Starting phenix.real_space_refine on Tue Dec 31 11:42:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vnq_32045/12_2024/7vnq_32045_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vnq_32045/12_2024/7vnq_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_32045/12_2024/7vnq_32045.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vnq_32045/12_2024/7vnq_32045.map" model { file = "/net/cci-nas-00/data/ceres_data/7vnq_32045/12_2024/7vnq_32045_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vnq_32045/12_2024/7vnq_32045_trim.cif" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 9.20, per 1000 atoms: 0.59 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: 4.30 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.47 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: 4.67 Time building geometry restraints manager: 4.84 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 588 or resid 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: 1.390 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: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 35.390 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.060 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:13.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.730 ------------------------------------------------------------------------------- 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= 0.637 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.030 0.003 TRP E 86 HIS 0.006 0.002 HIS G 292 PHE 0.030 0.003 PHE A 169 TYR 0.016 0.002 TYR G 101 ARG 0.008 0.001 ARG E 351 *********************** 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 : 1.764 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: 0.7999 (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: 0.8593 (mm-30) REVERT: C 104 PHE cc_start: 0.8715 (OUTLIER) cc_final: 0.8365 (t80) REVERT: C 329 GLN cc_start: 0.8811 (pt0) cc_final: 0.8364 (pp30) REVERT: C 330 HIS cc_start: 0.8497 (m90) cc_final: 0.8254 (m90) REVERT: C 333 LYS cc_start: 0.9606 (pptt) cc_final: 0.9327 (pptt) REVERT: E 104 PHE cc_start: 0.8731 (OUTLIER) cc_final: 0.8394 (t80) REVERT: E 333 LYS cc_start: 0.9629 (pptt) cc_final: 0.9424 (pptt) REVERT: G 86 TRP cc_start: 0.8449 (m100) cc_final: 0.7872 (m-90) REVERT: G 104 PHE cc_start: 0.8717 (OUTLIER) cc_final: 0.8259 (t80) REVERT: G 146 GLU cc_start: 0.8754 (mm-30) cc_final: 0.8544 (mm-30) outliers start: 112 outliers final: 16 residues processed: 483 average time/residue: 1.5547 time to fit residues: 813.0637 Evaluate side-chains 257 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 237 time to evaluate : 1.884 ------------------------------------------------------------------------------- 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 A residue 575 ARG 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 559 LYS Chi-restraints excluded: chain C residue 575 ARG 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 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 554 ARG 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 158 optimal weight: 0.8980 chunk 142 optimal weight: 8.9990 chunk 79 optimal weight: 6.9990 chunk 48 optimal weight: 7.9990 chunk 96 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 147 optimal weight: 5.9990 chunk 57 optimal weight: 9.9990 chunk 89 optimal weight: 10.0000 chunk 109 optimal weight: 0.9980 chunk 170 optimal weight: 0.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4638 moved from start: 0.4055 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= 0.281 Angle : 0.767 12.968 21360 Z= 0.390 Chirality : 0.042 0.172 2364 Planarity : 0.006 0.112 2692 Dihedral : 7.155 58.666 2240 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 6.10 % Allowed : 16.75 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.19), residues: 1888 helix: 0.85 (0.13), residues: 1540 sheet: None (None), residues: 0 loop : 0.05 (0.36), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 294 HIS 0.005 0.001 HIS E 102 PHE 0.026 0.002 PHE E 169 TYR 0.018 0.002 TYR C 147 ARG 0.009 0.001 ARG C 547 *********************** 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 387 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 288 time to evaluate : 1.704 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: A 139 MET cc_start: 0.7508 (OUTLIER) cc_final: 0.7124 (tmm) REVERT: A 220 ARG cc_start: 0.7646 (OUTLIER) cc_final: 0.7087 (pmt-80) REVERT: A 328 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8354 (tm-30) REVERT: B 18 LEU cc_start: -0.0259 (OUTLIER) cc_final: -0.0606 (tm) REVERT: C 104 PHE cc_start: 0.8766 (OUTLIER) cc_final: 0.8412 (t80) REVERT: C 139 MET cc_start: 0.7437 (OUTLIER) cc_final: 0.7044 (tmm) REVERT: C 182 PHE cc_start: 0.7392 (OUTLIER) cc_final: 0.7086 (t80) REVERT: C 207 ARG cc_start: 0.8203 (mtt180) cc_final: 0.7798 (mtp-110) REVERT: C 220 ARG cc_start: 0.7546 (OUTLIER) cc_final: 0.7051 (pmm150) REVERT: C 328 GLU cc_start: 0.8604 (tm-30) cc_final: 0.8331 (tm-30) REVERT: C 329 GLN cc_start: 0.8833 (pt0) cc_final: 0.8367 (pp30) REVERT: D 18 LEU cc_start: 0.0340 (OUTLIER) cc_final: -0.0372 (tm) REVERT: E 