Starting phenix.real_space_refine on Wed Feb 12 17:26:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8irm_35679/02_2025/8irm_35679.cif Found real_map, /net/cci-nas-00/data/ceres_data/8irm_35679/02_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_35679/02_2025/8irm_35679.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8irm_35679/02_2025/8irm_35679.map" model { file = "/net/cci-nas-00/data/ceres_data/8irm_35679/02_2025/8irm_35679.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8irm_35679/02_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 5.33, per 1000 atoms: 0.65 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: 2.31 Conformation dependent library (CDL) restraints added in 1.0 seconds 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1940 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 8 sheets defined 68.1% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 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: 2.58 Time building geometry restraints manager: 2.65 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.800 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: 0.250 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.470 Find NCS groups from input model: 0.300 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: 0.010 Load rotamer database and sin/cos tables:12.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.810 ------------------------------------------------------------------------------- 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 : 0.860 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: 1.3633 time to fit residues: 143.0667 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 : 0.870 ------------------------------------------------------------------------------- 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 = 43)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.092128 restraints weight = 10518.736| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 1.82 r_work: 0.2967 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 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 : 0.879 Fit side-chains REVERT: B 548 GLU cc_start: 0.7372 (tp30) cc_final: 0.6676 (mt-10) outliers start: 8 outliers final: 5 residues processed: 92 average time/residue: 1.2790 time to fit residues: 125.1966 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 : 0.845 ------------------------------------------------------------------------------- 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: 0.2980 chunk 5 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 88 optimal weight: 6.9990 chunk 89 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 61 optimal weight: 0.0040 chunk 13 optimal weight: 0.5980 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.117215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.091895 restraints weight = 10536.749| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.84 r_work: 0.2974 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1514 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= 0.110 Angle : 0.415 8.444 11320 Z= 0.215 Chirality : 0.037 0.128 1356 Planarity : 0.004 0.067 1398 Dihedral : 7.008 100.277 1230 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 20.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.63 % Allowed : 8.16 % Favored : 90.21 % 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: 2.27 (0.27), residues: 1076 helix: 2.54 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -0.25 (0.33), residues: 410 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 100 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.854 Fit side-chains REVERT: A 507 MET cc_start: 0.8778 (mmp) cc_final: 0.8522 (mmp) REVERT: B 401 MET cc_start: 0.8516 (OUTLIER) cc_final: 0.7102 (mtp) REVERT: B 548 GLU cc_start: 0.7432 (tp30) cc_final: 0.6763 (mt-10) outliers start: 14 outliers final: 5 residues processed: 92 average time/residue: 1.2126 time to fit residues: 118.8890 Evaluate side-chains 89 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL 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: 6.9990 chunk 13 optimal weight: 0.0570 chunk 24 optimal weight: 7.9990 chunk 6 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 25 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 chunk 96 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- 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** A 541 HIS ** B 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.117473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.092487 restraints weight = 10485.948| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 1.83 r_work: 0.2956 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8316 Z= 0.119 Angle : 0.407 8.859 11320 Z= 0.210 Chirality : 0.037 0.130 1356 Planarity : 0.004 0.069 1398 Dihedral : 6.572 97.392 1230 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 20.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.10 % Allowed : 8.39 % Favored : 89.51 % 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: 2.46 (0.27), residues: 1076 helix: 2.73 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -0.25 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 380 HIS 0.001 0.000 HIS B 364 PHE 0.013 0.001 PHE A 442 TYR 0.007 0.001 TYR B 399 ARG 0.001 0.000 ARG A 403 *********************** 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 104 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.921 Fit side-chains revert: symmetry clash REVERT: B 103 ARG cc_start: 0.7491 (ptt-90) cc_final: 0.7170 (ptt-90) REVERT: B 548 GLU cc_start: 0.7382 (tp30) cc_final: 0.6582 (mt-10) outliers start: 18 outliers final: 11 residues processed: 92 average time/residue: 1.2132 time to fit residues: 119.1371 Evaluate side-chains 95 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.934 ------------------------------------------------------------------------------- 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 B residue 33 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 162 THR 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: 0.0170 chunk 97 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 overall best weight: 1.1420 ------------------------------------------------------------------------------- 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 = 0.3368 r_free = 0.3368 target = 0.114335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.089171 restraints weight = 10461.110| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 1.83 r_work: 0.2913 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1698 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= 0.195 Angle : 0.447 9.752 11320 Z= 0.230 Chirality : 0.038 0.131 1356 Planarity : 0.004 0.065 1398 Dihedral : 6.296 92.190 1230 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 19.