Starting phenix.real_space_refine on Fri Aug 22 21:53:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8irm_35679/08_2025/8irm_35679.cif Found real_map, /net/cci-nas-00/data/ceres_data/8irm_35679/08_2025/8irm_35679.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8irm_35679/08_2025/8irm_35679.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8irm_35679/08_2025/8irm_35679.map" model { file = "/net/cci-nas-00/data/ceres_data/8irm_35679/08_2025/8irm_35679.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8irm_35679/08_2025/8irm_35679.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 52 5.16 5 C 5290 2.51 5 N 1316 2.21 5 O 1472 1.98 5 H 8 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8138 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 4026 Classifications: {'peptide': 540} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 516} Chain: "B" Number of atoms: 4026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 4026 Classifications: {'peptide': 540} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 516} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'ADE': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'ADE': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 2.22, per 1000 atoms: 0.27 Number of scatterers: 8138 At special positions: 0 Unit cell: (93.61, 104.673, 100.418, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 O 1472 8.00 N 1316 7.00 C 5290 6.00 H 8 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 78 " - pdb=" SG CYS A 123 " distance=2.03 Simple disulfide: pdb=" SG CYS A 83 " - pdb=" SG CYS A 111 " distance=2.03 Simple disulfide: pdb=" SG CYS A 87 " - pdb=" SG CYS A 97 " distance=2.03 Simple disulfide: pdb=" SG CYS A 254 " - pdb=" SG CYS A 287 " distance=2.03 Simple disulfide: pdb=" SG CYS B 78 " - pdb=" SG CYS B 123 " distance=2.03 Simple disulfide: pdb=" SG CYS B 83 " - pdb=" SG CYS B 111 " distance=2.03 Simple disulfide: pdb=" SG CYS B 87 " - pdb=" SG CYS B 97 " distance=2.03 Simple disulfide: pdb=" SG CYS B 254 " - pdb=" SG CYS B 287 " distance=2.03 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG C 1 " - " ASN A 270 " " NAG D 1 " - " ASN B 270 " Time building additional restraints: 0.86 Conformation dependent library (CDL) restraints added in 283.0 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1940 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 8 sheets defined 68.1% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 19 through 31 Processing helix chain 'A' and resid 31 through 37 Processing helix chain 'A' and resid 39 through 43 Processing helix chain 'A' and resid 46 through 61 Processing helix chain 'A' and resid 62 through 74 removed outlier: 4.389A pdb=" N ALA A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 93 through 97 Processing helix chain 'A' and resid 108 through 113 Processing helix chain 'A' and resid 117 through 149 Processing helix chain 'A' and resid 159 through 169 Processing helix chain 'A' and resid 180 through 202 removed outlier: 3.500A pdb=" N ILE A 201 " --> pdb=" O PHE A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 211 removed outlier: 3.969A pdb=" N VAL A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 232 removed outlier: 4.255A pdb=" N SER A 220 " --> pdb=" O ARG A 216 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ALA A 221 " --> pdb=" O ILE A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 257 No H-bonds generated for 'chain 'A' and resid 255 through 257' Processing helix chain 'A' and resid 294 through 313 Processing helix chain 'A' and resid 317 through 331 Processing helix chain 'A' and resid 343 through 355 removed outlier: 3.954A pdb=" N LYS A 355 " --> pdb=" O ASP A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 374 removed outlier: 4.562A pdb=" N GLY A 373 " --> pdb=" O SER A 370 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE A 374 " --> pdb=" O PHE A 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 370 through 374' Processing helix chain 'A' and resid 376 through 405 removed outlier: 3.586A pdb=" N TRP A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR A 399 " --> pdb=" O THR A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 435 Processing helix chain 'A' and resid 444 through 452 removed outlier: 4.039A pdb=" N GLY A 448 " --> pdb=" O GLU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 470 Processing helix chain 'A' and resid 472 through 477 Processing helix chain 'A' and resid 480 through 496 Proline residue: A 486 - end of helix