 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 : 0.592 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: 0.6502 time to fit residues: 339.3226 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 : 0.576 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.196964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.122021 restraints weight = 36555.252| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 6.19 r_work: 0.3223 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3187 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 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 = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| r_final: 0.3186 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.4085 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 : 0.771 12.397 21360 Z= 0.395 Chirality : 0.043 0.167 2364 Planarity : 0.006 0.110 2692 Dihedral : 7.020 57.263 2240 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 6.10 % Allowed : 16.69 % 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: 0.83 (0.19), residues: 1888 helix: 0.79 (0.13), residues: 1536 sheet: None (None), residues: 0 loop : -0.06 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 575 TYR 0.019 0.002 TYR C 147 PHE 0.026 0.002 PHE E 169 TRP 0.013 0.002 TRP E 294 HIS 0.005 0.001 HIS E 102 Details of bonding type rmsd covalent geometry : bond 0.00475 (15828) covalent geometry : angle 0.77106 (21360) hydrogen bonds : bond 0.04938 ( 1125) hydrogen bonds : angle 4.91848 ( 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 382 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 283 time to evaluate : 0.607 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: 0.7217 (OUTLIER) cc_final: 0.6917 (tmm) REVERT: A 182 PHE cc_start: 0.7853 (OUTLIER) cc_final: 0.7484 (t80) REVERT: A 207 ARG cc_start: 0.8373 (mtt180) cc_final: 0.7935 (mtp180) REVERT: A 217 MET cc_start: 0.5867 (ppp) cc_final: 0.4930 (ppp) REVERT: A 220 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.7989 (pmt-80) REVERT: A 328 GLU cc_start: 0.9270 (tm-30) cc_final: 0.9014 (tm-30) REVERT: A 340 MET cc_start: 0.9293 (mmm) cc_final: 0.9028 (tmm) REVERT: A 559 LYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8724 (pttt) REVERT: B 12 PHE cc_start: 0.6816 (m-10) cc_final: 0.6343 (m-80) REVERT: B 18 LEU cc_start: -0.0345 (OUTLIER) cc_final: -0.0672 (tm) REVERT: B 76 MET cc_start: 0.0180 (ptm) cc_final: -0.0501 (ptm) REVERT: B 126 ARG cc_start: 0.8781 (mtm-85) cc_final: 0.8465 (ptt90) REVERT: B 145 MET cc_start: 0.4079 (ttm) cc_final: 0.3770 (mmm) REVERT: C 139 MET cc_start: 0.7159 (OUTLIER) cc_final: 0.6856 (tmm) REVERT: C 220 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.7697 (pmm150) REVERT: C 328 GLU cc_start: 0.9237 (tm-30) cc_final: 0.8988 (tm-30) REVERT: C 335 PHE cc_start: 0.8282 (t80) cc_final: 0.7857 (t80) REVERT: C 340 MET cc_start: 0.9396 (mmm) cc_final: 0.9132 (tpp) REVERT: C 563 GLU cc_start: 0.9579 (tm-30) cc_final: 0.9365 (pp20) REVERT: D 18 LEU cc_start: 0.0065 (OUTLIER) cc_final: -0.0261 (tm) REVERT: D 24 ASP cc_start: 0.5649 (t0) cc_final: 0.5275 (p0) REVERT: D 126 ARG cc_start: 0.8602 (mtm-85) cc_final: 0.8212 (ptt90) REVERT: D 144 MET cc_start: 0.7756 (ptp) cc_final: 0.6982 (pp-130) REVERT: D 145 MET cc_start: 0.3817 (ttm) cc_final: 0.3610 (ttp) REVERT: E 139 MET cc_start: 0.7368 (OUTLIER) cc_final: 0.7013 (tmm) REVERT: E 182 PHE cc_start: 0.7957 (OUTLIER) cc_final: 0.7612 (t80) REVERT: E 207 ARG cc_start: 0.8556 (mtt-85) cc_final: 0.8305 (mtt180) REVERT: E 220 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7551 (pmm150) REVERT: E 328 GLU cc_start: 0.9239 (tm-30) cc_final: 0.8956 (tm-30) REVERT: E 335 PHE cc_start: 0.8290 (t80) cc_final: 0.7820 (t80) REVERT: E 340 MET cc_start: 0.9377 (mmm) cc_final: 0.9146 (tpp) REVERT: E 542 PHE cc_start: 0.7780 (t80) cc_final: 0.7117 (t80) REVERT: F 18 LEU cc_start: 0.0323 (OUTLIER) cc_final: -0.0050 (tm) REVERT: F 145 MET cc_start: 0.3624 (ttm) cc_final: 0.2917 (ttp) REVERT: G 220 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.7908 (pmm150) REVERT: G 328 GLU cc_start: 0.9331 (tm-30) cc_final: 0.9128 (tm-30) REVERT: G 563 GLU cc_start: 0.9558 (tm-30) cc_final: 0.9327 (pp20) REVERT: H 18 LEU cc_start: -0.0143 (OUTLIER) cc_final: -0.0449 (tm) REVERT: H 69 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.7321 (mt) REVERT: H 145 MET cc_start: 0.4081 (ttm) cc_final: 0.3827 (ttt) outliers start: 99 outliers final: 39 residues processed: 351 average time/residue: 0.5893 time to fit residues: 226.7714 Evaluate side-chains 265 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 211 time to evaluate : 0.476 ------------------------------------------------------------------------------- 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 182 PHE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 220 ARG 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 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: 0.7980 chunk 185 optimal weight: 1.9990 chunk 155 optimal weight: 0.6980 chunk 154 optimal weight: 0.9990 chunk 103 optimal weight: 10.0000 chunk 104 optimal weight: 7.9990 chunk 83 optimal weight: 0.0020 chunk 66 optimal weight: 0.8980 chunk 160 optimal weight: 0.9990 chunk 172 optimal weight: 8.9990 chunk 173 optimal weight: 5.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 HIS ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 HIS D 42 ASN ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 ASN E 124 HIS ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 111 ASN F 143 GLN 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4842 r_free = 0.4842 target = 0.197663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.120489 restraints weight = 37118.864| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 3.86 r_work: 0.3260 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3255 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3255 r_free = 0.3255 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 41 | |-----------------------------------------------------------------------------| r_final: 0.3254 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.4974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15828 Z= 0.142 Angle : 0.712 13.028 21360 Z= 0.355 Chirality : 0.040 0.178 2364 Planarity : 0.006 0.112 2692 Dihedral : 6.440 55.290 2222 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 5.67 % Allowed : 19.03 % Favored : 75.31 % 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: 1.42 (0.20), residues: 1888 helix: 1.27 (0.13), residues: 1528 sheet: None (None), residues: 0 loop : -0.21 (0.36), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 106 TYR 0.021 0.002 TYR E 556 PHE 0.025 0.001 PHE E 169 TRP 0.011 0.001 TRP A 350 HIS 0.007 0.001 HIS B 107 Details of bonding type rmsd covalent geometry : bond 0.00299 (15828) covalent geometry : angle 0.71185 (21360) hydrogen bonds : bond 0.04283 ( 1125) hydrogen bonds : angle 4.68850 ( 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 372 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 280 time to evaluate : 0.443 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: 0.7797 (OUTLIER) cc_final: 0.7562 (t) REVERT: A 220 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.8065 (pmm150) REVERT: A 563 GLU cc_start: 0.9539 (pp20) cc_final: 0.9337 (pp20) REVERT: B 18 LEU cc_start: -0.0550 (OUTLIER) cc_final: -0.0881 (tm) REVERT: B 76 MET cc_start: -0.0166 (ptm) cc_final: -0.0634 (ptm) REVERT: C 120 THR cc_start: 0.7771 (OUTLIER) cc_final: 0.7530 (t) REVERT: C 139 MET cc_start: 0.7158 (mtp) cc_final: 0.6948 (tmm) REVERT: C 217 MET cc_start: 0.5206 (ppp) cc_final: 0.4083 (ppp) REVERT: C 219 ARG cc_start: 0.8295 (mpp-170) cc_final: 0.7880 (ttp80) REVERT: C 220 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7836 (pmm150) REVERT: C 328 GLU cc_start: 0.9271 (tm-30) cc_final: 0.8949 (tm-30) REVERT: C 340 MET cc_start: 0.9427 (mmm) cc_final: 0.9221 (tmm) REVERT: C 357 MET cc_start: 0.4049 (ppp) cc_final: 0.3761 (ppp) REVERT: D 18 LEU cc_start: 0.0466 (OUTLIER) cc_final: 0.0170 (tm) REVERT: D 24 ASP cc_start: 0.5667 (t0) cc_final: 0.5268 (p0) REVERT: D 41 GLN cc_start: 0.6885 (tp-100) cc_final: 0.6551 (pt0) REVERT: D 144 MET cc_start: 0.8085 (ptp) cc_final: 0.7332 (pp-130) REVERT: E 120 THR cc_start: 0.7831 (OUTLIER) cc_final: 0.7597 (t) REVERT: E 139 MET cc_start: 0.7252 (OUTLIER) cc_final: 0.7011 (tmm) REVERT: E 182 PHE cc_start: 0.7919 (OUTLIER) cc_final: 0.7558 (t80) REVERT: E 220 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7709 (pmm150) REVERT: E 328 GLU cc_start: 0.9226 (tm-30) cc_final: 0.8885 (tm-30) REVERT: E 350 TRP cc_start: 0.6283 (t-100) cc_final: 0.5917 (t-100) REVERT: E 357 MET cc_start: 0.4636 (ppp) cc_final: 0.4160 (ppp) REVERT: F 18 LEU cc_start: 0.0576 (OUTLIER) cc_final: 0.0240 (tm) REVERT: F 111 ASN cc_start: 0.8664 (OUTLIER) cc_final: 0.8452 (p0) REVERT: F 145 MET cc_start: 0.3732 (ttm) cc_final: 0.3380 (tpp) REVERT: G 139 MET cc_start: 0.7240 (OUTLIER) cc_final: 0.6640 (tmm) REVERT: G 182 PHE cc_start: 0.7803 (t80) cc_final: 0.7601 (t80) REVERT: G 220 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.7762 (pmm150) REVERT: G 262 ASP cc_start: 0.9206 (p0) cc_final: 0.8993 (p0) REVERT: G 328 GLU cc_start: 0.9318 (tm-30) cc_final: 0.9009 (tm-30) REVERT: G 563 GLU cc_start: 0.9589 (tm-30) cc_final: 0.9233 (pp20) REVERT: H 18 LEU cc_start: -0.0103 (OUTLIER) cc_final: -0.0453 (tm) REVERT: H 41 GLN cc_start: 0.7012 (tp-100) cc_final: 0.6691 (pt0) REVERT: H 69 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7530 (mt) REVERT: H 109 MET cc_start: 0.7981 (ptm) cc_final: 0.7737 (ptm) outliers start: 92 outliers final: 32 residues processed: 344 average time/residue: 0.6740 time to fit residues: 252.5452 Evaluate side-chains 264 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 216 time to evaluate : 0.620 ------------------------------------------------------------------------------- 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 182 PHE 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 F residue 111 ASN 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 212 LEU 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 3 optimal weight: 9.9990 chunk 71 optimal weight: 2.9990 chunk 127 optimal weight: 20.0000 chunk 104 optimal weight: 5.9990 chunk 163 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 103 optimal weight: 20.0000 chunk 37 optimal weight: 5.9990 chunk 33 optimal weight: 0.1980 chunk 36 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4812 r_free = 0.4812 target = 0.194869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.113172 restraints weight = 36349.416| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 3.54 r_work: 0.3211 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3195 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 41 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 43 | |-----------------------------------------------------------------------------| r_final: 0.3195 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.5543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 15828 Z= 0.210 Angle : 0.762 11.079 21360 Z= 0.380 Chirality : 0.043 0.234 2364 Planarity : 0.006 0.112 2692 Dihedral : 5.291 54.993 2200 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 5.48 % Allowed : 21.98 % Favored : 72.54 % 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: 1.51 (0.20), residues: 1888 helix: 1.28 (0.13), residues: 1544 sheet: None (None), residues: 0 loop : 0.06 (0.37), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 547 TYR 0.020 0.002 TYR A 147 PHE 0.025 0.002 PHE E 169 TRP 0.013 0.001 TRP C 350 HIS 0.008 0.001 HIS B 107 Details of bonding type rmsd covalent geometry : bond 0.00471 (15828) covalent geometry : angle 0.76213 (21360) hydrogen bonds : bond 0.04446 ( 1125) hydrogen bonds : angle 4.68803 ( 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: 89 poor density : 241 time to evaluate : 0.758 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: A 120 THR cc_start: 0.7863 (OUTLIER) cc_final: 0.7597 (t) REVERT: A 220 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.8092 (pmm150) REVERT: B 18 LEU cc_start: -0.0352 (OUTLIER) cc_final: -0.0563 (tm) REVERT: B 72 MET cc_start: 0.3574 (tmm) cc_final: 0.3304 (pp-130) REVERT: B 84 GLU cc_start: 0.7116 (mm-30) cc_final: 0.6206 (pt0) REVERT: B 85 ILE cc_start: 0.5125 (mm) cc_final: 0.4395 (mt) REVERT: B 109 MET cc_start: 0.7093 (tmm) cc_final: 0.6859 (ppp) REVERT: B 124 MET cc_start: 0.6207 (ppp) cc_final: 0.5898 (ppp) REVERT: B 126 ARG cc_start: 0.8669 (mtm-85) cc_final: 0.8360 (ppt170) REVERT: C 207 ARG cc_start: 0.8532 (mtt180) cc_final: 0.8246 (mtp180) REVERT: C 220 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.8124 (pmm150) REVERT: C 262 ASP cc_start: 0.9207 (p0) cc_final: 0.8951 (p0) REVERT: C 328 GLU cc_start: 0.9292 (tm-30) cc_final: 0.8966 (tm-30) REVERT: D 18 LEU cc_start: 0.0423 (OUTLIER) cc_final: 0.0155 (tm) REVERT: D 72 MET