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.86 % Allowed : 9.32 % Favored : 88.81 % 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: 2.34 (0.27), residues: 1076 helix: 2.65 (0.20), residues: 666 sheet: -4.74 (0.63), residues: 20 loop : -0.05 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 380 HIS 0.003 0.001 HIS A 364 PHE 0.018 0.001 PHE A 442 TYR 0.008 0.001 TYR B 399 ARG 0.001 0.000 ARG A 508 *********************** 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: 16 poor density : 80 time to evaluate : 0.728 Fit side-chains revert: symmetry clash REVERT: A 494 MET cc_start: 0.8813 (OUTLIER) cc_final: 0.8440 (mtp) REVERT: B 103 ARG cc_start: 0.7447 (ptt-90) cc_final: 0.7175 (ptt-90) REVERT: B 401 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.6829 (mpp) REVERT: B 548 GLU cc_start: 0.7395 (tp30) cc_final: 0.6592 (mt-10) outliers start: 16 outliers final: 10 residues processed: 85 average time/residue: 1.3216 time to fit residues: 119.1938 Evaluate side-chains 92 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.958 ------------------------------------------------------------------------------- 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 468 LEU Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 105 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 92 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 76 optimal weight: 0.0030 overall best weight: 1.3594 ------------------------------------------------------------------------------- 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 = 0.3353 r_free = 0.3353 target = 0.113160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.088084 restraints weight = 10550.396| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 1.83 r_work: 0.2882 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8316 Z= 0.210 Angle : 0.458 10.369 11320 Z= 0.235 Chirality : 0.038 0.115 1356 Planarity : 0.004 0.065 1398 Dihedral : 6.005 85.565 1230 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 18.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.10 % Allowed : 9.56 % 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: 2.19 (0.27), residues: 1076 helix: 2.55 (0.20), residues: 666 sheet: -4.88 (0.58), residues: 20 loop : -0.13 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 380 HIS 0.002 0.001 HIS A 364 PHE 0.013 0.001 PHE A 442 TYR 0.008 0.001 TYR B 399 ARG 0.001 0.000 ARG B 42 *********************** 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 98 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.745 Fit side-chains revert: symmetry clash REVERT: A 103 ARG cc_start: 0.7509 (ptt-90) cc_final: 0.7204 (ptt-90) REVERT: A 470 MET cc_start: 0.7034 (ttp) cc_final: 0.6829 (mtp) REVERT: A 494 MET cc_start: 0.8834 (OUTLIER) cc_final: 0.8460 (mtp) REVERT: B 103 ARG cc_start: 0.7414 (ptt-90) cc_final: 0.7139 (ptt-90) REVERT: B 401 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.6691 (mpp) REVERT: B 548 GLU cc_start: 0.7395 (tp30) cc_final: 0.6597 (mt-10) outliers start: 18 outliers final: 9 residues processed: 89 average time/residue: 1.2592 time to fit residues: 119.6643 Evaluate side-chains 90 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.900 ------------------------------------------------------------------------------- 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 A residue 517 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: 2.9990 chunk 38 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 = 0.3339 r_free = 0.3339 target = 0.112107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.086975 restraints weight = 10619.283| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 1.83 r_work: 0.2864 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8316 Z= 0.229 Angle : 0.474 10.779 11320 Z= 0.243 Chirality : 0.039 0.118 1356 Planarity : 0.004 0.063 1398 Dihedral : 5.615 74.566 1230 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 19.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.86 % Allowed : 10.02 % Favored : 88.11 % 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: 2.14 (0.26), residues: 1076 helix: 2.48 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -0.41 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 380 HIS 0.002 0.001 HIS B 364 PHE 0.015 0.002 PHE A 442 TYR 0.008 0.001 TYR B 399 ARG 0.001 0.000 ARG B 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 96 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.905 Fit side-chains revert: symmetry clash REVERT: A 103 ARG cc_start: 0.7443 (ptt-90) cc_final: 0.7141 (ptt-90) REVERT: A 494 MET cc_start: 0.8827 (OUTLIER) cc_final: 0.8466 (mtp) REVERT: B 103 ARG cc_start: 0.7314 (ptt-90) cc_final: 0.7055 (ptt-90) REVERT: B 401 MET cc_start: 0.8581 (OUTLIER) cc_final: 0.6687 (mpp) REVERT: B 548 GLU cc_start: 0.7361 (tp30) cc_final: 0.6560 (mt-10) outliers start: 16 outliers final: 12 residues processed: 87 average time/residue: 1.3113 time to fit residues: 121.3998 Evaluate side-chains 93 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.927 ------------------------------------------------------------------------------- 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 468 LEU Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 517 MET Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 413 ASP Chi-restraints excluded: chain B residue 468 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 48 optimal weight: 0.6980 chunk 78 optimal weight: 5.9990 chunk 7 optimal weight: 0.0000 chunk 72 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 64 optimal weight: 0.2980 chunk 77 optimal weight: 0.0040 chunk 102 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 86 optimal weight: 0.3980 overall best weight: 0.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 541 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.117410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.092412 restraints weight = 10536.696| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 1.84 r_work: 0.2955 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.020 8316 Z= 0.095 Angle : 0.406 10.498 11320 Z= 0.206 Chirality : 0.036 0.119 1356 Planarity : 0.003 0.067 1398 Dihedral : 4.849 59.272 1230 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 22.