removed outlier: 3.566A pdb=" N ILE A 489 " --> pdb=" O GLY A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 502 removed outlier: 3.694A pdb=" N THR A 500 " --> pdb=" O LYS A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 523 Proline residue: A 512 - end of helix Proline residue: A 521 - end of helix Processing helix chain 'A' and resid 525 through 554 removed outlier: 4.581A pdb=" N TRP A 543 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ASP A 544 " --> pdb=" O LEU A 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 30 Processing helix chain 'B' and resid 31 through 37 Processing helix chain 'B' and resid 46 through 61 Processing helix chain 'B' and resid 62 through 74 removed outlier: 4.703A pdb=" N ALA B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER B 74 " --> pdb=" O ILE B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 83 Processing helix chain 'B' and resid 93 through 97 Processing helix chain 'B' and resid 108 through 113 Processing helix chain 'B' and resid 117 through 149 removed outlier: 3.519A pdb=" N VAL B 124 " --> pdb=" O TYR B 120 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU B 125 " --> pdb=" O ALA B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 169 removed outlier: 4.142A pdb=" N ALA B 164 " --> pdb=" O MET B 160 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N TYR B 165 " --> pdb=" O GLY B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 201 Processing helix chain 'B' and resid 203 through 209 Processing helix chain 'B' and resid 212 through 232 removed outlier: 4.145A pdb=" N SER B 220 " --> pdb=" O ARG B 216 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA B 221 " --> pdb=" O ILE B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 257 No H-bonds generated for 'chain 'B' and resid 255 through 257' Processing helix chain 'B' and resid 294 through 313 Processing helix chain 'B' and resid 317 through 331 Processing helix chain 'B' and resid 343 through 355 removed outlier: 3.884A pdb=" N LYS B 355 " --> pdb=" O ASP B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 405 removed outlier: 3.735A pdb=" N TRP B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE B 404 " --> pdb=" O SER B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 435 removed outlier: 3.537A pdb=" N MET B 422 " --> pdb=" O TYR B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 452 removed outlier: 4.232A pdb=" N GLY B 448 " --> pdb=" O GLU B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 470 Processing helix chain 'B' and resid 472 through 477 Processing helix chain 'B' and resid 480 through 496 Proline residue: B 486 - end of helix Processing helix chain 'B' and resid 497 through 502 removed outlier: 3.559A pdb=" N THR B 500 " --> pdb=" O LYS B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 523 Proline residue: B 512 - end of helix removed outlier: 3.769A pdb=" N MET B 520 " --> pdb=" O THR B 516 " (cutoff:3.500A) Proline residue: B 521 - end of helix Processing helix chain 'B' and resid 525 through 541 Processing helix chain 'B' and resid 541 through 554 Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 87 Processing sheet with id=AA2, first strand: chain 'A' and resid 156 through 158 Processing sheet with id=AA3, first strand: chain 'A' and resid 241 through 244 Processing sheet with id=AA4, first strand: chain 'A' and resid 274 through 275 removed outlier: 3.810A pdb=" N SER A 261 " --> pdb=" O VAL B 265 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER B 261 " --> pdb=" O VAL A 265 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 286 through 287 removed outlier: 3.810A pdb=" N SER A 261 " --> pdb=" O VAL B 265 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER B 261 " --> pdb=" O VAL A 265 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 86 through 87 Processing sheet with id=AA7, first strand: chain 'B' and resid 156 through 158 Processing sheet with id=AA8, first strand: chain 'B' and resid 241 through 242 517 hydrogen bonds defined for protein. 