cc_start: 0.3477 (tpt) cc_final: 0.3213 (pp-130) REVERT: D 122 ASP cc_start: 0.8676 (m-30) cc_final: 0.8340 (m-30) REVERT: D 126 ARG cc_start: 0.8463 (mtm-85) cc_final: 0.8020 (ppt170) REVERT: E 139 MET cc_start: 0.7409 (OUTLIER) cc_final: 0.7145 (tmm) REVERT: E 219 ARG cc_start: 0.8435 (mpp-170) cc_final: 0.7678 (ttm110) REVERT: E 220 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.8085 (pmm150) REVERT: E 262 ASP cc_start: 0.9180 (p0) cc_final: 0.8931 (p0) REVERT: E 328 GLU cc_start: 0.9266 (tm-30) cc_final: 0.8927 (tm-30) REVERT: F 18 LEU cc_start: 0.1002 (OUTLIER) cc_final: 0.0766 (tm) REVERT: G 139 MET cc_start: 0.7375 (OUTLIER) cc_final: 0.6773 (tmm) REVERT: G 220 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.8265 (pmm150) REVERT: G 262 ASP cc_start: 0.9195 (p0) cc_final: 0.8951 (p0) REVERT: G 328 GLU cc_start: 0.9337 (tm-30) cc_final: 0.9115 (tm-30) REVERT: H 18 LEU cc_start: 0.0302 (OUTLIER) cc_final: -0.0025 (tm) REVERT: H 76 MET cc_start: 0.1472 (ptt) cc_final: 0.0729 (ptt) REVERT: H 84 GLU cc_start: 0.7249 (mm-30) cc_final: 0.6492 (tt0) REVERT: H 106 ARG cc_start: 0.9254 (mmm160) cc_final: 0.8773 (mmp80) outliers start: 89 outliers final: 36 residues processed: 302 average time/residue: 0.6460 time to fit residues: 214.0617 Evaluate side-chains 261 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 214 time to evaluate : 0.619 ------------------------------------------------------------------------------- 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 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 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 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 137 PHE 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 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 64 optimal weight: 0.6980 chunk 160 optimal weight: 2.9990 chunk 47 optimal weight: 50.0000 chunk 106 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 166 optimal weight: 7.9990 chunk 162 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 152 optimal weight: 10.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 HIS A 344 ASN ** 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** ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 111 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4789 r_free = 0.4789 target = 0.195972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.116281 restraints weight = 36636.821| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 4.19 r_work: 0.3141 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3149 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 43 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 45 | |-----------------------------------------------------------------------------| r_final: 0.3149 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.6083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15828 Z= 0.149 Angle : 0.733 11.659 21360 Z= 0.363 Chirality : 0.041 0.190 2364 Planarity : 0.006 0.109 2692 Dihedral : 5.054 53.294 2192 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.37 % Allowed : 24.08 % Favored : 71.55 % 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: 1.48 (0.20), residues: 1888 helix: 1.31 (0.13), residues: 1540 sheet: None (None), residues: 0 loop : -0.25 (0.36), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 547 TYR 0.019 0.001 TYR A 147 PHE 0.024 0.002 PHE A 169 TRP 0.014 0.001 TRP E 350 HIS 0.009 0.001 HIS H 107 Details of bonding type rmsd covalent geometry : bond 0.00324 (15828) covalent geometry : angle 0.73304 (21360) hydrogen bonds : bond 0.04038 ( 1125) hydrogen bonds : angle 4.63602 ( 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 318 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 247 time to evaluate : 0.605 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: A 120 THR cc_start: 0.7697 (OUTLIER) cc_final: 0.7458 (t) REVERT: A 207 ARG cc_start: 0.8342 (mtt180) cc_final: 0.8109 (mtp180) REVERT: A 220 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.8087 (pmm150) REVERT: A 340 MET cc_start: 0.9410 (pp-130) cc_final: 0.9032 (mmp) REVERT: A 575 ARG cc_start: 0.7373 (ttt180) cc_final: 0.7130 (ttt-90) REVERT: B 72 MET cc_start: 0.3934 (tmm) cc_final: 0.3731 (pp-130) REVERT: B 84 GLU cc_start: 0.6994 (mm-30) cc_final: 0.6503 (mm-30) REVERT: B 145 MET cc_start: 0.3789 (OUTLIER) cc_final: 0.3567 (tpp) REVERT: C 120 THR cc_start: 0.7721 (OUTLIER) cc_final: 0.7482 (t) REVERT: C 214 MET cc_start: 0.7651 (tpt) cc_final: 0.7065 (tmm) REVERT: C 218 ASP cc_start: 0.7163 (OUTLIER) cc_final: 0.6226 (t0) REVERT: C 219 ARG cc_start: 0.8268 (mtm-85) cc_final: 0.7922 (ttm110) REVERT: C 220 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.8270 (pmm150) REVERT: C 262 ASP cc_start: 0.9244 (p0) cc_final: 0.9030 (p0) REVERT: C 328 GLU cc_start: 0.9271 (tm-30) cc_final: 0.8979 (tm-30) REVERT: C 572 MET cc_start: 0.9149 (tpt) cc_final: 0.8792 (mtt) REVERT: D 18 LEU cc_start: 0.0321 (OUTLIER) cc_final: 0.0066 (tm) REVERT: D 122 ASP cc_start: 0.8665 (m-30) cc_final: 0.8400 (m-30) REVERT: D 126 ARG cc_start: 0.8431 (mtm-85) cc_final: 0.8050 (ppt170) REVERT: D 144 MET cc_start: 0.7446 (ptt) cc_final: 0.6293 (pp-130) REVERT: E 120 THR cc_start: 0.7752 (OUTLIER) cc_final: 0.7509 (t) REVERT: E 139 MET cc_start: 0.7423 (mtp) cc_final: 0.7191 (tmm) REVERT: E 219 ARG cc_start: 0.8322 (mpp-170) cc_final: 0.7837 (ttm110) REVERT: E 220 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.8128 (pmm150) REVERT: E 262 ASP cc_start: 0.9218 (p0) cc_final: 0.9005 (p0) REVERT: E 328 GLU cc_start: 0.9251 (tm-30) cc_final: 0.8947 (tm-30) REVERT: E 335 PHE cc_start: 0.8579 (t80) cc_final: 0.8139 (t80) REVERT: F 18 LEU cc_start: 0.0550 (OUTLIER) cc_final: 0.0281 (tm) REVERT: F 72 MET cc_start: 0.4806 (tpt) cc_final: 0.4346 (pp-130) REVERT: F 84 GLU cc_start: 0.6997 (mm-30) cc_final: 0.6569 (mm-30) REVERT: G 139 MET cc_start: 0.7410 (OUTLIER) cc_final: 0.6865 (tmm) REVERT: G 182 PHE cc_start: 0.7967 (t80) cc_final: 0.7762 (t80) REVERT: G 219 ARG cc_start: 0.8297 (mtm-85) cc_final: 0.7940 (ttm110) REVERT: G 220 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.8212 (pmm150) REVERT: G 262 ASP cc_start: 0.9262 (p0) cc_final: 0.9058 (p0) REVERT: G 328 GLU cc_start: 0.9325 (tm-30) cc_final: 0.9074 (tm-30) REVERT: G 556 TYR cc_start: 0.4979 (OUTLIER) cc_final: 0.4614 (p90) REVERT: H 18 LEU cc_start: 0.0071 (OUTLIER) cc_final: -0.0235 (tm) REVERT: H 84 GLU cc_start: 0.7094 (mm-30) cc_final: 0.6299 (tt0) REVERT: H 106 ARG