104 PHE cc_start: 0.8752 (OUTLIER) cc_final: 0.8431 (t80) REVERT: E 139 MET cc_start: 0.7612 (OUTLIER) cc_final: 0.7181 (tmm) REVERT: E 214 MET cc_start: 0.8079 (tpt) cc_final: 0.7779 (tpt) REVERT: E 220 ARG cc_start: 0.7487 (OUTLIER) cc_final: 0.6981 (pmm150) REVERT: E 328 GLU cc_start: 0.8572 (tm-30) cc_final: 0.8286 (tm-30) REVERT: F 18 LEU cc_start: 0.0608 (OUTLIER) cc_final: 0.0078 (tm) REVERT: G 104 PHE cc_start: 0.8772 (OUTLIER) cc_final: 0.8551 (t80) REVERT: G 182 PHE cc_start: 0.7340 (OUTLIER) cc_final: 0.7124 (t80) REVERT: G 207 ARG cc_start: 0.8174 (mtt180) cc_final: 0.7775 (mtp-110) REVERT: G 220 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.7337 (pmm150) REVERT: H 145 MET cc_start: 0.1741 (ttm) cc_final: 0.1476 (mmm) outliers start: 99 outliers final: 37 residues processed: 355 average time/residue: 1.2542 time to fit residues: 491.4274 Evaluate side-chains 257 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 205 time to evaluate : 1.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 550 LYS 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 104 PHE 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 182 PHE 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 104 PHE Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 139 MET Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 220 ARG Chi-restraints excluded: chain E residue 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 104 PHE Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain G residue 182 PHE 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 H residue 29 THR Chi-restraints excluded: chain H residue 95 ASP Chi-restraints excluded: chain H residue 107 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 40.0000 chunk 52 optimal weight: 9.9990 chunk 142 optimal weight: 6.9990 chunk 116 optimal weight: 0.7980 chunk 47 optimal weight: 40.0000 chunk 171 optimal weight: 7.9990 chunk 184 optimal weight: 3.9990 chunk 152 optimal weight: 30.0000 chunk 169 optimal weight: 30.0000 chunk 58 optimal weight: 30.0000 chunk 137 optimal weight: 20.0000 overall best weight: 5.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 HIS A 344 ASN ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 HIS C 124 HIS C 569 HIS D 42 ASN ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 ASN ** D 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4779 moved from start: 0.5181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.070 15828 Z= 0.543 Angle : 0.823 12.480 21360 Z= 0.422 Chirality : 0.047 0.179 2364 Planarity : 0.007 0.111 2692 Dihedral : 6.722 55.799 2224 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 21.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 6.34 % Allowed : 19.89 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.19), residues: 1888 helix: 1.01 (0.13), residues: 1524 sheet: None (None), residues: 0 loop : -0.26 (0.35), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 294 HIS 0.008 0.002 HIS B 107 PHE 0.027 0.002 PHE E 169 TYR 0.022 0.002 TYR C 243 ARG 0.006 0.001 ARG H 106 *********************** 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 337 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 234 time to evaluate : 1.672 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 104 PHE cc_start: 0.8815 (OUTLIER) cc_final: 0.8526 (t80) REVERT: A 139 MET cc_start: 0.7607 (OUTLIER) cc_final: 0.7342 (tmm) REVERT: A 217 MET cc_start: 0.5680 (ppp) cc_final: 0.4852 (ppp) REVERT: A 219 ARG cc_start: 0.7838 (mpp-170) cc_final: 0.7168 (mtm-85) REVERT: A 220 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.8015 (pmt-80) REVERT: B 18 LEU cc_start: -0.0160 (OUTLIER) cc_final: -0.0875 (tm) REVERT: C 104 PHE cc_start: 0.8818 (t80) cc_final: 0.8564 (t80) REVERT: C 139 MET cc_start: 0.7524 (OUTLIER) cc_final: 0.7235 (tmm) REVERT: C 219 ARG cc_start: 0.7943 (mpp-170) cc_final: 0.7072 (mtm-85) REVERT: C 220 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.7951 (pmt-80) REVERT: D 18 LEU cc_start: 0.0196 (OUTLIER) cc_final: -0.0033 (tm) REVERT: D 144 MET cc_start: 0.4659 (pp-130) cc_final: 0.4401 (ptt) REVERT: E 104 PHE cc_start: 0.8776 (OUTLIER) cc_final: 0.8512 (t80) REVERT: E 214 MET cc_start: 0.8116 (tpt) cc_final: 0.7892 (tpt) REVERT: E 219 ARG cc_start: 0.8010 (mpp-170) cc_final: 0.7683 (mtm-85) REVERT: E 220 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.7928 (pmt-80) REVERT: F 18 LEU cc_start: 0.0739 (OUTLIER) cc_final: 0.0410 (tm) REVERT: F 145 MET cc_start: 0.1077 (OUTLIER) cc_final: 0.0801 (ttp) REVERT: G 104 PHE cc_start: 0.8808 (t80) cc_final: 0.8535 (t80) REVERT: G 139 MET cc_start: 0.7690 (OUTLIER) cc_final: 0.6816 (tmm) REVERT: G 219 ARG cc_start: 0.7962 (mpp-170) cc_final: 0.7189 (mtm-85) REVERT: G 220 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.8008 (pmt-80) REVERT: G 262 ASP cc_start: 0.8323 (p0) cc_final: 0.8081 (p0) outliers start: 103 outliers final: 49 residues processed: 302 average time/residue: 1.4183 time to fit residues: 469.1044 Evaluate side-chains 267 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 205 time to evaluate : 1.786 ------------------------------------------------------------------------------- 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 115 LEU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 137 PHE Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 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 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 239 ILE 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 D residue 142 VAL Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 220 ARG Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 542 PHE 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 126 ARG 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 115 LEU Chi-restraints excluded: chain G residue 120 THR 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 239 ILE Chi-restraints excluded: chain G residue 309 SER Chi-restraints excluded: chain G residue 359 ARG Chi-restraints excluded: chain G residue 569 HIS Chi-restraints excluded: chain G residue 575 ARG Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 95 ASP Chi-restraints excluded: chain H residue 107 HIS Chi-restraints excluded: chain H residue 136 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 8.9990 chunk 128 optimal weight: 9.9990 chunk 88 optimal weight: 30.0000 chunk 18 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 114 optimal weight: 0.8980 chunk 171 optimal weight: 6.9990 chunk 181 optimal weight: 7.9990 chunk 89 optimal weight: 10.0000 chunk 162 optimal weight: 0.6980 chunk 48 optimal weight: 5.9990 overall best weight: 1.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 ASN ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 GLN ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 143 GLN ** F 53 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4691 moved from start: 0.5575 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= 0.245 Angle : 0.722 11.975 21360 Z= 0.364 Chirality : 0.041 0.183 2364 Planarity : 0.006 0.111 2692 Dihedral : 6.091 54.247 2208 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 6.03 % Allowed : 21.86 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.20), residues: 1888 helix: 1.26 (0.13), residues: 1544 sheet: None (None), residues: 0 loop : -0.27 (0.37), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 350 HIS 0.004 0.001 HIS E 102 PHE 0.041 0.002 PHE B 89 TYR 0.021 0.001 TYR A 147 ARG 0.006 0.001 ARG F 106 *********************** 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 345 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 247 time to evaluate : 1.834 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: A 104 PHE cc_start: 0.8770 (t80) cc_final: 0.8487 (t80) REVERT: A 217 MET cc_start: 0.5248 (ppp) cc_final: 0.4672 (ppp) REVERT: A 220 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7714 (pmm150) REVERT: A 262 ASP cc_start: 0.8309 (p0) cc_final: 0.8066 (p0) REVERT: B 18 LEU cc_start: -0.0071 (OUTLIER) cc_final: -0.0396 (tm) REVERT: B 72 MET cc_start: 0.3571 (tmm) cc_final: 0.3217 (pp-130) REVERT: C 104 PHE cc_start: 0.8738 (t80) cc_final: 0.8439 (t80) REVERT: C 139 MET cc_start: 0.7446 (OUTLIER) cc_final: 0.7238 (tmm) REVERT: C 219 ARG cc_start: 0.7695 (mpp-170) cc_final: 0.7464 (ttm110) REVERT: C 220 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7772 (pmm150) REVERT: E 104 PHE cc_start: 0.8727 (t80) cc_final: 0.8510 (t80) REVERT: E 139 MET cc_start: 0.7772 (OUTLIER) cc_final: 0.6938 (tmm) REVERT: E 220 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.7844 (pmm150) REVERT: F 18 LEU cc_start: 0.0721 (OUTLIER) cc_final: 0.0413 (tm) REVERT: G 104 PHE cc_start: 0.8756 (t80) cc_final: 0.8451 (t80) REVERT: G 139 MET cc_start: 0.7693 (OUTLIER) cc_final: 0.6845 (tmm) REVERT: G 220 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7770 (pmm150) REVERT: G 262 ASP cc_start: 0.8285 (p0) cc_final: 0.8049 (p0) REVERT: G 556 TYR cc_start: 0.3907 (OUTLIER) cc_final: 0.3566 (p90) REVERT: H 72 MET cc_start: 0.3586 (tpt) cc_final: 0.3277 (pp-130) outliers start: 98 outliers final: 42 residues processed: 309 average time/residue: 1.4586 time to fit residues: 491.9165 Evaluate side-chains 263 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 211 time to evaluate : 1.680 ------------------------------------------------------------------------------- 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 212 LEU 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 559 LYS 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 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 137 PHE 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 330 HIS Chi-restraints excluded: chain C residue 569 HIS Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 107 HIS Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 139 MET Chi-restraints excluded: chain E residue 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 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 212 LEU Chi-restraints excluded: chain G residue 220 ARG Chi-restraints excluded: chain G residue 330 HIS Chi-restraints excluded: chain G residue 359 ARG 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 29 THR Chi-restraints excluded: chain H residue 95 ASP Chi-restraints excluded: chain H residue 107 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 7.9990 chunk 103 optimal weight: 8.9990 chunk 2 optimal weight: 3.9990 chunk 135 optimal weight: 0.9980 chunk 74 optimal weight: 20.0000 chunk 155 optimal weight: 0.9990 chunk 125 optimal weight: 5.9990 chunk 0 optimal weight: 50.0000 chunk 92 optimal weight: 30.0000 chunk 163 optimal weight: 0.9990 chunk 45 optimal weight: 8.