1467 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: 1.27 Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.86 - 1.05: 8 1.05 - 1.24: 1111 1.24 - 1.43: 2341 1.43 - 1.62: 4780 1.62 - 1.81: 84 Bond restraints: 8324 Sorted by residual: bond pdb=" C5 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.413 1.538 -0.125 2.00e-02 2.50e+03 3.93e+01 bond pdb=" C5 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.413 1.535 -0.122 2.00e-02 2.50e+03 3.75e+01 bond pdb=" C6 ADE A 701 " pdb=" N6 ADE A 701 " ideal model delta sigma weight residual 1.334 1.449 -0.115 2.00e-02 2.50e+03 3.30e+01 bond pdb=" C5 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.413 1.527 -0.114 2.00e-02 2.50e+03 3.26e+01 bond pdb=" C6 ADE B 701 " pdb=" N6 ADE B 701 " ideal model delta sigma weight residual 1.334 1.448 -0.114 2.00e-02 2.50e+03 3.26e+01 ... (remaining 8319 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 11135 2.26 - 4.51: 157 4.51 - 6.77: 30 6.77 - 9.03: 10 9.03 - 11.29: 2 Bond angle restraints: 11334 Sorted by residual: angle pdb=" C THR B 45 " pdb=" N PHE B 46 " pdb=" CA PHE B 46 " ideal model delta sigma weight residual 122.15 110.86 11.29 2.83e+00 1.25e-01 1.59e+01 angle pdb=" C THR A 45 " pdb=" N PHE A 46 " pdb=" CA PHE A 46 " ideal model delta sigma weight residual 122.15 111.15 11.00 2.83e+00 1.25e-01 1.51e+01 angle pdb=" C THR A 247 " pdb=" N LEU A 248 " pdb=" CA LEU A 248 " ideal model delta sigma weight residual 121.54 127.59 -6.05 1.91e+00 2.74e-01 1.00e+01 angle pdb=" N TYR B 524 " pdb=" CA TYR B 524 " pdb=" C TYR B 524 " ideal model delta sigma weight residual 112.58 108.84 3.74 1.22e+00 6.72e-01 9.42e+00 angle pdb=" C2 ADE A 701 " pdb=" N3 ADE A 701 " pdb=" C4 ADE A 701 " ideal model delta sigma weight residual 111.66 120.61 -8.95 3.00e+00 1.11e-01 8.90e+00 ... (remaining 11329 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.48: 4650 22.48 - 44.96: 213 44.96 - 67.44: 27 67.44 - 89.93: 3 89.93 - 112.41: 3 Dihedral angle restraints: 4896 sinusoidal: 1844 harmonic: 3052 Sorted by residual: dihedral pdb=" CA VAL B 484 " pdb=" C VAL B 484 " pdb=" N GLY B 485 " pdb=" CA GLY B 485 " ideal model delta harmonic sigma weight residual 180.00 142.58 37.42 0 5.00e+00 4.00e-02 5.60e+01 dihedral pdb=" CA VAL A 484 " pdb=" C VAL A 484 " pdb=" N GLY A 485 " pdb=" CA GLY A 485 " ideal model delta harmonic sigma weight residual 180.00 143.52 36.48 0 5.00e+00 4.00e-02 5.32e+01 dihedral pdb=" CA PHE B 332 " pdb=" C PHE B 332 " pdb=" N ARG B 333 " pdb=" CA ARG B 333 " ideal model delta harmonic sigma weight residual -180.00 -159.26 -20.74 0 5.00e+00 4.00e-02 1.72e+01 ... (remaining 4893 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1081 0.051 - 0.102: 242 0.102 - 0.154: 27 0.154 - 0.205: 3 0.205 - 0.256: 3 Chirality restraints: 1356 Sorted by residual: chirality pdb=" C5 NAG C 1 " pdb=" C4 NAG C 1 " pdb=" C6 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.41 -2.67 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CB THR B 250 " pdb=" CA THR B 250 " pdb=" OG1 THR B 250 " pdb=" CG2 THR B 250 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" C5 NAG C 2 " pdb=" C4 NAG C 2 " pdb=" C6 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.41 -2.63 0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 1353 not shown) Planarity restraints: 1402 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 248 " 0.017 2.00e-02 2.50e+03 3.40e-02 1.16e+01 pdb=" C LEU A 248 " -0.059 2.00e-02 2.50e+03 pdb=" O LEU A 248 " 0.022 2.00e-02 2.50e+03 pdb=" N VAL A 249 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 486 " -0.046 5.00e-02 4.00e+02 6.93e-02 7.68e+00 pdb=" N PRO A 487 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO A 487 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 487 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 486 " -0.041 5.00e-02 4.00e+02 6.16e-02 6.08e+00 pdb=" N PRO B 487 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO B 487 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 487 " -0.035 5.00e-02 4.00e+02 ... (remaining 1399 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.60: 73 2.60 - 3.10: 6265 3.10 - 3.60: 10557 3.60 - 4.10: 14423 4.10 - 4.60: 23235 Nonbonded interactions: 54553 Sorted by model distance: nonbonded pdb=" O VAL A 539 " pdb=" OH TYR B 309 " model vdw 2.101 2.800 nonbonded pdb=" OD1 ASN A 163 " pdb=" OG SER A 437 " model vdw 2.119 2.800 nonbonded pdb=" OD1 ASN B 67 " pdb=" ND2 ASN B 163 " model vdw 2.126 2.950 nonbonded pdb=" OG SER A 268 " pdb=" OD1 ASN A 270 " model vdw 2.157 2.800 nonbonded pdb=" OH TYR A 309 " pdb=" O VAL B 539 " model vdw 2.169 2.800 ... (remaining 54548 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.950 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: 0.080 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.630 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 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 : 0.007 0.125 8328 Z= 0.334 Angle : 0.690 11.285 11348 