Starting phenix.real_space_refine on Wed Mar 12 17:56:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8irm_35679/03_2025/8irm_35679.cif Found real_map, /net/cci-nas-00/data/ceres_data/8irm_35679/03_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_35679/03_2025/8irm_35679.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8irm_35679/03_2025/8irm_35679.map" model { file = "/net/cci-nas-00/data/ceres_data/8irm_35679/03_2025/8irm_35679.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8irm_35679/03_2025/8irm_35679.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.46, per 1000 atoms: 0.67 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: 2.50 Conformation dependent library (CDL) restraints added in 994.2 milliseconds 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: 1.02 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: 2.45 Time building geometry restraints manager: 2.85 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: 0.04 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: 0.750 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: 0.230 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.440 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.530 ------------------------------------------------------------------------------- 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 8316 Z= 0.453 Angle : 0.683 11.285 11320 Z= 0.335 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (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 TRP 0.009 0.001 TRP B 331 HIS 0.002 0.001 HIS A 364 PHE 0.035 0.002 PHE A 442 TYR 0.030 0.001 TYR A 418 ARG 0.001 0.000 ARG A 42 *********************** 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 : 1.095 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: 1.5185 time to fit residues: 159.1711 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 : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.6980 chunk 81 optimal weight: 0.0020 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 55 optimal weight: 0.5980 chunk 43 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 32 optimal weight: 0.0770 chunk 51 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 98 optimal weight: 0.7980 overall best weight: 0.4146 ------------------------------------------------------------------------------- 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 ** 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 = 0.3398 r_free = 0.3398 target = 0.116874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.092132 restraints weight = 10518.720| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 1.82 r_work: 0.2968 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8316 Z= 0.116 Angle : 0.455 8.291 11320 Z= 0.239 Chirality : 0.037 0.135 1356 Planarity : 0.004 0.066 1398 Dihedral : 7.602 102.989 1230 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.93 % Allowed : 6.99 % Favored : 92.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.27), residues: 1076 helix: 2.05 (0.20), residues: 664 sheet: -4.69 (0.63), residues: 20 loop : -0.14 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 482 HIS 0.002 0.001 HIS B 378 PHE 0.013 0.001 PHE A 442 TYR 0.008 0.001 TYR A 418 ARG 0.002 0.000 ARG A 42 *********************** 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 96 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.868 Fit side-chains REVERT: B 548 GLU cc_start: 0.7378 (tp30) cc_final: 0.6684 (mt-10) outliers start: 8 outliers final: 5 residues processed: 92 average time/residue: 1.2596 time to fit residues: 123.3406 Evaluate side-chains 87 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 413 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 88 optimal weight: 6.9990 chunk 89 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 61 optimal weight: 0.0050 chunk 13 optimal weight: 0.0770 overall best weight: 0.4952 ------------------------------------------------------------------------------- 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 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 = 0.3396 r_free = 0.3396 target = 0.116637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.091821 restraints weight = 10678.241| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 1.84 r_work: 0.2964 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8316 Z= 0.115 Angle : 0.418 8.050 11320 Z= 0.218 Chirality : 0.037 0.127 1356 Planarity : 0.004 0.066 1398 Dihedral : 7.161 101.069 1230 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 18.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.40 % Allowed : 8.16 % Favored : 90.