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 GLN ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4718 moved from start: 0.6080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15828 Z= 0.291 Angle : 0.755 12.923 21360 Z= 0.379 Chirality : 0.042 0.163 2364 Planarity : 0.006 0.109 2692 Dihedral : 5.856 58.689 2200 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 5.30 % Allowed : 23.95 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.20), residues: 1888 helix: 1.20 (0.13), residues: 1548 sheet: None (None), residues: 0 loop : -0.29 (0.37), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 350 HIS 0.004 0.001 HIS A 102 PHE 0.025 0.002 PHE E 169 TYR 0.021 0.001 TYR A 147 ARG 0.012 0.001 ARG A 554 *********************** 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 335 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 249 time to evaluate : 1.883 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 104 PHE cc_start: 0.8783 (t80) cc_final: 0.8494 (t80) REVERT: A 262 ASP cc_start: 0.8359 (p0) cc_final: 0.8117 (p0) REVERT: B 72 MET cc_start: 0.4204 (tmm) cc_final: 0.3801 (pp-130) REVERT: B 85 ILE cc_start: 0.1114 (mm) cc_final: 0.0798 (mt) REVERT: C 104 PHE cc_start: 0.8715 (t80) cc_final: 0.8457 (t80) REVERT: C 139 MET cc_start: 0.7516 (mtp) cc_final: 0.7276 (tmm) REVERT: C 182 PHE cc_start: 0.7286 (t80) cc_final: 0.6714 (t80) REVERT: C 217 MET cc_start: 0.5091 (ppp) cc_final: 0.4599 (ppp) REVERT: C 218 ASP cc_start: 0.7311 (OUTLIER) cc_final: 0.6688 (t0) REVERT: C 220 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.7812 (pmm150) REVERT: D 124 MET cc_start: 0.5010 (ppp) cc_final: 0.4651 (ppp) REVERT: E 104 PHE cc_start: 0.8705 (t80) cc_final: 0.8498 (t80) REVERT: E 139 MET cc_start: 0.7792 (OUTLIER) cc_final: 0.6984 (tmm) REVERT: E 220 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7911 (pmm150) REVERT: F 18 LEU cc_start: 0.0614 (OUTLIER) cc_final: 0.0344 (tm) REVERT: G 104 PHE cc_start: 0.8740 (t80) cc_final: 0.8426 (t80) REVERT: G 139 MET cc_start: 0.7711 (OUTLIER) cc_final: 0.6893 (tmm) REVERT: G 262 ASP cc_start: 0.8321 (p0) cc_final: 0.8076 (p0) REVERT: G 556 TYR cc_start: 0.3654 (OUTLIER) cc_final: 0.3281 (p90) outliers start: 86 outliers final: 39 residues processed: 308 average time/residue: 1.4025 time to fit residues: 472.8641 Evaluate side-chains 254 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 208 time to evaluate : 1.992 ------------------------------------------------------------------------------- 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 212 LEU Chi-restraints excluded: chain A residue 309 SER 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 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 137 PHE Chi-restraints excluded: chain C residue 212 LEU 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 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 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 95 ASP 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 359 ARG Chi-restraints excluded: chain G residue 556 TYR Chi-restraints excluded: chain G residue 569 HIS Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 95 ASP Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain H residue 107 HIS 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 61 optimal weight: 0.9990 chunk 163 optimal weight: 0.8980 chunk 35 optimal weight: 7.9990 chunk 106 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 181 optimal weight: 9.9990 chunk 150 optimal weight: 0.6980 chunk 84 optimal weight: 30.0000 chunk 15 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 95 optimal weight: 0.7980 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 344 ASN ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 HIS ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4681 moved from start: 0.6569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15828 Z= 0.225 Angle : 0.769 12.122 21360 Z= 0.386 Chirality : 0.041 0.174 2364 Planarity : 0.006 0.108 2692 Dihedral : 5.277 52.596 2200 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.56 % Favored : 95.34 % Rotamer: Outliers : 4.37 % Allowed : 26.48 % Favored : 69.