Z= 0.337 Chirality : 0.042 0.256 1356 Planarity : 0.005 0.069 1398 Dihedral : 13.129 112.406 2932 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.26), residues: 1076 helix: 1.25 (0.20), residues: 660 sheet: -4.69 (0.63), residues: 20 loop : -0.18 (0.33), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 42 TYR 0.030 0.001 TYR A 418 PHE 0.035 0.002 PHE A 442 TRP 0.009 0.001 TRP B 331 HIS 0.002 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00690 ( 8316) covalent geometry : angle 0.68272 (11320) SS BOND : bond 0.00123 ( 8) SS BOND : angle 1.50960 ( 16) hydrogen bonds : bond 0.16928 ( 513) hydrogen bonds : angle 6.28256 ( 1467) link_BETA1-4 : bond 0.00805 ( 2) link_BETA1-4 : angle 2.88367 ( 6) link_NAG-ASN : bond 0.00495 ( 2) link_NAG-ASN : angle 2.61063 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.290 Fit side-chains REVERT: A 32 ARG cc_start: 0.6316 (mpp-170) cc_final: 0.5980 (mtm-85) REVERT: B 32 ARG cc_start: 0.6378 (mpp-170) cc_final: 0.6040 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.6193 time to fit residues: 64.9782 Evaluate side-chains 83 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 0.0570 chunk 106 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.9704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 67 ASN B 163 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.111383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.086336 restraints weight = 10714.483| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 1.82 r_work: 0.2862 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 8328 Z= 0.200 Angle : 0.557 10.911 11348 Z= 0.286 Chirality : 0.041 0.145 1356 Planarity : 0.004 0.063 1398 Dihedral : 7.702 102.703 1230 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.07 % Favored : 96.84 % Rotamer: Outliers : 1.75 % Allowed : 6.41 % Favored : 91.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.39 (0.26), residues: 1076 helix: 1.79 (0.20), residues: 664 sheet: -4.63 (0.63), residues: 20 loop : -0.22 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 42 TYR 0.009 0.001 TYR A 399 PHE 0.031 0.002 PHE A 442 TRP 0.013 0.001 TRP B 380 HIS 0.003 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00456 ( 8316) covalent geometry : angle 0.54558 (11320) SS BOND : bond 0.00093 ( 8) SS BOND : angle 1.67303 ( 16) hydrogen bonds : bond 0.04288 ( 513) hydrogen bonds : angle 4.61184 ( 1467) link_BETA1-4 : bond 0.00458 ( 2) link_BETA1-4 : angle 2.93712 ( 6) link_NAG-ASN : bond 0.00269 ( 2) link_NAG-ASN : angle 3.09668 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.191 Fit side-chains REVERT: B 32 ARG cc_start: 0.6414 (mpp-170) cc_final: 0.5894 (mtm-85) REVERT: B 548 GLU cc_start: 0.7414 (tp30) cc_final: 0.6701 (mt-10) outliers start: 15 outliers final: 9 residues processed: 90 average time/residue: 0.5370 time to fit residues: 51.2529 Evaluate side-chains 90 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 413 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 14 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 76 optimal weight: 0.0570 chunk 16 optimal weight: 4.9990 chunk 93 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 25 optimal weight: 10.0000 overall best weight: 0.9700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.113205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.088289 restraints weight = 10618.435| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 1.82 r_work: 0.2896 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8328 Z= 0.116 Angle : 0.461 9.206 11348 Z= 0.237 Chirality : 0.038 0.126 1356 Planarity : 0.004 0.063 1398 Dihedral : 7.255 101.283 1230 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 17.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.52 % Allowed : 8.28 % Favored : 90.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.76 (0.27), residues: 1076 helix: 2.17 (0.20), residues: 666 sheet: -4.78 (0.64), residues: 20 loop : -0.24 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 103 TYR 0.007 0.001 TYR B 418 PHE 0.015 0.001 PHE A 442 TRP 0.010 0.001 TRP B 380 HIS 0.002 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 8316) covalent geometry : angle 0.45215 (11320) SS BOND : bond 0.00104 ( 8) SS BOND : angle 0.95966 ( 16) hydrogen bonds : bond 0.03721 ( 513) hydrogen bonds : angle 4.30382 ( 1467) link_BETA1-4 : bond 0.00454 ( 2) link_BETA1-4 : angle 2.88740 ( 6) link_NAG-ASN : bond 0.00326 ( 2) link_NAG-ASN : angle 2.33799 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.217 