Starting phenix.real_space_refine on Sun Aug 24 02:24:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wmq_37658/08_2025/8wmq_37658_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wmq_37658/08_2025/8wmq_37658.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wmq_37658/08_2025/8wmq_37658_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wmq_37658/08_2025/8wmq_37658_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wmq_37658/08_2025/8wmq_37658.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wmq_37658/08_2025/8wmq_37658.map" } resolution = 3.3 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= 0.003 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 5300 2.51 5 N 1316 2.21 5 O 1472 1.98 5 H 8208 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 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: 16348 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 8130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 8130 Classifications: {'peptide': 540} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 516} Chain: "A" Number of atoms: 8130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 8130 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: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'ZEA': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'ZEA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.74, per 1000 atoms: 0.23 Number of scatterers: 16348 At special positions: 0 Unit cell: (96.163, 114.885, 101.269, 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 5300 6.00 H 8208 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 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=2.04 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 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 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: 1.60 Conformation dependent library (CDL) restraints added in 560.2 milliseconds Enol-peptide restraints added in 953.7 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: 52 helices and 8 sheets defined 67.5% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'B' and resid 19 through 30 Processing helix chain 'B' and resid 31 through 37 Processing helix chain 'B' and resid 39 through 43 Processing helix chain 'B' and resid 46 through 61 Processing helix chain 'B' and resid 62 through 73 removed outlier: 4.203A pdb=" N ALA B 68 " --> pdb=" O LEU B 64 " (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 Processing helix chain 'B' and resid 159 through 169 removed outlier: 3.760A pdb=" N ALA B 164 " --> pdb=" O MET B 160 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR B 165 " --> pdb=" O GLY B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 201 removed outlier: 3.542A pdb=" N ILE B 201 " --> pdb=" O PHE B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 209 Processing helix chain 'B' and resid 212 through 232 removed outlier: 4.510A pdb=" N SER B 220 " --> pdb=" O ARG B 216 " (cutoff:3.500A) removed outlier: 4.480A 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 removed outlier: 3.509A pdb=" N TRP B 298 " --> pdb=" O SER B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 331 Processing helix chain 'B' and resid 343 through 355 removed outlier: 3.861A pdb=" N LYS B 355 " --> pdb=" O ASP B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 405 removed outlier: 3.728A pdb=" N TRP B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 435 Processing helix chain 'B' and resid 444 through 451 removed outlier: 4.268A 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: 4.000A pdb=" N THR B 500 " --> pdb=" O LYS B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 524 Proline residue: B 512 - end of helix removed outlier: 3.637A 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 554 removed outlier: 5.159A pdb=" N TRP B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N ASP B 544 " --> pdb=" O LEU B 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 30 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 60 Processing helix chain 'A' and resid 62 through 73 removed outlier: 4.200A 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 removed outlier: 3.862A pdb=" N ALA A 164 " --> pdb=" O MET A 160 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TYR A 165 " --> pdb=" O GLY A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 202 Processing helix chain 'A' and resid 203 through 211 removed outlier: 3.852A pdb=" N VAL A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 232 removed outlier: 4.510A pdb=" N SER A 220 " --> pdb=" O ARG A 216 " (cutoff:3.500A) removed outlier: 4.499A 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 330 Processing helix chain 'A' and resid 343 through 355 removed outlier: 3.862A pdb=" N LYS A 355 " --> pdb=" O ASP A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 406 removed outlier: 3.735A pdb=" N TRP A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 435 Processing helix chain 'A' and resid 445 through 451 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 Processing helix chain 'A' and resid 497 through 502 removed outlier: 4.006A pdb=" N THR A 500 " --> pdb=" O LYS A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 524 Proline residue: A 512 - end of helix removed outlier: 3.634A pdb=" N MET A 520 " --> pdb=" O THR A 516 " (cutoff:3.500A) Proline residue: A 521 - end of helix Processing helix chain 'A' and resid 525 through 554 removed outlier: 3.543A pdb=" N GLY A 529 " --> pdb=" O SER A 525 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N TRP A 543 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ASP A 544 " --> pdb=" O LEU A 540 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 86 through 87 Processing sheet with id=AA2, first strand: chain 'B' and resid 156 through 158 Processing sheet with id=AA3, first strand: chain 'B' and resid 241 through 242 removed outlier: 3.664A pdb=" N THR B 250 " --> pdb=" O GLY B 242 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 274 through 275 removed outlier: 3.766A pdb=" N SER B 274 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N SER B 261 " --> pdb=" O VAL A 265 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER A 261 " --> pdb=" O VAL B 265 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER A 274 " --> pdb=" O ILE A 266 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 286 through 287 removed outlier: 4.104A pdb=" N SER B 261 " --> pdb=" O VAL A 265 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER A 261 " --> pdb=" O VAL B 265 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 86 through 87 Processing sheet with id=AA7, first strand: chain 'A' and resid 156 through 158 Processing sheet with id=AA8, first strand: chain 'A' and resid 241 through 242 513 hydrogen bonds defined for protein. 1458 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: 4.04 Time building geometry restraints manager: 2.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8204 1.03 - 1.23: 14 1.23 - 1.42: 3414 1.42 - 1.62: 4820 1.62 - 1.81: 84 Bond restraints: 16536 Sorted by residual: bond pdb=" C6 ZEA A 701 " pdb=" N10 ZEA A 701 " ideal model delta sigma weight residual 1.336 1.466 -0.130 2.00e-02 2.50e+03 4.21e+01 bond pdb=" C6 ZEA B 701 " pdb=" N10 ZEA B 701 " ideal model delta sigma weight residual 1.336 1.466 -0.130 2.00e-02 2.50e+03 4.20e+01 bond pdb=" C13 ZEA A 701 " pdb=" C14 ZEA A 701 " ideal model delta sigma weight residual 1.502 1.596 -0.094 2.00e-02 2.50e+03 2.22e+01 bond pdb=" C13 ZEA B 701 " pdb=" C14 ZEA B 701 " ideal model delta sigma weight residual 1.502 1.596 -0.094 2.00e-02 2.50e+03 2.21e+01 bond pdb=" C13 ZEA A 701 " pdb=" C15 ZEA A 701 " ideal model delta sigma weight residual 1.500 1.557 -0.057 2.00e-02 2.50e+03 8.08e+00 ... (remaining 16531 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.39: 29912 8.39 - 16.79: 4 16.79 - 25.18: 0 25.18 - 33.58: 2 33.58 - 41.97: 4 Bond angle restraints: 29922 Sorted by residual: angle pdb=" C12 ZEA B 701 " pdb=" C13 ZEA B 701 " pdb=" C15 ZEA B 701 " ideal model delta sigma weight residual 125.58 167.55 -41.97 3.00e+00 1.11e-01 1.96e+02 angle pdb=" C12 ZEA A 701 " pdb=" C13 ZEA A 701 " pdb=" C15 ZEA A 701 " ideal model delta sigma weight residual 125.58 167.55 -41.97 3.00e+00 1.11e-01 1.96e+02 angle pdb=" C12 ZEA B 701 " pdb=" C13 ZEA B 701 " pdb=" C14 ZEA B 701 " ideal model delta sigma weight residual 121.92 87.91 34.01 3.00e+00 1.11e-01 1.28e+02 angle pdb=" C12 ZEA A 701 " pdb=" C13 ZEA A 701 " pdb=" C14 ZEA A 701 " ideal model delta sigma weight residual 121.92 87.94 33.98 3.00e+00 1.11e-01 1.28e+02 angle pdb=" C14 ZEA A 701 " pdb=" C13 ZEA A 701 " pdb=" C15 ZEA A 701 " ideal model delta sigma weight residual 112.50 79.62 32.88 3.00e+00 1.11e-01 1.20e+02 ... (remaining 29917 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.94: 7404 24.94 - 49.87: 339 49.87 - 74.80: 132 74.80 - 99.74: 4 99.74 - 124.67: 3 Dihedral angle restraints: 7882 sinusoidal: 4248 harmonic: 3634 Sorted by residual: dihedral pdb=" CB CYS A 78 " pdb=" SG CYS A 78 " pdb=" SG CYS A 123 " pdb=" CB CYS A 123 " ideal model