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.20), residues: 1888 helix: 1.21 (0.14), residues: 1528 sheet: None (None), residues: 0 loop : -0.30 (0.35), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 350 HIS 0.005 0.001 HIS E 102 PHE 0.039 0.002 PHE B 89 TYR 0.018 0.001 TYR A 147 ARG 0.011 0.001 ARG C 219 *********************** 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 322 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 251 time to evaluate : 1.708 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 104 PHE cc_start: 0.8731 (t80) cc_final: 0.8413 (t80) REVERT: A 120 THR cc_start: 0.8126 (OUTLIER) cc_final: 0.7925 (t) REVERT: A 214 MET cc_start: 0.7852 (tpt) cc_final: 0.7588 (tpt) REVERT: A 218 ASP cc_start: 0.7103 (OUTLIER) cc_final: 0.6762 (m-30) REVERT: A 262 ASP cc_start: 0.8316 (p0) cc_final: 0.8116 (p0) REVERT: A 357 MET cc_start: 0.3111 (ppp) cc_final: 0.2857 (ppp) REVERT: B 72 MET cc_start: 0.4392 (OUTLIER) cc_final: 0.4007 (pp-130) REVERT: B 124 MET cc_start: 0.5191 (ppp) cc_final: 0.4928 (ppp) REVERT: C 104 PHE cc_start: 0.8705 (t80) cc_final: 0.8381 (t80) REVERT: C 214 MET cc_start: 0.7818 (tpt) cc_final: 0.6731 (tmm) REVERT: E 104 PHE cc_start: 0.8719 (t80) cc_final: 0.8451 (t80) REVERT: E 139 MET cc_start: 0.7792 (OUTLIER) cc_final: 0.7005 (tmm) REVERT: E 569 HIS cc_start: 0.2867 (OUTLIER) cc_final: 0.2445 (t70) REVERT: F 18 LEU cc_start: 0.0789 (OUTLIER) cc_final: 0.0457 (tm) REVERT: F 72 MET cc_start: 0.4449 (tpt) cc_final: 0.4078 (pp-130) REVERT: F 124 MET cc_start: 0.4515 (ppp) cc_final: 0.4302 (ppp) REVERT: G 104 PHE cc_start: 0.8702 (t80) cc_final: 0.8372 (t80) REVERT: G 139 MET cc_start: 0.7728 (OUTLIER) cc_final: 0.6954 (tmm) REVERT: G 214 MET cc_start: 0.7807 (tpt) cc_final: 0.7587 (tpt) REVERT: G 218 ASP cc_start: 0.7130 (OUTLIER) cc_final: 0.6756 (m-30) REVERT: G 556 TYR cc_start: 0.4248 (OUTLIER) cc_final: 0.3884 (p90) outliers start: 71 outliers final: 35 residues processed: 295 average time/residue: 1.3763 time to fit residues: 448.3153 Evaluate side-chains 251 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 207 time to evaluate : 1.847 ------------------------------------------------------------------------------- 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 218 ASP Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 330 HIS 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 B residue 18 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 72 MET 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 137 PHE 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 95 ASP Chi-restraints excluded: chain D residue 107 HIS Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 137 PHE Chi-restraints excluded: chain E residue 139 MET Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 569 HIS Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 95 ASP Chi-restraints excluded: chain F residue 99 TYR Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 139 MET Chi-restraints excluded: chain G residue 218 ASP Chi-restraints excluded: chain G residue 330 HIS Chi-restraints excluded: chain G residue 359 ARG Chi-restraints excluded: chain G residue 556 TYR Chi-restraints excluded: chain G residue 569 HIS Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 95 ASP Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain H residue 107 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 20.0000 chunk 20 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 chunk 132 optimal weight: 30.0000 chunk 102 optimal weight: 9.9990 chunk 153 optimal weight: 0.0670 chunk 101 optimal weight: 8.9990 chunk 181 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 110 optimal weight: 0.6980 chunk 83 optimal weight: 5.9990 overall best weight: 2.3524 ------------------------------------------------------------------------------- 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** ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4729 moved from start: 0.6998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15828 Z= 0.289 Angle : 0.822 12.520 21360 Z= 0.415 Chirality : 0.043 0.186 2364 Planarity : 0.006 0.106 2692 Dihedral : 5.175 52.906 2194 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.08 % Favored : 95.71 % Rotamer: Outliers : 4.62 % Allowed : 27.77 % Favored : 67.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.20), residues: 1888 helix: 1.08 (0.13), residues: 1548 sheet: None (None), residues: 0 loop : -0.40 (0.36), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 350 HIS 0.013 0.001 HIS F 107 PHE 0.046 0.002 PHE H 89 TYR 0.016 0.001 TYR B 99 ARG 0.012 0.001 ARG G 547 *********************** 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 314 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 239 time to evaluate : 2.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 PHE cc_start: 0.8718 (t80) cc_final: 0.8399 (t80) REVERT: A 214 MET cc_start: 0.7804 (tpt) cc_final: 0.7548 (tpt) REVERT: A 218 ASP cc_start: 0.7311 (OUTLIER) cc_final: 0.6920 (m-30) REVERT: A 262 ASP cc_start: 0.8357 (p0) cc_final: 0.8148 (p0) REVERT: B 72 MET cc_start: 0.4506 (OUTLIER) cc_final: 0.4060 (pp-130) REVERT: B 84 GLU cc_start: 0.2422 (tp30) cc_final: 0.2151 (tp30) REVERT: C 104 PHE cc_start: 0.8732 (t80) cc_final: 0.8390 (t80) REVERT: C 214 MET cc_start: 0.7915 (tpt) cc_final: 0.7478 (tpt) REVERT: E 104 PHE cc_start: 0.8711 (t80) cc_final: 0.8392 (t80) REVERT: E 139 MET cc_start: 0.7816 (OUTLIER) cc_final: 0.7029 (tmm) REVERT: E 214 MET cc_start: 0.7711 (tpt) cc_final: 0.7382 (tpt) REVERT: E 217 MET cc_start: 0.6019 (OUTLIER) cc_final: 0.4689 (ppp) REVERT: E 