Fit side-chains revert: symmetry clash REVERT: A 494 MET cc_start: 0.8795 (OUTLIER) cc_final: 0.8438 (mtp) REVERT: B 32 ARG cc_start: 0.6390 (mpp-170) cc_final: 0.5833 (mtm-85) REVERT: B 401 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.7376 (mtp) REVERT: B 548 GLU cc_start: 0.7460 (tp30) cc_final: 0.6777 (mt-10) outliers start: 13 outliers final: 6 residues processed: 86 average time/residue: 0.5946 time to fit residues: 54.2397 Evaluate side-chains 87 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 413 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 43 optimal weight: 6.9990 chunk 77 optimal weight: 0.7980 chunk 59 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.110501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.085366 restraints weight = 10729.313| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 1.83 r_work: 0.2849 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 8328 Z= 0.210 Angle : 0.535 10.590 11348 Z= 0.274 Chirality : 0.041 0.136 1356 Planarity : 0.004 0.061 1398 Dihedral : 7.029 98.168 1230 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.98 % Allowed : 7.81 % Favored : 90.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.63 (0.26), residues: 1076 helix: 2.05 (0.20), residues: 664 sheet: None (None), residues: 0 loop : -0.54 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 403 TYR 0.010 0.001 TYR B 399 PHE 0.019 0.002 PHE A 442 TRP 0.011 0.001 TRP B 380 HIS 0.003 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00486 ( 8316) covalent geometry : angle 0.52521 (11320) SS BOND : bond 0.00110 ( 8) SS BOND : angle 1.50461 ( 16) hydrogen bonds : bond 0.04201 ( 513) hydrogen bonds : angle 4.39827 ( 1467) link_BETA1-4 : bond 0.00521 ( 2) link_BETA1-4 : angle 2.93436 ( 6) link_NAG-ASN : bond 0.00332 ( 2) link_NAG-ASN : angle 2.51016 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 77 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: A 470 MET cc_start: 0.7236 (OUTLIER) cc_final: 0.6965 (mtp) REVERT: A 494 MET cc_start: 0.8871 (OUTLIER) cc_final: 0.8515 (mtp) REVERT: B 32 ARG cc_start: 0.6462 (mpp-170) cc_final: 0.5764 (mtm-85) REVERT: B 401 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.7097 (mtp) REVERT: B 548 GLU cc_start: 0.7437 (tp30) cc_final: 0.6782 (mt-10) outliers start: 17 outliers final: 12 residues processed: 83 average time/residue: 0.5677 time to fit residues: 49.9989 Evaluate side-chains 91 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 388 TYR Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 470 MET Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 413 ASP Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 517 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 7 optimal weight: 10.0000 chunk 92 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 29 optimal weight: 0.0470 chunk 11 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 79 optimal weight: 9.9990 chunk 36 optimal weight: 0.6980 chunk 70 optimal weight: 5.9990 overall best weight: 0.9480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.112924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.087286 restraints weight = 10558.416| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 1.86 r_work: 0.2887 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8328 Z= 0.111 Angle : 0.454 9.298 11348 Z= 0.231 Chirality : 0.037 0.132 1356 Planarity : 0.004 0.062 1398 Dihedral : 6.652 96.111 1230 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 19.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.75 % Allowed : 9.09 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.95 (0.27), residues: 1076 helix: 2.34 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -0.50 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 403 TYR 0.007 0.001 TYR B 399 PHE 0.010 0.001 PHE A 166 TRP 0.010 0.001 TRP B 380 HIS 0.001 0.000 HIS B 541 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 8316) covalent geometry : angle 0.44380 (11320) SS BOND : bond 0.00063 ( 8) SS BOND : angle 1.24871 ( 16) hydrogen bonds : bond 0.03432 ( 513) hydrogen bonds : angle 4.19233 ( 1467) link_BETA1-4 : bond 0.00515 ( 2) link_BETA1-4 : angle 3.01473 ( 6) link_NAG-ASN : bond 0.00312 ( 2) link_NAG-ASN : angle 2.18643 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: A 401 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.7226 (mpp) REVERT: A 470 MET cc_start: 0.7138 (OUTLIER) cc_final: 0.6889 (mtp) REVERT: A 494 MET cc_start: 0.8847 (OUTLIER) cc_final: 0.8498 (mtp) REVERT: B 32 ARG cc_start: 0.6430 (mpp-170) cc_final: 0.5695 (mtm-85) REVERT: B 401 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.6928 (mtp) REVERT: B 548 GLU cc_start: 0.7399 (tp30) cc_final: 0.6707 (mt-10) outliers start: 15 outliers final: 7 residues processed: 87 average time/residue: 0.6002 time to fit residues: 55.4890 Evaluate side-chains 88 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 388 TYR Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 470 MET Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 413 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 88 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 chunk 102 optimal weight: 8.9990 chunk 57 optimal weight: 4.9990 chunk 58 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.112645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.087325 restraints weight = 10525.101| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 1.84 r_work: 0.2874 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8328 Z= 0.121 Angle : 0.456 9.717 11348 Z= 0.232 Chirality : 0.038 0.130 1356 Planarity : 0.004 0.063 1398 Dihedral : 6.374 92.353 1230 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 18.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.33 % Allowed : 8.97 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.07 (0.26), residues: 1076 helix: 2.45 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -0.47 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 403 TYR 0.008 0.001 TYR B 399 PHE 0.011 0.001 PHE A 166 TRP 0.009 0.001 TRP B 380 HIS 0.001 0.001 HIS B 541 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 8316) covalent geometry : angle 0.44592 (11320) SS BOND : bond 0.00079 ( 8) SS BOND : angle 1.21914 ( 16) hydrogen bonds : bond 0.03452 ( 513) hydrogen bonds : angle 4.13565 ( 1467) link_BETA1-4 : bond 0.00561 ( 2) link_BETA1-4 : angle 3.05059 ( 6) link_NAG-ASN : bond 0.00296 ( 2) link_NAG-ASN : angle 2.15668 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 77 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: A 103 ARG cc_start: 0.7465 (ptt-90) cc_final: 0.7124 (ptt-90) REVERT: A 401 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.7101 (mpp) REVERT: A 470 MET cc_start: 0.7101 (OUTLIER) cc_final: 0.6866 (mtp) REVERT: A 494 MET cc_start: 0.8826 (OUTLIER) cc_final: 0.8477 (mtp) REVERT: B 32 ARG cc_start: 0.6375 (mpp-170) cc_final: 0.5603 (mtm-85) REVERT: B 401 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.6750 (mtp) REVERT: B 548 GLU cc_start: 0.7339 (tp30) cc_final: 0.6527 (mt-10) outliers start: 20 outliers final: 11 residues processed: 87 average time/residue: 0.6205 time to fit residues: 57.4057 Evaluate side-chains 91 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 388 TYR Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain A residue 470 MET Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 413 ASP Chi-restraints excluded: chain B residue 468 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 92 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 62 optimal weight: 0.0870 chunk 91 optimal weight: 0.6980 chunk 94 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 95 optimal weight: 5.9990 chunk 99 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.114271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.088373 restraints weight = 10604.647| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 1.89 r_work: 0.2908 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8328 Z= 0.097 Angle : 0.436 10.358 11348 Z= 0.220 Chirality : 0.037 0.119 1356 Planarity : 0.004 0.064 1398 Dihedral : 5.948 86.047 1230 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 19.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.98 % Allowed : 9.67 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.28 (0.27), residues: 1076 helix: 2.62 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -0.38 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 291 TYR 0.006 0.001 TYR B 399 PHE 0.010 0.001 PHE A 166 TRP 0.009 0.001 TRP B 380 HIS 0.001 0.000 HIS B 364 Details of bonding type rmsd covalent geometry : bond 0.00207 ( 8316) covalent geometry : angle 0.42546 (11320) SS BOND : bond 0.00064 ( 8) SS BOND : angle 1.19509 ( 16) hydrogen bonds : bond 0.03165 ( 513) hydrogen bonds : angle 4.02961 ( 1467) link_BETA1-4 : bond 0.00555 ( 2) link_BETA1-4 : angle 3.28233 ( 6) link_NAG-ASN : bond 0.00285 ( 2) link_NAG-ASN : angle 2.04055 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: A 103 ARG