delta sinusoidal sigma weight residual -86.00 -145.94 59.94 1 1.00e+01 1.00e-02 4.79e+01 dihedral pdb=" CB CYS B 78 " pdb=" SG CYS B 78 " pdb=" SG CYS B 123 " pdb=" CB CYS B 123 " ideal model delta sinusoidal sigma weight residual -86.00 -144.84 58.84 1 1.00e+01 1.00e-02 4.63e+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 180.00 150.51 29.49 0 5.00e+00 4.00e-02 3.48e+01 ... (remaining 7879 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1137 0.053 - 0.105: 191 0.105 - 0.158: 27 0.158 - 0.210: 0 0.210 - 0.263: 1 Chirality restraints: 1356 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN B 270 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA ILE A 362 " pdb=" N ILE A 362 " pdb=" C ILE A 362 " pdb=" CB ILE A 362 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.90e-01 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 2.42 0.13 2.00e-01 2.50e+01 4.38e-01 ... (remaining 1353 not shown) Planarity restraints: 2434 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 486 " -0.043 5.00e-02 4.00e+02 6.49e-02 6.74e+00 pdb=" N PRO A 487 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 487 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 487 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 486 " -0.043 5.00e-02 4.00e+02 6.46e-02 6.68e+00 pdb=" N PRO B 487 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 487 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 487 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 340 " 0.043 5.00e-02 4.00e+02 6.32e-02 6.39e+00 pdb=" N PRO A 341 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 341 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 341 " 0.035 5.00e-02 4.00e+02 ... (remaining 2431 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.19: 766 2.19 - 2.79: 32112 2.79 - 3.39: 45274 3.39 - 4.00: 56801 4.00 - 4.60: 89965 Nonbonded interactions: 224918 Sorted by model distance: nonbonded pdb=" O LEU A 519 " pdb=" HG1 THR A 523 " model vdw 1.583 2.450 nonbonded pdb=" O LEU B 519 " pdb=" HG1 THR B 523 " model vdw 1.584 2.450 nonbonded pdb=" HG SER A 268 " pdb=" OD1 ASN A 270 " model vdw 1.608 2.450 nonbonded pdb=" O SER B 88 " pdb="HD21 ASN A 270 " model vdw 1.630 2.450 nonbonded pdb=" O PHE B 332 " pdb=" HG1 THR B 338 " model vdw 1.633 2.450 ... (remaining 224913 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: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.120 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.320 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.130 8340 Z= 0.213 Angle : 1.070 41.971 11362 Z= 0.456 Chirality : 0.040 0.263 1356 Planarity : 0.005 0.065 1400 Dihedral : 14.040 124.675 2938 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % 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: 0.89 (0.26), residues: 1076 helix: 1.65 (0.21), residues: 642 sheet: None (None), residues: 0 loop : -1.07 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 23 TYR 0.013 0.001 TYR B 309 PHE 0.010 0.001 PHE A 189 TRP 0.011 0.001 TRP A 482 HIS 0.003 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 8328) covalent geometry : angle 1.07007 (11334) SS BOND : bond 0.00223 ( 8) SS BOND : angle 0.74306 ( 16) hydrogen bonds : bond 0.13654 ( 509) hydrogen bonds : angle 5.56263 ( 1458) link_BETA1-4 : bond 0.00262 ( 2) link_BETA1-4 : angle 1.54546 ( 6) link_NAG-ASN : bond 0.00177 ( 2) link_NAG-ASN : angle 1.42070 ( 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 132 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.441 Fit side-chains REVERT: B 390 ASP cc_start: 0.7078 (m-30) cc_final: 0.6821 (m-30) REVERT: B 444 GLU cc_start: 0.6848 (mp0) cc_final: 0.6634 (mp0) REVERT: A 390 ASP cc_start: 0.7144 (m-30) cc_final: 0.6882 (m-30) REVERT: A 444 GLU cc_start: 0.6869 (mp0) cc_final: 0.6630 (mp0) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.1316 time to fit residues: 28.0081 Evaluate side-chains 108 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.430 ------------------------------------------------------------------------------- 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: 6.