cc_start: 0.9322 (mmm160) cc_final: 0.8932 (mmp80) REVERT: H 145 MET cc_start: 0.4340 (tpt) cc_final: 0.3930 (mmm) outliers start: 71 outliers final: 28 residues processed: 298 average time/residue: 0.6460 time to fit residues: 210.3430 Evaluate side-chains 267 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 225 time to evaluate : 0.506 ------------------------------------------------------------------------------- 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 309 SER 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 29 THR 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 B residue 145 MET 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 587 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 220 ARG 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 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 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 136 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 12 optimal weight: 7.9990 chunk 172 optimal weight: 6.9990 chunk 153 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 104 optimal weight: 0.0670 chunk 0 optimal weight: 40.0000 chunk 68 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 73 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 overall best weight: 1.1922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 HIS B 41 GLN ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 569 HIS ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 41 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4792 r_free = 0.4792 target = 0.196505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.115939 restraints weight = 36339.575| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 3.76 r_work: 0.3166 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3164 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 45 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| r_final: 0.3164 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.6440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15828 Z= 0.148 Angle : 0.760 12.065 21360 Z= 0.373 Chirality : 0.041 0.186 2364 Planarity : 0.006 0.106 2692 Dihedral : 5.052 54.185 2192 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 4.50 % Allowed : 24.94 % Favored : 70.57 % 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: 1.43 (0.20), residues: 1888 helix: 1.28 (0.14), residues: 1524 sheet: None (None), residues: 0 loop : -0.20 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 554 TYR 0.016 0.001 TYR C 147 PHE 0.024 0.001 PHE A 169 TRP 0.014 0.001 TRP E 350 HIS 0.004 0.001 HIS E 102 Details of bonding type rmsd covalent geometry : bond 0.00322 (15828) covalent geometry : angle 0.76002 (21360) hydrogen bonds : bond 0.03974 ( 1125) hydrogen bonds : angle 4.61955 ( 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 326 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 253 time to evaluate : 0.593 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: A 120 THR cc_start: 0.7751 (OUTLIER) cc_final: 0.7518 (t) REVERT: A 219 ARG cc_start: 0.9192 (mtt90) cc_final: 0.8383 (mpp-170) REVERT: A 220 ARG cc_start: 0.8637 (OUTLIER) cc_final: 0.8176 (pmm150) REVERT: A 260 GLU cc_start: 0.8595 (pt0) cc_final: 0.8130 (mt-10) REVERT: A 340 MET cc_start: 0.9356 (pp-130) cc_final: 0.9041 (mmp) REVERT: A 351 ARG cc_start: 0.6221 (mtt90) cc_final: 0.5944 (tpt170) REVERT: B 41 GLN cc_start: 0.6051 (OUTLIER) cc_final: 0.5809 (pp30) REVERT: B 124 MET cc_start: 0.5544 (ppp) cc_final: 0.5242 (ppp) REVERT: B 126 ARG cc_start: 0.8696 (mtm-85) cc_final: 0.8404 (ppt170) REVERT: C 120 THR cc_start: 0.7775 (OUTLIER) cc_final: 0.7544 (t) REVERT: C 207 ARG cc_start: 0.8481 (mtt180) cc_final: 0.8272 (mtp180) REVERT: C 214 MET cc_start: 0.7603 (tpt) cc_final: 0.7033 (tmm) REVERT: C 218 ASP cc_start: 0.7146 (OUTLIER) cc_final: 0.6227 (t0) REVERT: C 220 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.8222 (pmm150) REVERT: C 262 ASP cc_start: 0.9250 (p0) cc_final: 0.9041 (p0) REVERT: C 328 GLU cc_start: 0.9259 (tm-30) cc_final: 0.8971 (tm-30) REVERT: D 18 LEU cc_start: 0.0174 (OUTLIER) cc_final: -0.0088 (tm) REVERT: D 72 MET cc_start: 0.4745 (tpt) cc_final: 0.4237 (pp-130) REVERT: D 84 GLU cc_start: 0.6928 (mm-30) cc_final: 0.6592 (mm-30) REVERT: D 122 ASP cc_start: 0.8674 (m-30) cc_final: 0.8429 (m-30) REVERT: D 126 ARG cc_start: 0.8424 (mtm-85) cc_final: 0.8048 (ppt170) REVERT: D 145 MET cc_start: 0.4200 (ttt) cc_final: 0.3791 (mmt) REVERT: E 120 THR cc_start: 0.7824 (OUTLIER) cc_final: 0.7595 (t) REVERT: E 214 MET cc_start: 0.7565 (tpt) cc_final: 0.6885 (tmm) REVERT: E 219 ARG cc_start: 0.8180 (mpp-170) cc_final: 0.7913 (ttm110) REVERT: E 220 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.8155 (pmm150) REVERT: E 262 ASP cc_start: 0.9214 (p0) cc_final: 0.9006 (p0) REVERT: E 328 GLU cc_start: 0.9247 (tm-30) cc_final: 0.8959 (tm-30) REVERT: E 340 MET cc_start: 0.9490 (pp-130) cc_final: 0.9067 (mmp) REVERT: F 18 LEU cc_start: 0.0478 (OUTLIER) cc_final: 0.0244 (tm) REVERT: F 72 MET cc_start: 0.4863 (tpt) cc_final: 0.4562 (pp-130) REVERT: F 84 GLU cc_start: 0.6990 (mm-30) cc_final: 0.6498 (mm-30) REVERT: F 109 MET cc_start: 0.7878 (ppp) cc_final: 0.7647 (ppp) REVERT: G 139 MET cc_start: 0.7475 (OUTLIER) cc_final: 0.6938 (tmm) REVERT: G 214 MET cc_start: 0.7632 (tpt) cc_final: 0.6931 (tmm) REVERT: G 219 ARG cc_start: 0.8230 (mtm-85) cc_final: 0.8012 (ttm110) REVERT: G 220 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.8289 (pmm150) REVERT: G 262 ASP cc_start: 0.9253 (p0) cc_final: 0.9050 (p0) REVERT: G 328 GLU cc_start: 0.9319 (tm-30) cc_final: 0.9046 (tm-30) REVERT: G 340 MET cc_start: 0.9542 (ppp) cc_final: 0.9155 (mmp) REVERT: G 556 TYR cc_start: 0.5043 (OUTLIER) cc_final: 0.4609 (p90) REVERT: H 18 LEU cc_start: -0.0018 (OUTLIER) cc_final: -0.0341 (tm) REVERT: H 84 GLU cc_start: 0.7200 (mm-30) cc_final: 0.6376 (pt0) REVERT: H 85 ILE cc_start: 0.5028 (mm) cc_final: 0.4661 (mt) REVERT: H 106 ARG cc_start: 0.9306 (mmm160) cc_final: 0.8907 (mmt90) REVERT: H 145 MET cc_start: 0.4535 (tpt) cc_final: 0.4171 (mmm) outliers start: 73 outliers final: 36 residues processed: 307 average time/residue: 0.6856 time to fit residues: 229.4102 Evaluate side-chains 270 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 220 time to evaluate : 0.570 ------------------------------------------------------------------------------- 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 124 HIS Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 309 SER 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 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 137 PHE 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 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 136 VAL 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 220 ARG Chi-restraints excluded: chain E residue 552 THR 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 142 VAL Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 124 HIS 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 120 optimal weight: 1.9990 chunk 148 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 180 optimal weight: 5.9990 chunk 58 optimal weight: 40.0000 chunk 170 optimal weight: 8.9990 chunk 56 optimal weight: 3.9990 chunk 35 optimal weight: 30.0000 chunk 172 optimal weight: 9.9990 chunk 42 optimal weight: 30.0000 chunk 40 optimal weight: 5.