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.27), residues: 1076 helix: 2.44 (0.20), residues: 666 sheet: -4.68 (0.65), residues: 20 loop : -0.08 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 482 HIS 0.001 0.000 HIS A 364 PHE 0.012 0.001 PHE A 442 TYR 0.008 0.001 TYR B 418 ARG 0.001 0.000 ARG A 103 *********************** 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 97 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.827 Fit side-chains REVERT: A 32 ARG cc_start: 0.6449 (mtm-85) cc_final: 0.6243 (mtm-85) REVERT: B 60 MET cc_start: 0.9047 (ptp) cc_final: 0.8842 (ptm) REVERT: B 401 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.7245 (mtp) REVERT: B 548 GLU cc_start: 0.7440 (tp30) cc_final: 0.6780 (mt-10) outliers start: 12 outliers final: 6 residues processed: 89 average time/residue: 1.2915 time to fit residues: 122.9814 Evaluate side-chains 91 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 0.701 ------------------------------------------------------------------------------- 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 B residue 33 VAL Chi-restraints excluded: chain B residue 162 THR 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 60 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 6 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 59 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 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 = 0.3329 r_free = 0.3329 target = 0.111370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.085752 restraints weight = 10513.578| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 1.84 r_work: 0.2865 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 8316 Z= 0.258 Angle : 0.492 9.697 11320 Z= 0.255 Chirality : 0.040 0.135 1356 Planarity : 0.004 0.065 1398 Dihedral : 6.938 98.015 1230 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 18.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.98 % Allowed : 8.62 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.26), residues: 1076 helix: 2.32 (0.20), residues: 664 sheet: -4.68 (0.63), residues: 20 loop : -0.15 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 380 HIS 0.003 0.001 HIS A 364 PHE 0.025 0.002 PHE A 442 TYR 0.011 0.001 TYR B 399 ARG 0.002 0.000 ARG B 42 *********************** 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 96 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.904 Fit side-chains revert: symmetry clash REVERT: A 494 MET cc_start: 0.8797 (OUTLIER) cc_final: 0.8420 (mtp) REVERT: B 401 MET cc_start: 0.8506 (OUTLIER) cc_final: 0.6917 (mtp) REVERT: B 548 GLU cc_start: 0.7377 (tp30) cc_final: 0.6701 (mt-10) outliers start: 17 outliers final: 8 residues processed: 87 average time/residue: 1.5745 time to fit residues: 145.4539 Evaluate side-chains 88 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 1.500 ------------------------------------------------------------------------------- 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 468 LEU 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 401 MET Chi-restraints excluded: chain B residue 413 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 6 optimal weight: 0.0000 chunk 97 optimal weight: 6.9990 chunk 42 optimal weight: 0.0070 chunk 101 optimal weight: 4.9990 chunk 104 optimal weight: 0.0970 chunk 33 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 overall best weight: 0.3600 ------------------------------------------------------------------------------- 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 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 = 0.3399 r_free = 0.3399 target = 0.116571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.091581 restraints weight = 10447.490| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.82 r_work: 0.2942 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8316 Z= 0.111 Angle : 0.412 9.187 11320 Z= 0.212 Chirality : 0.037 0.130 1356 Planarity : 0.003 0.065 1398 Dihedral : 6.518 96.066 1230 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 19.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.40 % Allowed : 9.32 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.27), residues: 1076 helix: 2.62 (0.20), residues: 666 sheet: -4.88 (0.62), residues: 20 loop : -0.07 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 380 HIS 0.001 0.000 HIS A 350 PHE 0.009 0.001 PHE A 166 TYR 0.008 0.001 TYR B 418 ARG 0.001 0.000 ARG B 216 *********************** 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 96 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.856 Fit side-chains revert: symmetry clash REVERT: A 470 MET cc_start: 0.7039 (ttp) cc_final: 0.6792 (mtp) REVERT: B 103 ARG cc_start: 0.7477 (ptt-90) cc_final: 0.7164 (ptt-90) REVERT: B 548 GLU cc_start: 0.7396 (tp30) cc_final: 0.6597 (mt-10) outliers start: 12 outliers final: 7 residues processed: 87 average time/residue: 1.1807 time to fit residues: 109.6207 Evaluate side-chains 88 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 388 TYR Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 123 CYS 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 92 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 25 optimal weight: 8.9990 chunk 39 optimal weight: 7.9990 chunk 103 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 76 optimal weight: 0.0970 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 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 = 0.3344 r_free = 0.3344 target = 0.112705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.087666 restraints weight = 10578.210| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 1.81 r_work: 0.2887 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8316 Z= 0.212 Angle : 0.454 9.694 11320 Z= 0.233 Chirality : 0.038 0.131 1356 Planarity : 0.004 0.064 1398 Dihedral : 6.364 92.433 1230 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 18.