218 ASP cc_start: 0.7572 (OUTLIER) cc_final: 0.6548 (m-30) REVERT: E 569 HIS cc_start: 0.2757 (OUTLIER) cc_final: 0.2320 (t70) REVERT: F 18 LEU cc_start: 0.0818 (OUTLIER) cc_final: 0.0397 (tm) REVERT: F 72 MET cc_start: 0.4638 (tpt) cc_final: 0.4317 (pp-130) REVERT: G 104 PHE cc_start: 0.8704 (t80) cc_final: 0.8391 (t80) REVERT: G 139 MET cc_start: 0.7814 (OUTLIER) cc_final: 0.7034 (tmm) REVERT: G 182 PHE cc_start: 0.7103 (t80) cc_final: 0.6624 (t80) REVERT: G 214 MET cc_start: 0.7688 (tpt) cc_final: 0.7408 (tpt) REVERT: G 218 ASP cc_start: 0.7289 (OUTLIER) cc_final: 0.6870 (m-30) REVERT: G 556 TYR cc_start: 0.4049 (OUTLIER) cc_final: 0.3708 (p90) REVERT: H 84 GLU cc_start: 0.2749 (OUTLIER) cc_final: 0.2519 (tt0) outliers start: 75 outliers final: 36 residues processed: 289 average time/residue: 1.3246 time to fit residues: 422.5463 Evaluate side-chains 251 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 204 time to evaluate : 1.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 309 SER 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 B residue 18 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 72 MET 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 110 THR Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 124 HIS Chi-restraints excluded: chain C residue 137 PHE 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 107 HIS Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 124 HIS Chi-restraints excluded: chain E residue 137 PHE Chi-restraints excluded: chain E residue 139 MET Chi-restraints excluded: chain E residue 217 MET Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 569 HIS Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 95 ASP Chi-restraints excluded: chain F residue 99 TYR Chi-restraints excluded: chain F residue 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 218 ASP Chi-restraints excluded: chain G residue 359 ARG Chi-restraints excluded: chain G residue 556 TYR Chi-restraints excluded: chain G residue 569 HIS Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain H residue 95 ASP Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain H residue 107 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 54 optimal weight: 9.9990 chunk 35 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 123 optimal weight: 6.9990 chunk 89 optimal weight: 9.9990 chunk 16 optimal weight: 0.9980 chunk 142 optimal weight: 9.9990 chunk 164 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 102 HIS ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 330 HIS ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 HIS ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4670 moved from start: 0.7371 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= 0.221 Angle : 0.826 13.087 21360 Z= 0.413 Chirality : 0.043 0.275 2364 Planarity : 0.006 0.106 2692 Dihedral : 5.084 52.813 2192 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.71 % Favored : 96.08 % Rotamer: Outliers : 3.69 % Allowed : 29.00 % Favored : 67.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.20), residues: 1888 helix: 1.09 (0.14), residues: 1532 sheet: None (None), residues: 0 loop : -0.33 (0.35), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 350 HIS 0.007 0.001 HIS F 107 PHE 0.042 0.002 PHE B 89 TYR 0.015 0.001 TYR A 556 ARG 0.009 0.001 ARG C 554 *********************** 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 297 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 237 time to evaluate : 1.737 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 104 PHE cc_start: 0.8681 (t80) cc_final: 0.8333 (t80) REVERT: A 139 MET cc_start: 0.7917 (ppp) cc_final: 0.7669 (ptt) REVERT: A 357 MET cc_start: 0.2805 (ppp) cc_final: 0.2558 (ppp) REVERT: B 72 MET cc_start: 0.4549 (OUTLIER) cc_final: 0.4013 (pp-130) REVERT: B 84 GLU cc_start: 0.2539 (tp30) cc_final: 0.2327 (tp30) REVERT: B 85 ILE cc_start: 0.1606 (mm) cc_final: 0.1161 (mt) REVERT: B 145 MET cc_start: 0.2808 (mmp) cc_final: 0.1134 (tpt) REVERT: C 104 PHE cc_start: 0.8622 (t80) cc_final: 0.8230 (t80) REVERT: C 359 ARG cc_start: 0.4301 (mmt180) cc_final: 0.4071 (mmp-170) REVERT: D 84 GLU cc_start: 0.2195 (tt0) cc_final: 0.1953 (tt0) REVERT: E 139 MET cc_start: 0.7787 (OUTLIER) cc_final: 0.7047 (tmm) REVERT: F 18 LEU cc_start: 0.0909 (OUTLIER) cc_final: 0.0514 (tm) REVERT: G 139 MET cc_start: 0.7823 (OUTLIER) cc_final: 0.7111 (tmm) REVERT: G 140 ILE cc_start: 0.7580 (OUTLIER) cc_final: 0.7165 (tt) REVERT: H 145 MET cc_start: 0.2720 (mmp) cc_final: 0.2485 (tpt) outliers start: 60 outliers final: 34 residues processed: 273 average time/residue: 1.3647 time to fit residues: 410.7592 Evaluate side-chains 245 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 206 time to evaluate : 1.