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 HIS B 41 GLN B 42 ASN ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 HIS D 41 GLN ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4757 r_free = 0.4757 target = 0.193209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.111068 restraints weight = 36136.829| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 3.91 r_work: 0.3081 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3082 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 46 | |-----------------------------------------------------------------------------| r_final: 0.3082 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.6719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 15828 Z= 0.256 Angle : 0.827 12.382 21360 Z= 0.413 Chirality : 0.045 0.174 2364 Planarity : 0.006 0.105 2692 Dihedral : 5.229 54.156 2192 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 18.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 4.37 % Allowed : 26.05 % Favored : 69.58 % 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: 1.17 (0.20), residues: 1888 helix: 1.07 (0.13), residues: 1540 sheet: None (None), residues: 0 loop : -0.22 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 547 TYR 0.016 0.002 TYR B 99 PHE 0.025 0.002 PHE C 169 TRP 0.016 0.001 TRP E 350 HIS 0.016 0.002 HIS C 569 Details of bonding type rmsd covalent geometry : bond 0.00583 (15828) covalent geometry : angle 0.82720 (21360) hydrogen bonds : bond 0.04496 ( 1125) hydrogen bonds : angle 4.80098 ( 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 307 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 236 time to evaluate : 0.651 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: A 219 ARG cc_start: 0.9201 (mtt90) cc_final: 0.8661 (mpt180) REVERT: A 340 MET cc_start: 0.9391 (pp-130) cc_final: 0.8994 (mpp) REVERT: A 351 ARG cc_start: 0.6293 (mtt90) cc_final: 0.6052 (tpt170) REVERT: B 41 GLN cc_start: 0.5916 (OUTLIER) cc_final: 0.5604 (pp30) REVERT: B 115 LYS cc_start: 0.9245 (mmmm) cc_final: 0.8993 (mmmt) REVERT: B 124 MET cc_start: 0.5912 (ppp) cc_final: 0.5673 (ppp) REVERT: C 214 MET cc_start: 0.7547 (tpt) cc_final: 0.7241 (tpt) REVERT: C 219 ARG cc_start: 0.9271 (ttm110) cc_final: 0.8770 (ttm170) REVERT: C 262 ASP cc_start: 0.9275 (p0) cc_final: 0.9009 (p0) REVERT: C 328 GLU cc_start: 0.9300 (tm-30) cc_final: 0.9070 (tm-30) REVERT: D 18 LEU cc_start: 0.0138 (OUTLIER) cc_final: -0.0112 (tm) REVERT: D 72 MET cc_start: 0.4778 (tpt) cc_final: 0.4334 (pp-130) REVERT: D 84 GLU cc_start: 0.7021 (mm-30) cc_final: 0.6701 (mm-30) REVERT: D 106 ARG cc_start: 0.8745 (mmm160) cc_final: 0.8233 (mmt90) REVERT: D 122 ASP cc_start: 0.8636 (m-30) cc_final: 0.8365 (m-30) REVERT: D 126 ARG cc_start: 0.8422 (mtm-85) cc_final: 0.8158 (ppt170) REVERT: D 145 MET cc_start: 0.4504 (OUTLIER) cc_final: 0.4156 (mmt) REVERT: E 214 MET cc_start: 0.7590 (tpt) cc_final: 0.7342 (tpt) REVERT: E 218 ASP cc_start: 0.7407 (OUTLIER) cc_final: 0.6993 (m-30) REVERT: E 262 ASP cc_start: 0.9253 (p0) cc_final: 0.8988 (p0) REVERT: E 328 GLU cc_start: 0.9290 (tm-30) cc_final: 0.9042 (tm-30) REVERT: E 340 MET cc_start: 0.9440 (OUTLIER) cc_final: 0.9008 (mpp) REVERT: F 18 LEU cc_start: 0.0572 (OUTLIER) cc_final: 0.0351 (tm) REVERT: F 84 GLU cc_start: 0.7013 (mm-30) cc_final: 0.6504 (mm-30) REVERT: F 145 MET cc_start: 0.4793 (ttt) cc_final: 0.4156 (mmp) REVERT: G 139 MET cc_start: 0.7494 (OUTLIER) cc_final: 0.6896 (tmm) REVERT: G 262 ASP cc_start: 0.9264 (p0) cc_final: 0.9004 (p0) REVERT: G 328 GLU cc_start: 0.9327 (tm-30) cc_final: 0.9094 (tm-30) REVERT: G 340 MET cc_start: 0.9556 (ppp) cc_final: 0.9155 (mmp) REVERT: G 556 TYR cc_start: 0.4942 (OUTLIER) cc_final: 0.4633 (p90) REVERT: H 18 LEU cc_start: -0.0150 (OUTLIER) cc_final: -0.0466 (tm) REVERT: H 71 MET cc_start: 0.4168 (mpt) cc_final: 0.3884 (mtt) REVERT: H 84 GLU cc_start: 0.7107 (mm-30) cc_final: 0.6370 (tt0) REVERT: H 106 ARG cc_start: 0.9217 (mmm160) cc_final: 0.8867 (mmp80) REVERT: H 145 MET cc_start: 0.5026 (tpt) cc_final: 0.4613 (mmm) outliers start: 71 outliers final: 32 residues processed: 287 average time/residue: 0.6269 time to fit residues: 197.0215 Evaluate side-chains 254 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 213 time to evaluate : 0.631 ------------------------------------------------------------------------------- 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 124 HIS 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 552 THR 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 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 218 ASP Chi-restraints excluded: chain E residue 340 MET 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 142 VAL Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 124 HIS Chi-restraints excluded: chain G residue 137 PHE Chi-restraints excluded: chain G residue 139 MET 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 136 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 125 optimal weight: 0.9990 chunk 92 optimal weight: 30.0000 chunk 39 optimal weight: 6.9990 chunk 75 optimal weight: 20.0000 chunk 68 optimal weight: 0.1980 chunk 89 optimal weight: 7.9990 chunk 140 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 165 optimal weight: 0.6980 chunk 59 optimal weight: 20.0000 chunk 123 optimal weight: 8.