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.52 % Allowed : 9.91 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.27), residues: 1076 helix: 2.56 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -0.38 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 380 HIS 0.002 0.001 HIS A 364 PHE 0.015 0.001 PHE A 442 TYR 0.009 0.001 TYR B 399 ARG 0.001 0.000 ARG B 508 *********************** 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 91 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.821 Fit side-chains revert: symmetry clash REVERT: A 103 ARG cc_start: 0.7478 (ptt-90) cc_final: 0.7176 (ptt-90) REVERT: A 494 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.8433 (mtp) REVERT: B 103 ARG cc_start: 0.7413 (ptt-90) cc_final: 0.7069 (ptt-90) REVERT: B 401 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.6867 (mpp) REVERT: B 548 GLU cc_start: 0.7366 (tp30) cc_final: 0.6560 (mt-10) outliers start: 13 outliers final: 9 residues processed: 84 average time/residue: 1.2530 time to fit residues: 112.2139 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 : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 388 TYR Chi-restraints excluded: chain A residue 468 LEU 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 401 MET Chi-restraints excluded: chain B residue 413 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 37 optimal weight: 0.0040 chunk 38 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 overall best weight: 0.9794 ------------------------------------------------------------------------------- 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 = 0.3358 r_free = 0.3358 target = 0.113614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.087987 restraints weight = 10534.278| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 1.86 r_work: 0.2910 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8316 Z= 0.164 Angle : 0.434 10.249 11320 Z= 0.222 Chirality : 0.037 0.118 1356 Planarity : 0.004 0.065 1398 Dihedral : 6.038 87.367 1230 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 19.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.63 % Allowed : 10.37 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.27), residues: 1076 helix: 2.63 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -0.35 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 380 HIS 0.002 0.001 HIS B 364 PHE 0.010 0.001 PHE A 442 TYR 0.007 0.001 TYR B 399 ARG 0.001 0.000 ARG A 291 *********************** 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 94 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.810 Fit side-chains revert: symmetry clash REVERT: A 103 ARG cc_start: 0.7510 (ptt-90) cc_final: 0.7214 (ptt-90) REVERT: A 494 MET cc_start: 0.8818 (OUTLIER) cc_final: 0.8455 (mtp) REVERT: B 103 ARG cc_start: 0.7439 (ptt-90) cc_final: 0.7172 (ptt-90) REVERT: B 401 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.6801 (mpp) REVERT: B 548 GLU cc_start: 0.7399 (tp30) cc_final: 0.6602 (mt-10) outliers start: 14 outliers final: 10 residues processed: 86 average time/residue: 1.2684 time to fit residues: 116.2278 Evaluate side-chains 91 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 105 ILE 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 468 LEU 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 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 48 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 64 optimal weight: 0.0770 chunk 77 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 overall best weight: 1.2142 ------------------------------------------------------------------------------- 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 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 = 0.3352 r_free = 0.3352 target = 0.113204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.088038 restraints weight = 10579.235| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 1.83 r_work: 0.2895 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8316 Z= 0.196 Angle : 0.453 10.684 11320 Z= 0.232 Chirality : 0.038 0.117 1356 Planarity : 0.004 0.064 1398 Dihedral : 5.739 79.616 1230 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 18.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.52 % Allowed : 10.49 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.27), residues: 1076 helix: 2.58 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -0.37 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 380 HIS 0.002 0.001 HIS B 541 PHE 0.012 0.001 PHE A 442 TYR 0.009 0.001 TYR B 399 ARG 0.001 0.000 ARG A 403 *********************** 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 90 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.840 Fit side-chains revert: symmetry clash REVERT: A 103 ARG cc_start: 0.7482 (ptt-90) cc_final: 0.7186 (ptt-90) REVERT: A 494 MET cc_start: 0.8834 (OUTLIER) cc_final: 0.8474 (mtp) REVERT: B 103 ARG cc_start: 0.7442 (ptt-90) cc_final: 0.7152 (ptt-90) REVERT: B 401 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.6739 (mpp) REVERT: B 548 GLU cc_start: 0.7388 (tp30) cc_final: 0.6608 (mt-10) outliers start: 13 outliers final: 11 residues processed: 83 average time/residue: 1.2710 time to fit residues: 112.2226 Evaluate side-chains 90 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 105 ILE 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 468 LEU 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 401 MET Chi-restraints excluded: chain B residue 413 ASP Chi-restraints excluded: chain B residue 468 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 85 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 93 optimal weight: 7.9990 chunk 78 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 84 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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 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 = 0.3297 r_free = 0.3297 target = 0.109238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.083226 restraints weight = 10563.018| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 1.89 r_work: 0.2792 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 8316 Z= 0.366 Angle : 0.543 10.717 11320 Z= 0.280 Chirality : 0.042 0.119 1356 Planarity : 0.004 0.062 1398 Dihedral : 5.656 69.250 1230 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 17.