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.123234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.100281 restraints weight = 39859.916| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.49 r_work: 0.3254 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.0967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8340 Z= 0.131 Angle : 0.997 37.687 11362 Z= 0.405 Chirality : 0.039 0.212 1356 Planarity : 0.005 0.065 1400 Dihedral : 8.579 111.371 1236 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.35 % Allowed : 6.53 % Favored : 93.12 % 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: 1.18 (0.26), residues: 1076 helix: 1.83 (0.20), residues: 652 sheet: None (None), residues: 0 loop : -0.90 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 23 TYR 0.010 0.001 TYR B 524 PHE 0.016 0.001 PHE B 555 TRP 0.007 0.001 TRP A 482 HIS 0.003 0.001 HIS B 360 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 8328) covalent geometry : angle 0.99580 (11334) SS BOND : bond 0.00117 ( 8) SS BOND : angle 0.76990 ( 16) hydrogen bonds : bond 0.05739 ( 509) hydrogen bonds : angle 4.63369 ( 1458) link_BETA1-4 : bond 0.00271 ( 2) link_BETA1-4 : angle 2.46330 ( 6) link_NAG-ASN : bond 0.00413 ( 2) link_NAG-ASN : angle 1.67065 ( 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 116 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 113 time to evaluate : 0.440 Fit side-chains REVERT: B 390 ASP cc_start: 0.7556 (m-30) cc_final: 0.7266 (m-30) REVERT: B 444 GLU cc_start: 0.7493 (mp0) cc_final: 0.7216 (mp0) REVERT: A 390 ASP cc_start: 0.7565 (m-30) cc_final: 0.7285 (m-30) outliers start: 3 outliers final: 2 residues processed: 114 average time/residue: 0.1498 time to fit residues: 26.9153 Evaluate side-chains 106 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 104 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain A residue 335 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 73 optimal weight: 3.9990 chunk 53 optimal weight: 0.4980 chunk 106 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 7 optimal weight: 0.0270 chunk 99 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 overall best weight: 2.3044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.121222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.098339 restraints weight = 40155.030| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.48 r_work: 0.3223 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 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 : 0.004 0.031 8340 Z= 0.160 Angle : 0.999 37.669 11362 Z= 0.405 Chirality : 0.040 0.206 1356 Planarity : 0.005 0.067 1400 Dihedral : 8.133 104.961 1236 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.93 % Allowed : 8.39 % Favored : 90.68 % 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: 1.09 (0.26), residues: 1076 helix: 1.83 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -1.04 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 454 TYR 0.008 0.001 TYR B 524 PHE 0.014 0.001 PHE B 189 TRP 0.006 0.001 TRP B 482 HIS 0.003 0.001 HIS B 360 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 8328) covalent geometry : angle 0.99687 (11334) SS BOND : bond 0.00199 ( 8) SS BOND : angle 1.00125 ( 16) hydrogen bonds : bond 0.05758 ( 509) hydrogen bonds : angle 4.52628 ( 1458) link_BETA1-4 : bond 0.00169 ( 2) link_BETA1-4 : angle 2.43268 ( 6) link_NAG-ASN : bond 0.00407 ( 2) link_NAG-ASN : angle 1.84319 ( 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 113 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 105 time to evaluate : 0.496 Fit side-chains REVERT: B 390 ASP cc_start: 0.7646 (m-30) cc_final: 0.7389 (m-30) REVERT: A 86 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7646 (mm) REVERT: A 390 ASP cc_start: 0.7622 (m-30) cc_final: 0.7355 (m-30) outliers start: 8 outliers final: 7 residues processed: 110 average time/residue: 0.1533 time to fit residues: 25.8641 Evaluate side-chains 110 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 551 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.121250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.098895 restraints weight = 39901.439| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.44 r_work: 0.3234 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8340 Z= 0.127 Angle : 0.986 37.226 11362 Z= 0.393 Chirality : 0.039 0.205 1356 Planarity : 0.005 0.066 1400 Dihedral : 7.830 98.156 1236 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.05 % Allowed : 9.09 % Favored : 89.86 % 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: 1.31 (0.26), residues: 1076 helix: 2.01 (0.21), residues: 646 sheet: None (None), residues: 0 loop : -0.93 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 51 TYR 0.008 0.001 TYR B 524 PHE 0.014 0.001 PHE B 555 TRP 0.006 0.001 TRP B 482 HIS 0.002 0.001 HIS B 541 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 8328) covalent geometry : angle 0.98420 (11334) SS BOND : bond 0.00172 ( 8) SS BOND : angle 0.86581 ( 16) hydrogen