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 HIS ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 569 HIS ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 143 GLN E 102 HIS ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 143 GLN ** G 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 143 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4781 r_free = 0.4781 target = 0.196229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.117332 restraints weight = 36605.813| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 4.15 r_work: 0.3133 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3138 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 46 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| r_final: 0.3138 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.7054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15828 Z= 0.158 Angle : 0.820 13.126 21360 Z= 0.404 Chirality : 0.043 0.277 2364 Planarity : 0.006 0.105 2692 Dihedral : 5.135 54.628 2192 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.66 % Favored : 95.29 % Rotamer: Outliers : 3.20 % Allowed : 27.59 % Favored : 69.21 % 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: 1.19 (0.20), residues: 1888 helix: 1.11 (0.14), residues: 1524 sheet: None (None), residues: 0 loop : -0.26 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 547 TYR 0.014 0.001 TYR B 99 PHE 0.026 0.002 PHE D 12 TRP 0.017 0.001 TRP E 350 HIS 0.020 0.001 HIS G 569 Details of bonding type rmsd covalent geometry : bond 0.00351 (15828) covalent geometry : angle 0.82042 (21360) hydrogen bonds : bond 0.04044 ( 1125) hydrogen bonds : angle 4.70798 ( 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 295 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 243 time to evaluate : 0.622 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: 0.7805 (OUTLIER) cc_final: 0.7569 (t) REVERT: A 219 ARG cc_start: 0.9077 (mtt90) cc_final: 0.8863 (mtt90) REVERT: A 260 GLU cc_start: 0.8756 (pt0) cc_final: 0.8213 (mt-10) REVERT: A 262 ASP cc_start: 0.9299 (p0) cc_final: 0.9053 (p0) REVERT: A 340 MET cc_start: 0.9404 (pp-130) cc_final: 0.9012 (mmp) REVERT: A 351 ARG cc_start: 0.6238 (mtt90) cc_final: 0.5940 (mmt180) REVERT: A 575 ARG cc_start: 0.8156 (ttt180) cc_final: 0.7844 (ttt180) REVERT: B 51 MET cc_start: 0.8555 (ppp) cc_final: 0.7797 (pmm) REVERT: B 115 LYS cc_start: 0.9205 (mmmm) cc_final: 0.8939 (mmmt) REVERT: C 120 THR cc_start: 0.7795 (OUTLIER) cc_final: 0.7559 (t) REVERT: C 214 MET cc_start: 0.7491 (tpt) cc_final: 0.7205 (tpt) REVERT: C 217 MET cc_start: 0.6789 (tpt) cc_final: 0.5053 (pp-130) REVERT: C 219 ARG cc_start: 0.9147 (ttm110) cc_final: 0.8604 (ttm170) REVERT: C 262 ASP cc_start: 0.9262 (p0) cc_final: 0.9033 (p0) REVERT: C 328 GLU cc_start: 0.9297 (tm-30) cc_final: 0.9042 (tm-30) REVERT: D 18 LEU cc_start: 0.0032 (OUTLIER) cc_final: -0.0173 (tm) REVERT: D 72 MET cc_start: 0.5125 (tpt) cc_final: 0.4741 (pp-130) REVERT: D 84 GLU cc_start: 0.6922 (mm-30) cc_final: 0.6473 (mm-30) REVERT: D 106 ARG cc_start: 0.8748 (mmm160) cc_final: 0.8270 (mmt90) REVERT: D 122 ASP cc_start: 0.8702 (m-30) cc_final: 0.8444 (m-30) REVERT: D 126 ARG cc_start: 0.8464 (mtm-85) cc_final: 0.8204 (ppt170) REVERT: D 144 MET cc_start: 0.7215 (ptt) cc_final: 0.6750 (ppp) REVERT: D 145 MET cc_start: 0.5238 (ttt) cc_final: 0.4836 (mmm) REVERT: E 120 THR cc_start: 0.7800 (OUTLIER) cc_final: 0.7565 (t) REVERT: E 217 MET cc_start: 0.5906 (tpt) cc_final: 0.4591 (ppp) REVERT: E 219 ARG cc_start: 0.9182 (ttm110) cc_final: 0.8625 (tmm-80) REVERT: E 260 GLU cc_start: 0.8785 (pt0) cc_final: 0.8240 (mt-10) REVERT: E 262 ASP cc_start: 0.9265 (p0) cc_final: 0.9031 (p0) REVERT: E 328 GLU cc_start: 0.9281 (tm-30) cc_final: 0.9013 (tm-30) REVERT: E 340 MET cc_start: 0.9430 (OUTLIER) cc_final: 0.9027 (mpp) REVERT: F 18 LEU cc_start: 0.0529 (OUTLIER) cc_final: 0.0328 (tm) REVERT: F 72 MET cc_start: 0.4911 (tpt) cc_final: 0.4403 (pp-130) REVERT: F 145 MET cc_start: 0.5093 (OUTLIER) cc_final: 0.4553 (mmp) REVERT: G 139 MET cc_start: 0.7573 (OUTLIER) cc_final: 0.7069 (tmm) REVERT: G 217 MET cc_start: 0.6036 (tpt) cc_final: 0.4141 (ppp) REVERT: G 219 ARG cc_start: 0.8737 (mtm-85) cc_final: 0.8376 (ttm-80) REVERT: G 260 GLU cc_start: 0.8773 (pt0) cc_final: 0.8189 (mt-10) REVERT: G 262 ASP cc_start: 0.9267 (p0) cc_final: 0.9037 (p0) REVERT: G 328 GLU cc_start: 0.9326 (tm-30) cc_final: 0.9088 (tm-30) REVERT: G 340 MET cc_start: 0.9556 (ppp) cc_final: 0.9304 (tmm) REVERT: G 351 ARG cc_start: 0.6374 (mtt90) cc_final: 0.5918 (mmt180) REVERT: G 556 TYR cc_start: 0.4874 (OUTLIER) cc_final: 0.4666 (p90) REVERT: H 18 LEU cc_start: -0.0150 (OUTLIER) cc_final: -0.0468 (tm) REVERT: H 51 MET cc_start: 0.8578 (ppp) cc_final: 0.7977 (pmm) REVERT: H 84 GLU cc_start: 0.7051 (mm-30) cc_final: 0.6610 (mm-30) REVERT: H 106 ARG cc_start: 0.9166 (mmm160) cc_final: 0.8912 (mmp80) REVERT: H 111 ASN cc_start: 0.8501 (p0) cc_final: 0.8200 (p0) REVERT: H 144 MET cc_start: 0.7351 (ptt) cc_final: 0.6645 (ppp) REVERT: H 145 MET cc_start: 0.5300 (OUTLIER) cc_final: 0.5065 (tpt) outliers start: 52 outliers final: 25 residues processed: 280 average time/residue: 0.6639 time to fit residues: 203.0640 Evaluate side-chains 253 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 217 time to evaluate : 0.576 ------------------------------------------------------------------------------- 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 308 ILE Chi-restraints excluded: chain A residue 309 SER 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 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 146 GLU Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 569 HIS Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 340 MET 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 142 VAL Chi-restraints excluded: chain F residue 145 MET Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 139 MET Chi-restraints excluded: chain G residue 330 HIS 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 136 VAL Chi-restraints excluded: chain H residue 145 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 159 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 chunk 129 optimal weight: 7.9990 chunk 101 optimal weight: 7.9990 chunk 155 optimal weight: 0.7980 chunk 167 optimal weight: 9.9990 chunk 125 optimal weight: 20.0000 chunk 161 optimal weight: 0.5980 chunk 176 optimal weight: 6.9990 chunk 59 optimal weight: 6.9990 chunk 153 optimal weight: 1.