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.52 % Allowed : 10.49 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.26), residues: 1076 helix: 2.20 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -0.50 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 380 HIS 0.004 0.001 HIS A 364 PHE 0.022 0.002 PHE A 442 TYR 0.012 0.001 TYR B 399 ARG 0.002 0.000 ARG A 403 *********************** 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 87 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.843 Fit side-chains revert: symmetry clash REVERT: A 103 ARG cc_start: 0.7415 (ptt-90) cc_final: 0.7110 (ptt-90) REVERT: A 286 MET cc_start: 0.9143 (ttt) cc_final: 0.8758 (ttt) REVERT: A 494 MET cc_start: 0.8920 (OUTLIER) cc_final: 0.8577 (mtp) REVERT: B 103 ARG cc_start: 0.7341 (ptt-90) cc_final: 0.7055 (ptt-90) REVERT: B 401 MET cc_start: 0.8608 (OUTLIER) cc_final: 0.6754 (mpp) REVERT: B 548 GLU cc_start: 0.7446 (tp30) cc_final: 0.6628 (mt-10) outliers start: 13 outliers final: 8 residues processed: 81 average time/residue: 1.3313 time to fit residues: 114.9121 Evaluate side-chains 83 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.819 ------------------------------------------------------------------------------- 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 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 401 MET Chi-restraints excluded: chain B residue 413 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 103 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 54 optimal weight: 9.9990 chunk 101 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 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 = 0.113188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.087475 restraints weight = 10309.098| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 1.86 r_work: 0.2880 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8316 Z= 0.151 Angle : 0.441 10.253 11320 Z= 0.225 Chirality : 0.037 0.117 1356 Planarity : 0.004 0.063 1398 Dihedral : 4.979 55.862 1230 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 19.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.93 % Allowed : 10.84 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.27), residues: 1076 helix: 2.52 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -0.42 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 380 HIS 0.002 0.001 HIS A 364 PHE 0.009 0.001 PHE A 442 TYR 0.007 0.001 TYR B 399 ARG 0.001 0.000 ARG A 403 ********************** 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 85 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 1.354 Fit side-chains revert: symmetry clash REVERT: A 103 ARG cc_start: 0.7436 (ptt-90) cc_final: 0.7140 (ptt-90) REVERT: A 470 MET cc_start: 0.6988 (ttp) cc_final: 0.6774 (mtp) REVERT: B 103 ARG cc_start: 0.7354 (ptt-90) cc_final: 0.7066 (ptt-90) REVERT: B 401 MET cc_start: 0.8568 (OUTLIER) cc_final: 0.6700 (mpp) REVERT: B 548 GLU cc_start: 0.7378 (tp30) cc_final: 0.6585 (mt-10) outliers start: 8 outliers final: 7 residues processed: 81 average time/residue: 1.5113 time to fit residues: 129.7021 Evaluate side-chains 84 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.822 ------------------------------------------------------------------------------- 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 B residue 123 CYS Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 413 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 15 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 94 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 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 = 0.3341 r_free = 0.3341 target = 0.112702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.086867 restraints weight = 10454.776| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 1.89 r_work: 0.2882 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8316 Z= 0.161 Angle : 0.434 8.739 11320 Z= 0.223 Chirality : 0.037 0.117 1356 Planarity : 0.004 0.063 1398 Dihedral : 4.618 40.656 1230 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 20.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.17 % Allowed : 10.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.27), residues: 1076 helix: 2.60 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -0.38 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 380 HIS 0.002 0.001 HIS B 541 PHE 0.010 0.001 PHE A 166 TYR 0.007 0.001 TYR B 399 ARG 0.001 0.000 ARG A 216 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5812.38 seconds wall clock time: 103 minutes 43.48 seconds (6223.48 seconds total)