Starting phenix.real_space_refine on Sat Jun 14 16:37:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wmq_37658/06_2025/8wmq_37658_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wmq_37658/06_2025/8wmq_37658.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wmq_37658/06_2025/8wmq_37658.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wmq_37658/06_2025/8wmq_37658.map" model { file = "/net/cci-nas-00/data/ceres_data/8wmq_37658/06_2025/8wmq_37658_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wmq_37658/06_2025/8wmq_37658_trim.cif" } resolution = 3.3 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 52 5.16 5 C 5300 2.51 5 N 1316 2.21 5 O 1472 1.98 5 H 8208 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16348 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 8130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 8130 Classifications: {'peptide': 540} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 516} Chain: "A" Number of atoms: 8130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 8130 Classifications: {'peptide': 540} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 516} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'ZEA': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'ZEA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.06, per 1000 atoms: 0.49 Number of scatterers: 16348 At special positions: 0 Unit cell: (96.163, 114.885, 101.269, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 O 1472 8.00 N 1316 7.00 C 5300 6.00 H 8208 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS B 78 " - pdb=" SG CYS B 123 " distance=2.03 Simple disulfide: pdb=" SG CYS B 83 " - pdb=" SG CYS B 111 " distance=2.04 Simple disulfide: pdb=" SG CYS B 87 " - pdb=" SG CYS B 97 " distance=2.03 Simple disulfide: pdb=" SG CYS B 254 " - pdb=" SG CYS B 287 " distance=2.03 Simple disulfide: pdb=" SG CYS A 78 " - pdb=" SG CYS A 123 " distance=2.03 Simple disulfide: pdb=" SG CYS A 83 " - pdb=" SG CYS A 111 " distance=2.03 Simple disulfide: pdb=" SG CYS A 87 " - pdb=" SG CYS A 97 " distance=2.03 Simple disulfide: pdb=" SG CYS A 254 " - pdb=" SG CYS A 287 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG C 1 " - " ASN A 270 " " NAG D 1 " - " ASN B 270 " Time building additional restraints: 4.19 Conformation dependent library (CDL) restraints added in 2.7 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: 52 helices and 8 sheets defined 67.5% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'B' and resid 19 through 30 Processing helix chain 'B' and resid 31 through 37 Processing helix chain 'B' and resid 39 through 43 Processing helix chain 'B' and resid 46 through 61 Processing helix chain 'B' and resid 62 through 73 removed outlier: 4.203A pdb=" N ALA B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 83 Processing helix chain 'B' and resid 93 through 97 Processing helix chain 'B' and resid 108 through 113 Processing helix chain 'B' and resid 117 through 149 Processing helix chain 'B' and resid 159 through 169 removed outlier: 3.760A pdb=" N ALA B 164 " --> pdb=" O MET B 160 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR B 165 " --> pdb=" O GLY B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 201 removed outlier: 3.542A pdb=" N ILE B 201 " --> pdb=" O PHE B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 209 Processing helix chain 'B' and resid 212 through 232 removed outlier: 4.510A pdb=" N SER B 220 " --> pdb=" O ARG B 216 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ALA B 221 " --> pdb=" O ILE B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 257 No H-bonds generated for 'chain 'B' and resid 255 through 257' Processing helix chain 'B' and resid 294 through 313 removed outlier: 3.509A pdb=" N TRP B 298 " --> pdb=" O SER B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 331 Processing helix chain 'B' and resid 343 through 355 removed outlier: 3.861A pdb=" N LYS B 355 " --> pdb=" O ASP B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 405 removed outlier: 3.728A pdb=" N TRP B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 435 Processing helix chain 'B' and resid 444 through 451 removed outlier: 4.268A pdb=" N GLY B 448 " --> pdb=" O GLU B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 470 Processing helix chain 'B' and resid 472 through 477 Processing helix chain 'B' and resid 480 through 496 Proline residue: B 486 - end of helix Processing helix chain 'B' and resid 497 through 502 removed outlier: 4.000A pdb=" N THR B 500 " --> pdb=" O LYS B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 524 Proline residue: B 512 - end of helix removed outlier: 3.637A pdb=" N MET B 520 " --> pdb=" O THR B 516 " (cutoff:3.500A) Proline residue: B 521 - end of helix Processing helix chain 'B' and resid 525 through 554 removed outlier: 5.159A pdb=" N TRP B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N