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.05 % Allowed : 10.84 % 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 (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: 2.49 (0.27), residues: 1076 helix: 2.78 (0.20), residues: 672 sheet: None (None), residues: 0 loop : -0.33 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 380 HIS 0.001 0.000 HIS B 541 PHE 0.009 0.001 PHE A 166 TYR 0.006 0.001 TYR A 418 ARG 0.001 0.000 ARG A 291 *********************** 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 94 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.808 Fit side-chains revert: symmetry clash REVERT: A 103 ARG cc_start: 0.7496 (ptt-90) cc_final: 0.7204 (ptt-90) REVERT: B 103 ARG cc_start: 0.7391 (ptt-90) cc_final: 0.7137 (ptt-90) REVERT: B 401 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.6620 (mpp) REVERT: B 548 GLU cc_start: 0.7341 (tp30) cc_final: 0.6608 (mt-10) outliers start: 9 outliers final: 5 residues processed: 87 average time/residue: 1.2745 time to fit residues: 118.1181 Evaluate side-chains 90 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 388 TYR Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 413 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 85 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 35 optimal weight: 0.0000 chunk 90 optimal weight: 4.9990 chunk 93 optimal weight: 0.4980 chunk 78 optimal weight: 0.4980 chunk 53 optimal weight: 5.9990 chunk 84 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 = 0.3340 r_free = 0.3340 target = 0.112487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.087334 restraints weight = 10780.872| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 1.83 r_work: 0.2878 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8316 Z= 0.216 Angle : 0.452 9.185 11320 Z= 0.232 Chirality : 0.038 0.117 1356 Planarity : 0.004 0.065 1398 Dihedral : 4.710 45.596 1230 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 19.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.93 % Allowed : 11.31 % Favored : 87.76 % 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: 2.65 (0.20), residues: 666 sheet: -4.92 (0.57), residues: 20 loop : -0.09 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 380 HIS 0.002 0.001 HIS A 364 PHE 0.012 0.001 PHE A 442 TYR 0.008 0.001 TYR B 399 ARG 0.001 0.000 ARG A 333 *********************** 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 89 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.840 Fit side-chains revert: symmetry clash REVERT: A 103 ARG cc_start: 0.7456 (ptt-90) cc_final: 0.7165 (ptt-90) REVERT: A 163 ASN cc_start: 0.7443 (m-40) cc_final: 0.7122 (m-40) REVERT: B 103 ARG cc_start: 0.7351 (ptt-90) cc_final: 0.7100 (ptt-90) REVERT: B 401 MET cc_start: 0.8606 (OUTLIER) cc_final: 0.6650 (mpp) REVERT: B 548 GLU cc_start: 0.7350 (tp30) cc_final: 0.6650 (mt-10) outliers start: 8 outliers final: 6 residues processed: 83 average time/residue: 1.3252 time to fit residues: 116.8357 Evaluate side-chains 86 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 123 CYS Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 413 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 103 optimal weight: 0.2980 chunk 12 optimal weight: 0.8980 chunk 82 optimal weight: 0.0970 chunk 2 optimal weight: 0.0000 chunk 43 optimal weight: 0.9980 chunk 54 optimal weight: 9.9990 chunk 101 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 overall best weight: 0.4182 ------------------------------------------------------------------------------- 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 = 0.3386 r_free = 0.3386 target = 0.115971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.091099 restraints weight = 10538.893| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 1.82 r_work: 0.2953 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8316 Z= 0.107 Angle : 0.398 7.727 11320 Z= 0.205 Chirality : 0.036 0.117 1356 Planarity : 0.003 0.066 1398 Dihedral : 4.271 30.427 1230 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 22.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.82 % Allowed : 11.31 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 2.51 (0.27), residues: 1076 helix: 2.79 (0.20), residues: 672 sheet: None (None), residues: 0 loop : -0.31 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 380 HIS 0.001 0.000 HIS A 364 PHE 0.009 0.001 PHE A 166 TYR 0.006 0.001 TYR A 418 ARG 0.001 0.000 ARG B 454 ********************** 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 92 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.927 Fit side-chains revert: symmetry clash REVERT: A 103 ARG cc_start: 0.7481 (ptt-90) cc_final: 0.7187 (ptt-90) REVERT: B 103 ARG cc_start: 0.7352 (ptt-90) cc_final: 0.7094 (ptt-90) REVERT: B 401 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.6589 (mpp) REVERT: B 548 GLU cc_start: 0.7327 (tp30) cc_final: 0.6558 (mt-10) outliers start: 7 outliers final: 6 residues processed: 87 average time/residue: 1.3244 time to fit residues: 122.4227 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 : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 388 TYR Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 470 MET Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 413 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 15 optimal weight: 6.9990 chunk 67 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 94 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3369 r_free = 0.3369 target = 0.114582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.088816 restraints weight = 10531.148| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 1.87 r_work: 0.2913 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8316 Z= 0.143 Angle : 0.407 7.905 11320 Z= 0.211 Chirality : 0.037 0.116 1356 Planarity : 0.003 0.065 1398 Dihedral : 4.239 31.801 1230 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 20.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.93 % Allowed : 11.31 % Favored : 87.76 % 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: 2.51 (0.27), residues: 1076 helix: 2.79 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -0.28 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 482 HIS 0.001 0.000 HIS B 364 PHE 0.009 0.001 PHE A 166 TYR 0.006 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: 5554.34 seconds wall clock time: 98 minutes 57.27 seconds (5937.27 seconds total)