cc_start: 0.7441 (ptt-90) cc_final: 0.7169 (ptt-90) REVERT: A 470 MET cc_start: 0.7005 (OUTLIER) cc_final: 0.6794 (mtp) REVERT: A 494 MET cc_start: 0.8791 (OUTLIER) cc_final: 0.8438 (mtp) REVERT: B 32 ARG cc_start: 0.6392 (mpp-170) cc_final: 0.5584 (mtm-85) REVERT: B 401 MET cc_start: 0.8507 (OUTLIER) cc_final: 0.6667 (mtp) REVERT: B 548 GLU cc_start: 0.7332 (tp30) cc_final: 0.6538 (mt-10) outliers start: 17 outliers final: 10 residues processed: 88 average time/residue: 0.5885 time to fit residues: 54.9381 Evaluate side-chains 92 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 388 TYR Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain A residue 470 MET Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 413 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 61 optimal weight: 0.4980 chunk 36 optimal weight: 4.9990 chunk 96 optimal weight: 0.6980 chunk 75 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 48 optimal weight: 0.0370 chunk 38 optimal weight: 3.9990 chunk 73 optimal weight: 0.0980 chunk 56 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 overall best weight: 0.8660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.113583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.088225 restraints weight = 10622.588| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 1.84 r_work: 0.2898 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8328 Z= 0.106 Angle : 0.444 10.736 11348 Z= 0.223 Chirality : 0.037 0.117 1356 Planarity : 0.004 0.064 1398 Dihedral : 5.578 77.581 1230 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 20.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.52 % Allowed : 10.26 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.32 (0.27), residues: 1076 helix: 2.64 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -0.35 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 32 TYR 0.007 0.001 TYR B 399 PHE 0.010 0.001 PHE A 166 TRP 0.008 0.001 TRP B 380 HIS 0.001 0.001 HIS B 541 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 8316) covalent geometry : angle 0.43235 (11320) SS BOND : bond 0.00064 ( 8) SS BOND : angle 1.19240 ( 16) hydrogen bonds : bond 0.03240 ( 513) hydrogen bonds : angle 4.01614 ( 1467) link_BETA1-4 : bond 0.00461 ( 2) link_BETA1-4 : angle 3.59101 ( 6) link_NAG-ASN : bond 0.00276 ( 2) link_NAG-ASN : angle 2.06775 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.321 Fit side-chains revert: symmetry clash REVERT: A 103 ARG cc_start: 0.7462 (ptt-90) cc_final: 0.7163 (ptt-90) REVERT: A 470 MET cc_start: 0.6994 (OUTLIER) cc_final: 0.6774 (mtp) REVERT: A 494 MET cc_start: 0.8799 (OUTLIER) cc_final: 0.8431 (mtp) REVERT: B 32 ARG cc_start: 0.6332 (mpp-170) cc_final: 0.5517 (mtm-85) REVERT: B 401 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.6606 (mtp) REVERT: B 548 GLU cc_start: 0.7301 (tp30) cc_final: 0.6534 (mt-10) outliers start: 13 outliers final: 9 residues processed: 86 average time/residue: 0.6807 time to fit residues: 61.9433 Evaluate side-chains 90 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 388 TYR Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 470 MET Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 413 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 80 optimal weight: 0.0870 chunk 48 optimal weight: 0.0570 chunk 37 optimal weight: 0.0170 chunk 96 optimal weight: 0.6980 chunk 77 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 73 optimal weight: 0.0070 chunk 27 optimal weight: 0.7980 overall best weight: 0.1732 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 541 HIS B 541 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.118953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.094042 restraints weight = 10647.266| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.84 r_work: 0.2982 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.019 8328 Z= 0.068 Angle : 0.414 10.349 11348 Z= 0.205 Chirality : 0.036 0.119 1356 Planarity : 0.003 0.067 1398 Dihedral : 4.702 58.239 1230 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 23.