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 HIS ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 569 HIS ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 330 HIS ** H 53 ASN ** 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 = 0.4773 r_free = 0.4773 target = 0.195203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.112187 restraints weight = 36710.132| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 3.82 r_work: 0.3100 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3096 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3096 r_free = 0.3096 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3096 r_free = 0.3096 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 45 | |-----------------------------------------------------------------------------| r_final: 0.3096 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.7367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15828 Z= 0.198 Angle : 0.853 13.697 21360 Z= 0.422 Chirality : 0.045 0.287 2364 Planarity : 0.006 0.104 2692 Dihedral : 5.291 54.727 2192 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.56 % Favored : 95.34 % Rotamer: Outliers : 3.02 % Allowed : 28.57 % Favored : 68.41 % 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: 1.04 (0.20), residues: 1888 helix: 1.01 (0.14), residues: 1524 sheet: None (None), residues: 0 loop : -0.35 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 168 TYR 0.022 0.002 TYR F 99 PHE 0.037 0.002 PHE H 89 TRP 0.021 0.001 TRP E 350 HIS 0.012 0.001 HIS G 569 Details of bonding type rmsd covalent geometry : bond 0.00448 (15828) covalent geometry : angle 0.85340 (21360) hydrogen bonds : bond 0.04317 ( 1125) hydrogen bonds : angle 4.80659 ( 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 278 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 229 time to evaluate : 0.544 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: 0.7955 (OUTLIER) cc_final: 0.7730 (t) REVERT: A 139 MET cc_start: 0.7502 (ptt) cc_final: 0.7183 (pp-130) REVERT: A 213 ARG cc_start: 0.5689 (OUTLIER) cc_final: 0.5376 (ttt180) REVERT: A 219 ARG cc_start: 0.9091 (mtt90) cc_final: 0.8676 (mpt180) REVERT: A 340 MET cc_start: 0.9428 (pp-130) cc_final: 0.9007 (mmp) REVERT: A 351 ARG cc_start: 0.6343 (mtt90) cc_final: 0.6108 (mmt180) REVERT: B 72 MET cc_start: 0.2232 (pp-130) cc_final: 0.1857 (pp-130) REVERT: C 120 THR cc_start: 0.7952 (OUTLIER) cc_final: 0.7722 (t) REVERT: C 139 MET cc_start: 0.7297 (ptt) cc_final: 0.7056 (pp-130) REVERT: C 219 ARG cc_start: 0.9121 (ttm110) cc_final: 0.8554 (tmm-80) REVERT: C 262 ASP cc_start: 0.9250 (p0) cc_final: 0.9015 (p0) REVERT: C 328 GLU cc_start: 0.9278 (tm-30) cc_final: 0.9018 (tm-30) REVERT: D 18 LEU cc_start: -0.0076 (OUTLIER) cc_final: -0.0291 (tm) REVERT: D 84 GLU cc_start: 0.7030 (mm-30) cc_final: 0.6639 (mm-30) REVERT: D 106 ARG cc_start: 0.8791 (mmm160) cc_final: 0.8338 (mmt90) REVERT: D 122 ASP cc_start: 0.8690 (m-30) cc_final: 0.8451 (m-30) REVERT: D 126 ARG cc_start: 0.8395 (mtm-85) cc_final: 0.8140 (ppt170) REVERT: D 144 MET cc_start: 0.6985 (ptt) cc_final: 0.6587 (ppp) REVERT: D 145 MET cc_start: 0.5336 (OUTLIER) cc_final: 0.4743 (mmm) REVERT: E 104 PHE cc_start: 0.9298 (t80) cc_final: 0.9078 (t80) REVERT: E 120 THR cc_start: 0.7938 (OUTLIER) cc_final: 0.7711 (t) REVERT: E 219 ARG cc_start: 0.9158 (ttm110) cc_final: 0.8606 (tmm-80) REVERT: E 262 ASP cc_start: 0.9274 (p0) cc_final: 0.9031 (p0) REVERT: E 328 GLU cc_start: 0.9284 (tm-30) cc_final: 0.9016 (tm-30) REVERT: E 340 MET cc_start: 0.9456 (OUTLIER) cc_final: 0.9022 (mpp) REVERT: F 18 LEU cc_start: 0.0628 (OUTLIER) cc_final: 0.0410 (tm) REVERT: F 84 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6663 (mm-30) REVERT: F 145 MET cc_start: 0.5041 (ttt) cc_final: 0.4653 (mmp) REVERT: G 139 MET cc_start: 0.7554 (OUTLIER) cc_final: 0.6961 (tmm) REVERT: G 182 PHE cc_start: 0.7793 (t80) cc_final: 0.7563 (t80) REVERT: G 219 ARG cc_start: 0.8743 (mtm-85) cc_final: 0.8533 (ttm-80) REVERT: G 220 ARG cc_start: 0.8899 (pmt-80) cc_final: 0.8585 (pmm150) REVERT: G 262 ASP cc_start: 0.9279 (p0) cc_final: 0.9037 (p0) REVERT: G 328 GLU cc_start: 0.9301 (tm-30) cc_final: 0.9069 (tm-30) REVERT: G 340 MET cc_start: 0.9576 (ppp) cc_final: 0.9332 (tmm) REVERT: G 351 ARG cc_start: 0.6524 (mtt90) cc_final: 0.6214 (mmt180) REVERT: H 18 LEU cc_start: -0.0278 (OUTLIER) cc_final: -0.0575 (tm) REVERT: H 72 MET cc_start: 0.2491 (pp-130) cc_final: 0.2110 (pp-130) REVERT: H 84 GLU cc_start: 0.7147 (mm-30) cc_final: 0.6349 (pt0) REVERT: H 85 ILE cc_start: 0.5836 (tt) cc_final: 0.5010 (mm) REVERT: H 106 ARG cc_start: 0.9075 (mmm160) cc_final: 0.8740 (mmt90) REVERT: H 121 VAL cc_start: 0.6681 (OUTLIER) cc_final: 0.6409 (t) REVERT: H 122 ASP cc_start: 0.8648 (t0) cc_final: 0.8137 (m-30) REVERT: H 145 MET cc_start: 0.5571 (OUTLIER) cc_final: 0.4988 (tpt) outliers start: 49 outliers final: 24 residues processed: 264 average time/residue: 0.6224 time to fit residues: 180.0622 Evaluate side-chains 248 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 212 time to evaluate : 0.618 ------------------------------------------------------------------------------- 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 213 ARG Chi-restraints excluded: chain A residue 308 ILE 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 552 THR Chi-restraints excluded: chain C residue 569 HIS Chi-restraints excluded: chain D residue 18 LEU 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 340 MET 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 142 VAL Chi-restraints excluded: chain F residue 144 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 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 121 VAL Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 145 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 0 optimal weight: 40.0000 chunk 19 optimal weight: 4.9990 chunk 67 optimal weight: 0.2980 chunk 124 optimal weight: 5.9990 chunk 138 optimal weight: 4.9990 chunk 175 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 chunk 162 optimal weight: 0.0980 chunk 153 optimal weight: 7.9990 chunk 147 optimal weight: 5.9990 chunk 48 optimal weight: 20.0000 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4794 r_free = 0.4794 target = 0.194439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.115209 restraints weight = 35916.827| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 4.06 r_work: 0.3202 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3180 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 45 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 47 | |-----------------------------------------------------------------------------| r_final: 0.3180 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.7566 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= 0.225 Angle : 0.892 14.202 21360 