bonds : bond 0.05227 ( 509) hydrogen bonds : angle 4.32154 ( 1458) link_BETA1-4 : bond 0.00339 ( 2) link_BETA1-4 : angle 2.46703 ( 6) link_NAG-ASN : bond 0.00397 ( 2) link_NAG-ASN : angle 1.71633 ( 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 110 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.460 Fit side-chains REVERT: B 390 ASP cc_start: 0.7590 (m-30) cc_final: 0.7323 (m-30) REVERT: A 86 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7280 (mm) REVERT: A 390 ASP cc_start: 0.7607 (m-30) cc_final: 0.7354 (m-30) outliers start: 9 outliers final: 8 residues processed: 106 average time/residue: 0.1472 time to fit residues: 24.2406 Evaluate side-chains 108 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 551 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 79 optimal weight: 10.0000 chunk 85 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 4 optimal weight: 0.9980 chunk 19 optimal weight: 0.1980 chunk 58 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.123120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.100680 restraints weight = 39520.613| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.46 r_work: 0.3256 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8340 Z= 0.106 Angle : 0.973 36.635 11362 Z= 0.381 Chirality : 0.038 0.200 1356 Planarity : 0.005 0.065 1400 Dihedral : 7.327 90.192 1236 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.93 % Allowed : 9.79 % Favored : 89.28 % 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: 1.56 (0.27), residues: 1076 helix: 2.21 (0.21), residues: 646 sheet: None (None), residues: 0 loop : -0.83 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 259 TYR 0.007 0.001 TYR A 181 PHE 0.011 0.001 PHE B 555 TRP 0.006 0.001 TRP A 482 HIS 0.001 0.001 HIS B 541 Details of bonding type rmsd covalent geometry : bond 0.00219 ( 8328) covalent geometry : angle 0.97118 (11334) SS BOND : bond 0.00179 ( 8) SS BOND : angle 0.73727 ( 16) hydrogen bonds : bond 0.04651 ( 509) hydrogen bonds : angle 4.12648 ( 1458) link_BETA1-4 : bond 0.00355 ( 2) link_BETA1-4 : angle 2.57799 ( 6) link_NAG-ASN : bond 0.00327 ( 2) link_NAG-ASN : angle 1.58005 ( 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 113 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 105 time to evaluate : 0.452 Fit side-chains REVERT: B 390 ASP cc_start: 0.7556 (m-30) cc_final: 0.7291 (m-30) REVERT: A 390 ASP cc_start: 0.7616 (m-30) cc_final: 0.7342 (m-30) outliers start: 8 outliers final: 6 residues processed: 111 average time/residue: 0.1442 time to fit residues: 24.9659 Evaluate side-chains 109 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 103 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 551 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 68 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.121126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.099019 restraints weight = 39829.881| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.42 r_work: 0.3233 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8340 Z= 0.140 Angle : 0.986 36.793 11362 Z= 0.391 Chirality : 0.039 0.199 1356 Planarity : 0.005 0.067 1400 Dihedral : 7.222 84.751 1236 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.28 % Allowed : 10.61 % 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: 1.46 (0.26), residues: 1076 helix: 2.11 (0.20), residues: 648 sheet: None (None), residues: 0 loop : -0.86 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 204 TYR 0.008 0.001 TYR A 181 PHE 0.019 0.001 PHE B 555 TRP 0.005 0.001 TRP B 482 HIS 0.002 0.001 HIS A 350 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 8328) covalent geometry : angle 0.98422 (11334) SS BOND : bond 0.00182 ( 8) SS BOND : angle 0.95563 ( 16) hydrogen bonds : bond 0.05032 ( 509) hydrogen bonds : angle 4.17458 ( 1458) link_BETA1-4 : bond 0.00297 ( 2) link_BETA1-4 : angle 2.77853 ( 6) link_NAG-ASN : bond 0.00379 ( 2) link_NAG-ASN : angle 1.58239 ( 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 111 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 0.265 Fit side-chains REVERT: B 390 ASP cc_start: 0.7562 (m-30) cc_final: 0.7295 (m-30) REVERT: B 524 TYR cc_start: 0.8831 (OUTLIER) cc_final: 0.8084 (m-80) REVERT: A 390 ASP cc_start: 0.7570 (m-30) cc_final: 0.7305 (m-30) outliers start: 11 outliers final: 10 residues processed: 107 average time/residue: 0.1350 time to fit residues: 22.1217 Evaluate side-chains 110 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 524 TYR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 10 