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.70 % Allowed : 11.19 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.66 (0.27), residues: 1076 helix: 2.90 (0.20), residues: 672 sheet: None (None), residues: 0 loop : -0.25 (0.33), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 128 TYR 0.007 0.001 TYR B 418 PHE 0.008 0.001 PHE A 166 TRP 0.009 0.001 TRP B 482 HIS 0.001 0.000 HIS B 541 Details of bonding type rmsd covalent geometry : bond 0.00139 ( 8316) covalent geometry : angle 0.39858 (11320) SS BOND : bond 0.00073 ( 8) SS BOND : angle 1.12436 ( 16) hydrogen bonds : bond 0.02640 ( 513) hydrogen bonds : angle 3.83013 ( 1467) link_BETA1-4 : bond 0.00257 ( 2) link_BETA1-4 : angle 4.21439 ( 6) link_NAG-ASN : bond 0.00238 ( 2) link_NAG-ASN : angle 1.97148 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: B 32 ARG cc_start: 0.6333 (mpp-170) cc_final: 0.5523 (mtm-85) REVERT: B 548 GLU cc_start: 0.7274 (tp30) cc_final: 0.6494 (mt-10) outliers start: 6 outliers final: 7 residues processed: 90 average time/residue: 0.6194 time to fit residues: 59.3683 Evaluate side-chains 92 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 388 TYR Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 413 ASP Chi-restraints excluded: chain B residue 468 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 4 optimal weight: 0.5980 chunk 75 optimal weight: 0.2980 chunk 25 optimal weight: 7.9990 chunk 87 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.116038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.090824 restraints weight = 10565.085| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.84 r_work: 0.2938 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8328 Z= 0.093 Angle : 0.423 8.983 11348 Z= 0.211 Chirality : 0.037 0.116 1356 Planarity : 0.003 0.065 1398 Dihedral : 4.403 43.580 1230 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 20.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.82 % Allowed : 11.19 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.65 (0.27), residues: 1076 helix: 2.89 (0.20), residues: 672 sheet: None (None), residues: 0 loop : -0.25 (0.33), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 32 TYR 0.004 0.001 TYR A 168 PHE 0.009 0.001 PHE A 166 TRP 0.007 0.001 TRP B 482 HIS 0.001 0.000 HIS B 364 Details of bonding type rmsd covalent geometry : bond 0.00202 ( 8316) covalent geometry : angle 0.40554 (11320) SS BOND : bond 0.00062 ( 8) SS BOND : angle 1.12127 ( 16) hydrogen bonds : bond 0.02939 ( 513) hydrogen bonds : angle 3.86133 ( 1467) link_BETA1-4 : bond 0.00115 ( 2) link_BETA1-4 : angle 4.44228 ( 6) link_NAG-ASN : bond 0.00254 ( 2) link_NAG-ASN : angle 2.13668 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: B 32 ARG cc_start: 0.6339 (mpp-170) cc_final: 0.5529 (mtm-85) REVERT: B 548 GLU cc_start: 0.7302 (tp30) cc_final: 0.6517 (mt-10) outliers start: 7 outliers final: 7 residues processed: 88 average time/residue: 0.6613 time to fit residues: 61.8561 Evaluate side-chains 89 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 82 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 388 TYR Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 413 ASP Chi-restraints excluded: chain B residue 468 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 87 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 9 optimal weight: 8.9990 chunk 17 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 79 optimal weight: 0.0570 chunk 15 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 8 optimal weight: 4.9990 chunk 6 optimal weight: 0.1980 overall best weight: 0.7702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.115263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.089946 restraints weight = 10601.249| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 1.84 r_work: 0.2923 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8328 Z= 0.095 Angle : 0.423 7.891 11348 Z= 0.213 Chirality : 0.037 0.116 1356 Planarity : 0.004 0.065 1398 Dihedral : 4.223 31.536 1230 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 20.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.82 % Allowed : 11.31 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.62 (0.27), residues: 1076 helix: 2.87 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -0.22 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 103 TYR 0.005 0.001 TYR B 399 PHE 0.009 0.001 PHE B 166 TRP 0.008 0.001 TRP B 380 HIS 0.001 0.000 HIS A 350 Details of bonding type rmsd covalent geometry : bond 0.00205 ( 8316) covalent geometry : angle 0.40655 (11320) SS BOND : bond 0.00059 ( 8) SS BOND : angle 1.18072 ( 16) hydrogen bonds : bond 0.03042 ( 513) hydrogen bonds : angle 3.89310 ( 1467) link_BETA1-4 : bond 0.00081 ( 2) link_BETA1-4 : angle 4.30098 ( 6) link_NAG-ASN : bond 0.00274 ( 2) link_NAG-ASN : angle 2.21459 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2820.24 seconds wall clock time: 48 minutes 56.88 seconds (2936.88 seconds total)