Z= 0.440 Chirality : 0.046 0.276 2364 Planarity : 0.006 0.103 2692 Dihedral : 5.347 55.071 2192 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 18.25 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.87 % Favored : 95.07 % Rotamer: Outliers : 2.52 % Allowed : 29.19 % Favored : 68.29 % 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: 0.90 (0.20), residues: 1888 helix: 0.91 (0.14), residues: 1520 sheet: None (None), residues: 0 loop : -0.37 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 168 TYR 0.024 0.002 TYR E 147 PHE 0.028 0.002 PHE D 12 TRP 0.022 0.001 TRP E 350 HIS 0.012 0.001 HIS C 569 Details of bonding type rmsd covalent geometry : bond 0.00513 (15828) covalent geometry : angle 0.89224 (21360) hydrogen bonds : bond 0.04420 ( 1125) hydrogen bonds : angle 4.90873 ( 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 268 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 227 time to evaluate : 0.596 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: 0.8064 (OUTLIER) cc_final: 0.7820 (t) REVERT: A 139 MET cc_start: 0.7475 (ptt) cc_final: 0.7088 (pp-130) REVERT: A 262 ASP cc_start: 0.9212 (p0) cc_final: 0.8898 (p0) REVERT: A 340 MET cc_start: 0.9413 (pp-130) cc_final: 0.8963 (mmm) REVERT: A 351 ARG cc_start: 0.6472 (mtt90) cc_final: 0.6203 (mmt180) REVERT: B 72 MET cc_start: 0.2365 (pp-130) cc_final: 0.2016 (pp-130) REVERT: B 126 ARG cc_start: 0.8541 (mtm-85) cc_final: 0.8040 (tmt170) REVERT: B 145 MET cc_start: 0.4168 (tpt) cc_final: 0.3810 (tpp) REVERT: C 139 MET cc_start: 0.7345 (ptt) cc_final: 0.7054 (pp-130) REVERT: C 219 ARG cc_start: 0.9144 (ttm110) cc_final: 0.8773 (ttm-80) REVERT: C 262 ASP cc_start: 0.9238 (p0) cc_final: 0.8956 (p0) REVERT: C 328 GLU cc_start: 0.9327 (tm-30) cc_final: 0.9035 (tm-30) REVERT: D 18 LEU cc_start: -0.0393 (OUTLIER) cc_final: -0.0624 (tm) REVERT: D 65 PHE cc_start: 0.6583 (t80) cc_final: 0.6363 (t80) REVERT: D 72 MET cc_start: 0.4897 (tpt) cc_final: 0.4381 (pp-130) REVERT: D 84 GLU cc_start: 0.6961 (mm-30) cc_final: 0.6476 (mm-30) REVERT: D 106 ARG cc_start: 0.8723 (mmm160) cc_final: 0.8264 (mmt90) REVERT: D 122 ASP cc_start: 0.8700 (m-30) cc_final: 0.8452 (m-30) REVERT: D 126 ARG cc_start: 0.8414 (mtm-85) cc_final: 0.8100 (ppt170) REVERT: E 104 PHE cc_start: 0.9286 (t80) cc_final: 0.9081 (t80) REVERT: E 219 ARG cc_start: 0.9111 (ttm110) cc_final: 0.8623 (tmm-80) REVERT: E 262 ASP cc_start: 0.9268 (p0) cc_final: 0.8986 (p0) REVERT: E 328 GLU cc_start: 0.9334 (tm-30) cc_final: 0.9055 (tm-30) REVERT: E 340 MET cc_start: 0.9452 (OUTLIER) cc_final: 0.9022 (mpp) REVERT: F 18 LEU cc_start: 0.0714 (OUTLIER) cc_final: 0.0506 (tm) REVERT: F 145 MET cc_start: 0.5148 (ttt) cc_final: 0.4765 (mmp) REVERT: G 139 MET cc_start: 0.7615 (OUTLIER) cc_final: 0.6995 (tmm) REVERT: G 182 PHE cc_start: 0.7609 (t80) cc_final: 0.7387 (t80) REVERT: G 262 ASP cc_start: 0.9275 (p0) cc_final: 0.8996 (p0) REVERT: G 328 GLU cc_start: 0.9371 (tm-30) cc_final: 0.9149 (tm-30) REVERT: G 340 MET cc_start: 0.9566 (ppp) cc_final: 0.9321 (tmm) REVERT: G 351 ARG cc_start: 0.6681 (mtt90) cc_final: 0.6415 (mmt180) REVERT: H 18 LEU cc_start: -0.0470 (OUTLIER) cc_final: -0.0770 (tm) REVERT: H 72 MET cc_start: 0.2561 (pp-130) cc_final: 0.2168 (pp-130) REVERT: H 84 GLU cc_start: 0.7240 (mm-30) cc_final: 0.6393 (pt0) REVERT: H 85 ILE cc_start: 0.5707 (tt) cc_final: 0.5062 (mm) REVERT: H 122 ASP cc_start: 0.8659 (t0) cc_final: 0.8110 (m-30) REVERT: H 145 MET cc_start: 0.5730 (OUTLIER) cc_final: 0.5050 (tpt) outliers start: 41 outliers final: 24 residues processed: 258 average time/residue: 0.6206 time to fit residues: 175.2606 Evaluate side-chains 239 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 208 time to evaluate : 0.489 ------------------------------------------------------------------------------- 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 308 ILE 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 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 552 THR Chi-restraints excluded: chain D residue 18 LEU 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 340 MET Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 95 ASP Chi-restraints excluded: chain F residue 99 TYR Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 139 MET 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 145 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 115 optimal weight: 0.0570 chunk 28 optimal weight: 8.9990 chunk 149 optimal weight: 5.9990 chunk 110 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 157 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 chunk 152 optimal weight: 50.0000 chunk 72 optimal weight: 0.9980 chunk 101 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 569 HIS ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 53 ASN ** 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 = 0.4815 r_free = 0.4815 target = 0.196961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.118064 restraints weight = 35127.205| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 3.44 r_work: 0.3325 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3325 ------------------------------------------------------------------------------- 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: 47 | |-----------------------------------------------------------------------------| |-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: 47 | |-----------------------------------------------------------------------------| r_final: 0.3286 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.7864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15828 Z= 0.153 Angle : 0.896 14.170 21360 Z= 0.439 Chirality : 0.045 0.359 2364 Planarity : 0.006 0.104 2692 Dihedral : 5.263 55.630 2192 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.61 % Favored : 95.29 % Rotamer: Outliers : 2.40 % Allowed : 29.80 % Favored : 67.80 % 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: 0.96 (0.14), residues: 1516 sheet: None (None), residues: 0 loop : -0.14 (0.35), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 554 TYR 0.020 0.001 TYR B 99 PHE 0.030 0.002 PHE B 141 TRP 0.026 0.001 TRP E 350 HIS 0.012 0.001 HIS F 107 Details of bonding type rmsd covalent geometry : bond 0.00333 (15828) covalent geometry : angle 0.89620 (21360) hydrogen bonds : bond 0.04117 ( 1125) hydrogen bonds : angle 4.83377 ( 3363) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9400.68 seconds wall clock time: 159 minutes 58.69 seconds (9598.69 seconds total)