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 239 ILE 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 B residue 18 LEU Chi-restraints excluded: chain B residue 72 MET 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 124 HIS Chi-restraints excluded: chain C residue 137 PHE Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 330 HIS Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain D residue 107 HIS Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 124 HIS Chi-restraints excluded: chain E residue 137 PHE Chi-restraints excluded: chain E residue 139 MET Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 48 LEU 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 140 ILE Chi-restraints excluded: chain G residue 239 ILE Chi-restraints excluded: chain G residue 260 GLU Chi-restraints excluded: chain G residue 330 HIS Chi-restraints excluded: chain G residue 359 ARG Chi-restraints excluded: chain G residue 569 HIS Chi-restraints excluded: chain H residue 95 ASP Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain H residue 107 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 173 optimal weight: 7.9990 chunk 158 optimal weight: 0.7980 chunk 168 optimal weight: 9.9990 chunk 101 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 132 optimal weight: 40.0000 chunk 51 optimal weight: 0.9980 chunk 152 optimal weight: 6.9990 chunk 159 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 178 optimal weight: 4.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 HIS A 330 HIS ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 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** ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4728 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 : 0.004 0.038 15828 Z= 0.282 Angle : 0.887 13.585 21360 Z= 0.437 Chirality : 0.045 0.292 2364 Planarity : 0.006 0.108 2692 Dihedral : 5.154 52.713 2192 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.97 % Favored : 95.82 % Rotamer: Outliers : 3.20 % Allowed : 30.17 % Favored : 66.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.20), residues: 1888 helix: 1.00 (0.13), residues: 1540 sheet: None (None), residues: 0 loop : -0.28 (0.37), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 350 HIS 0.006 0.001 HIS A 102 PHE 0.036 0.002 PHE B 89 TYR 0.018 0.001 TYR E 147 ARG 0.026 0.001 ARG A 219 *********************** 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 273 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 221 time to evaluate : 1.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 MET cc_start: 0.7974 (ppp) cc_final: 0.7706 (ptt) REVERT: A 217 MET cc_start: 0.7748 (tpp) cc_final: 0.7432 (tpp) REVERT: A 357 MET cc_start: 0.2660 (ppp) cc_final: 0.2443 (ppp) REVERT: B 85 ILE cc_start: 0.1633 (OUTLIER) cc_final: 0.1203 (mt) REVERT: B 145 MET cc_start: 0.2927 (mmp) cc_final: 0.1191 (tpt) REVERT: C 217 MET cc_start: 0.7730 (tpp) cc_final: 0.7392 (tpp) REVERT: D 72 MET cc_start: 0.4672 (tpt) cc_final: 0.4441 (tpt) REVERT: D 84 GLU cc_start: 0.2322 (tt0) cc_final: 0.2102 (tt0) REVERT: E 139 MET cc_start: 0.7813 (OUTLIER) cc_final: 0.7057 (tmm) REVERT: E 217 MET cc_start: 0.5720 (OUTLIER) cc_final: 0.4381 (ppp) REVERT: F 18 LEU cc_start: 0.0823 (OUTLIER) cc_final: 0.0419 (tm) REVERT: F 72 MET cc_start: 0.4695 (tpt) cc_final: 0.4071 (pp-130) REVERT: F 145 MET cc_start: 0.2651 (mmp) cc_final: 0.0037 (tpt) REVERT: G 139 MET cc_start: 0.7776 (OUTLIER) cc_final: 0.7077 (tmm) REVERT: G 140 ILE cc_start: 0.7598 (OUTLIER) cc_final: 0.7182 (tt) REVERT: G 217 MET cc_start: 0.7821 (tpp) cc_final: 0.7561 (tpp) REVERT: H 72 MET cc_start: 0.2218 (pp-130) cc_final: -0.0020 (pp-130) REVERT: H 145 MET cc_start: 0.2717 (mmp) cc_final: 0.2314 (tpt) outliers start: 52 outliers final: 30 residues processed: 258 average time/residue: 1.3414 time to fit residues: 383.0121 Evaluate side-chains 236 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 200 time to evaluate : 1.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 330 HIS 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 B residue 18 LEU Chi-restraints excluded: chain B residue 85 ILE 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 124 HIS 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 99 TYR Chi-restraints excluded: chain D residue 107 HIS Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 124 HIS Chi-restraints excluded: chain E residue 137 PHE Chi-restraints excluded: chain E residue 139 MET Chi-restraints excluded: chain E residue 217 MET Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 48 LEU 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 140 ILE Chi-restraints excluded: chain G residue 359 ARG Chi-restraints excluded: chain G residue 569 HIS Chi-restraints excluded: chain H residue 95 ASP Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain H residue 107 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 6.9990 chunk 84 optimal weight: 7.9990 chunk 124 optimal weight: 9.9990 chunk 187 optimal weight: 6.9990 chunk 172 optimal weight: 0.7980 chunk 149 optimal weight: 0.0770 chunk 15 optimal weight: 0.9990 chunk 115 optimal weight: 0.0980 chunk 91 optimal weight: 7.9990 chunk 118 optimal weight: 0.9990 chunk 158 optimal weight: 1.9990 overall best weight: 0.5942 ------------------------------------------------------------------------------- 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 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 143 GLN ** E 569 HIS ** 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 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4659 moved from start: 0.7888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15828 Z= 0.221 Angle : 0.900 14.035 21360 Z= 0.440 Chirality : 0.045 0.256 2364 Planarity : 0.006 0.109 2692 Dihedral : 5.140 52.380 2192 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.13 % Favored : 95.66 % Rotamer: Outliers : 2.34 % Allowed : 30.91 % Favored : 66.