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 30 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.118303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.096349 restraints weight = 40078.781| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.41 r_work: 0.3196 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8340 Z= 0.175 Angle : 1.009 36.917 11362 Z= 0.408 Chirality : 0.040 0.206 1356 Planarity : 0.005 0.067 1400 Dihedral : 7.099 75.701 1236 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 1.52 % Allowed : 10.96 % Favored : 87.53 % 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: 1.24 (0.26), residues: 1076 helix: 1.96 (0.20), residues: 648 sheet: None (None), residues: 0 loop : -1.01 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 259 TYR 0.010 0.001 TYR B 27 PHE 0.022 0.002 PHE A 555 TRP 0.007 0.001 TRP A 543 HIS 0.003 0.001 HIS A 350 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 8328) covalent geometry : angle 1.00546 (11334) SS BOND : bond 0.00201 ( 8) SS BOND : angle 1.22265 ( 16) hydrogen bonds : bond 0.05636 ( 509) hydrogen bonds : angle 4.30211 ( 1458) link_BETA1-4 : bond 0.00211 ( 2) link_BETA1-4 : angle 3.08564 ( 6) link_NAG-ASN : bond 0.00406 ( 2) link_NAG-ASN : angle 1.71556 ( 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 117 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.440 Fit side-chains revert: symmetry clash REVERT: B 390 ASP cc_start: 0.7583 (m-30) cc_final: 0.7349 (m-30) REVERT: B 524 TYR cc_start: 0.8874 (OUTLIER) cc_final: 0.8028 (m-80) REVERT: A 517 MET cc_start: 0.8592 (mtp) cc_final: 0.8285 (mtm) outliers start: 13 outliers final: 10 residues processed: 112 average time/residue: 0.1596 time to fit residues: 26.4485 Evaluate side-chains 113 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 524 TYR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 551 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 86 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.118413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.096602 restraints weight = 40087.996| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.40 r_work: 0.3200 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8340 Z= 0.140 Angle : 0.995 36.852 11362 Z= 0.397 Chirality : 0.039 0.203 1356 Planarity : 0.005 0.067 1400 Dihedral : 6.683 66.982 1236 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.40 % Allowed : 11.42 % Favored : 87.18 % 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: 1.31 (0.26), residues: 1076 helix: 2.01 (0.20), residues: 648 sheet: None (None), residues: 0 loop : -0.96 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 259 TYR 0.008 0.001 TYR A 181 PHE 0.020 0.001 PHE B 555 TRP 0.007 0.001 TRP B 482 HIS 0.002 0.001 HIS B 289 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 8328) covalent geometry : angle 0.99155 (11334) SS BOND : bond 0.00172 ( 8) SS BOND : angle 1.02898 ( 16) hydrogen bonds : bond 0.05329 ( 509) hydrogen bonds : angle 4.19950 ( 1458) link_BETA1-4 : bond 0.00137 ( 2) link_BETA1-4 : angle 3.47706 ( 6) link_NAG-ASN : bond 0.00385 ( 2) link_NAG-ASN : angle 1.73968 ( 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 113 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 524 TYR cc_start: 0.8869 (OUTLIER) cc_final: 0.8132 (m-80) REVERT: A 517 MET cc_start: 0.8526 (mtp) cc_final: 0.8232 (mtm) outliers start: 12 outliers final: 10 residues processed: 109 average time/residue: 0.1504 time to fit residues: 24.1173 Evaluate side-chains 113 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 309 TYR Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 524 TYR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 60 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 chunk 27 optimal weight: 0.4980 chunk 106 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 chunk 49 optimal weight: 3.9990 chunk 79 optimal weight: 10.0000 chunk 8 optimal weight: 0.6980 chunk 30 optimal weight: 4.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 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 = 0.3645 r_free = 0.3645 target = 0.120170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.098153 restraints weight = 39730.498| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.42 r_work: 0.3222 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8340 Z= 0.115 Angle : 0.985 36.683 11362 Z= 0.388 Chirality : 0.039 0.197 1356 Planarity : 0.005 0.066 1400 Dihedral : 5.891 53.761 1236 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 1.52 % Allowed : 11.42 % Favored : 87.06 % 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: 1.53 (0.27), residues: 1076 helix: 2.18 (0.21), residues: 648 sheet: None (None), residues: 0 loop : -0.85 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 259 TYR 0.008 0.001 TYR A 181 PHE 0.023 0.001 PHE B 555 TRP 0.007 0.001 TRP B 482 HIS 0.002 0.001 HIS A 289 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 8328) covalent geometry : angle 0.97959 (11334) SS BOND : bond 0.00151 ( 8) SS BOND : angle 0.81318 ( 16) hydrogen bonds : bond 0.04808 ( 509) hydrogen bonds : angle 4.05872 ( 1458) link_BETA1-4 : bond 0.00218 ( 2) link_BETA1-4 : angle 4.22633 ( 6) link_NAG-ASN : bond 0.00306 ( 2) link_NAG-ASN : angle 1.80254 ( 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 113 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 524 TYR cc_start: 0.8846 (OUTLIER) cc_final: 0.8161 (m-80) outliers start: 13 outliers final: 12 residues processed: 109 average time/residue: 0.1566 time to fit residues: 25.0766 Evaluate side-chains 113 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 309 TYR Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 524 TYR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 84 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 107 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 85 optimal weight: 0.4980 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 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 = 0.3639 r_free = 0.3639 target = 0.119563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.097890 restraints weight = 39885.742| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.40 r_work: 0.3225 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8340 Z= 0.118 Angle : 0.980 36.739 11362 Z= 0.386 Chirality : 0.039 0.204 1356 Planarity : 0.005 0.066 1400 Dihedral : 5.508 54.645 1236 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.52 % Allowed : 11.89 % Favored : 86.60 % 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: 1.61 (0.26), residues: 1076 helix: 2.24 (0.20), residues: 648 sheet: None (None), residues: 0 loop : -0.82 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 259 TYR 0.008 0.001 TYR A 181 PHE 0.027 0.001 PHE A 555 TRP 0.007 0.001 TRP B 482 HIS 0.002 0.001 HIS B 289 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 8328) covalent geometry : angle 0.97445 (11334) SS BOND : bond 0.00162 ( 8) SS BOND : angle 0.83879 ( 16) hydrogen bonds : bond 0.04770 ( 509) hydrogen bonds : angle 4.01620 ( 1458) link_BETA1-4 : bond 0.00348 ( 2) link_BETA1-4 : angle 4.25168 ( 6) link_NAG-ASN : bond 0.00341 ( 2) link_NAG-ASN : angle 2.13541 ( 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 112 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 524 TYR cc_start: 0.8836 (OUTLIER) cc_final: 0.8161 (m-80) outliers start: 13 outliers final: 11 residues processed: 108 average time/residue: 0.1490 time to fit residues: 24.0179 Evaluate side-chains 110 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 309 TYR Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 524 TYR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 105 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 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 = 0.3644 r_free = 0.3644 target = 0.119929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.098101 restraints weight = 39939.939| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.41 r_work: 0.3226 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8340 Z= 0.118 Angle : 0.979 36.632 11362 Z= 0.385 Chirality : 0.038 0.206 1356 Planarity : 0.005 0.066 1400 Dihedral : 5.582 54.369 1236 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.28 % Allowed : 12.24 % Favored : 86.48 % 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: 1.64 (0.27), residues: 1076 helix: 2.28 (0.21), residues: 648 sheet: None (None), residues: 0 loop : -0.82 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 259 TYR 0.008 0.001 TYR A 181 PHE 0.024 0.001 PHE A 555 TRP 0.007 0.001 TRP B 482 HIS 0.002 0.001 HIS B 289 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 8328) covalent geometry : angle 0.97430 (11334) SS BOND : bond 0.00154 ( 8) SS BOND : angle 0.83403 ( 16) hydrogen bonds : bond 0.04725 ( 509) hydrogen bonds : angle 4.00120 ( 1458) link_BETA1-4 : bond 0.00181 ( 2) link_BETA1-4 : angle 3.67779 ( 6) link_NAG-ASN : bond 0.00357 ( 2) link_NAG-ASN : angle 2.16067 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3798.21 seconds wall clock time: 65 minutes 8.68 seconds (3908.68 seconds total)