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.20), residues: 1888 helix: 0.92 (0.13), residues: 1520 sheet: None (None), residues: 0 loop : -0.20 (0.36), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 350 HIS 0.012 0.001 HIS E 569 PHE 0.033 0.002 PHE B 89 TYR 0.023 0.001 TYR A 147 ARG 0.022 0.001 ARG A 219 ********************** 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 262 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 224 time to evaluate : 1.903 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 217 MET cc_start: 0.7641 (tpp) cc_final: 0.7352 (tpp) REVERT: A 357 MET cc_start: 0.2746 (ppp) cc_final: 0.2525 (ppp) REVERT: B 85 ILE cc_start: 0.1532 (OUTLIER) cc_final: 0.1144 (mt) REVERT: B 145 MET cc_start: 0.2905 (mmp) cc_final: 0.1216 (tpt) REVERT: C 217 MET cc_start: 0.7612 (tpp) cc_final: 0.7321 (tpp) REVERT: D 84 GLU cc_start: 0.2132 (tt0) cc_final: 0.1372 (tp30) REVERT: E 139 MET cc_start: 0.7824 (ttm) cc_final: 0.7071 (tmm) REVERT: E 217 MET cc_start: 0.5359 (OUTLIER) cc_final: 0.4174 (ppp) REVERT: F 18 LEU cc_start: 0.0887 (OUTLIER) cc_final: 0.0488 (tm) REVERT: F 72 MET cc_start: 0.4809 (tpt) cc_final: 0.4159 (pp-130) REVERT: F 145 MET cc_start: 0.2738 (mmp) cc_final: 0.0094 (tpt) REVERT: G 139 MET cc_start: 0.7831 (OUTLIER) cc_final: 0.7127 (tmm) REVERT: G 140 ILE cc_start: 0.7579 (OUTLIER) cc_final: 0.7288 (tp) REVERT: G 217 MET cc_start: 0.7653 (tpp) cc_final: 0.7427 (tpp) REVERT: H 71 MET cc_start: 0.5057 (mmt) cc_final: 0.4743 (mtt) REVERT: H 72 MET cc_start: 0.2099 (pp-130) cc_final: -0.0060 (pp-130) REVERT: H 145 MET cc_start: 0.2912 (mmp) cc_final: 0.2425 (tpt) outliers start: 38 outliers final: 25 residues processed: 248 average time/residue: 1.3201 time to fit residues: 360.4821 Evaluate side-chains 231 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 201 time to evaluate : 1.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL 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 B residue 18 LEU Chi-restraints excluded: chain B residue 85 ILE 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 137 PHE Chi-restraints excluded: chain C residue 139 MET Chi-restraints excluded: chain C residue 260 GLU Chi-restraints excluded: chain C residue 569 HIS Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 107 HIS Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 137 PHE Chi-restraints excluded: chain E residue 217 MET Chi-restraints excluded: chain F residue 18 LEU 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 140 ILE Chi-restraints excluded: chain G residue 359 ARG Chi-restraints excluded: chain G residue 569 HIS Chi-restraints excluded: chain H residue 95 ASP Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain H residue 107 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 45 optimal weight: 7.9990 chunk 137 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 149 optimal weight: 30.0000 chunk 62 optimal weight: 0.9990 chunk 153 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 131 optimal weight: 0.6980 chunk 8 optimal weight: 30.0000 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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** ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 143 GLN ** E 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** 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 = 0.4798 r_free = 0.4798 target = 0.195268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.119226 restraints weight = 35593.718| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 4.61 r_work: 0.3234 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3207 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3207 r_free = 0.3207 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 40 | |-----------------------------------------------------------------------------| r_final: 0.3206 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.8029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 15828 Z= 0.278 Angle : 0.915 17.883 21360 Z= 0.450 Chirality : 0.046 0.254 2364 Planarity : 0.006 0.108 2692 Dihedral : 5.220 53.163 2192 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.29 % Favored : 95.50 % Rotamer: Outliers : 2.40 % Allowed : 31.10 % Favored : 66.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.20), residues: 1888 helix: 0.86 (0.13), residues: 1540 sheet: None (None), residues: 0 loop : -0.24 (0.38), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 350 HIS 0.010 0.001 HIS E 569 PHE 0.029 0.002 PHE B 89 TYR 0.021 0.001 TYR F 99 ARG 0.022 0.001 ARG G 331 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7176.20 seconds wall clock time: 129 minutes 52.65 seconds (7792.65 seconds total)