ASP B 544 " --> pdb=" O LEU B 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 30 Processing helix chain 'A' and resid 31 through 37 Processing helix chain 'A' and resid 39 through 43 Processing helix chain 'A' and resid 46 through 60 Processing helix chain 'A' and resid 62 through 73 removed outlier: 4.200A pdb=" N ALA A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 93 through 97 Processing helix chain 'A' and resid 108 through 113 Processing helix chain 'A' and resid 117 through 149 Processing helix chain 'A' and resid 159 through 169 removed outlier: 3.862A pdb=" N ALA A 164 " --> pdb=" O MET A 160 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TYR A 165 " --> pdb=" O GLY A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 202 Processing helix chain 'A' and resid 203 through 211 removed outlier: 3.852A pdb=" N VAL A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 232 removed outlier: 4.510A pdb=" N SER A 220 " --> pdb=" O ARG A 216 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ALA A 221 " --> pdb=" O ILE A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 257 No H-bonds generated for 'chain 'A' and resid 255 through 257' Processing helix chain 'A' and resid 294 through 313 Processing helix chain 'A' and resid 317 through 330 Processing helix chain 'A' and resid 343 through 355 removed outlier: 3.862A pdb=" N LYS A 355 " --> pdb=" O ASP A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 406 removed outlier: 3.735A pdb=" N TRP A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 435 Processing helix chain 'A' and resid 445 through 451 Processing helix chain 'A' and resid 456 through 470 Processing helix chain 'A' and resid 472 through 477 Processing helix chain 'A' and resid 480 through 496 Proline residue: A 486 - end of helix Processing helix chain 'A' and resid 497 through 502 removed outlier: 4.006A pdb=" N THR A 500 " --> pdb=" O LYS A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 524 Proline residue: A 512 - end of helix removed outlier: 3.634A pdb=" N MET A 520 " --> pdb=" O THR A 516 " (cutoff:3.500A) Proline residue: A 521 - end of helix Processing helix chain 'A' and resid 525 through 554 removed outlier: 3.543A pdb=" N GLY A 529 " --> pdb=" O SER A 525 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N TRP A 543 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ASP A 544 " --> pdb=" O LEU A 540 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 86 through 87 Processing sheet with id=AA2, first strand: chain 'B' and resid 156 through 158 Processing sheet with id=AA3, first strand: chain 'B' and resid 241 through 242 removed outlier: 3.664A pdb=" N THR B 250 " --> pdb=" O GLY B 242 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 274 through 275 removed outlier: 3.766A pdb=" N SER B 274 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N SER B 261 " --> pdb=" O VAL A 265 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER A 261 " --> pdb=" O VAL B 265 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER A 274 " --> pdb=" O ILE A 266 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 286 through 287 removed outlier: 4.104A pdb=" N SER B 261 " --> pdb=" O VAL A 265 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER A 261 " --> pdb=" O VAL B 265 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 86 through 87 Processing sheet with id=AA7, first strand: chain 'A' and resid 156 through 158 Processing sheet with id=AA8, first strand: chain 'A' and resid 241 through 242 513 hydrogen bonds defined for protein. 1458 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.67 Time building geometry restraints manager: 4.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8204 1.03 - 1.23: 14 1.23 - 1.42: 3414 1.42 - 1.62: 4820 1.62 - 1.81: 84 Bond restraints: 16536 Sorted by residual: bond pdb=" C6 ZEA A 701 " pdb=" N10 ZEA A 701 " ideal model delta sigma weight residual 1.336 1.466 -0.130 2.00e-02 2.50e+03 4.21e+01 bond pdb=" C6 ZEA B 701 " pdb=" N10 ZEA B 701 " ideal model delta sigma weight residual 1.336 1.466 -0.130 2.00e-02 2.50e+03 4.20e+01 bond pdb=" C13 ZEA A 701 " pdb=" C14 ZEA A 701 " ideal model delta sigma weight residual 1.502 1.596 -0.094 2.00e-02 2.50e+03 2.22e+01 bond pdb=" C13 ZEA B 701 " pdb=" C14 ZEA B 701 " ideal model delta sigma weight residual 1.502 1.596 -0.094 2.00e-02 2.50e+03 2.21e+01 bond pdb=" C13 ZEA A 701 " pdb=" C15 ZEA A 701 " ideal model delta sigma weight residual 1.500 1.557 -0.057 2.00e-02 2.50e+03 8.08e+00 ... (remaining 16531 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.39: 29912 8.39 - 16.79: 4 16.79 - 25.18: 0 25.18 - 33.58: 2 33.58 - 41.97: 4 Bond angle restraints: 29922 Sorted by residual: angle pdb=" C12 ZEA B 701 " pdb=" C13 ZEA B 701 " pdb=" C15 ZEA B 701 " ideal model delta sigma weight residual 125.58 167.55 -41.97 3.00e+00 1.11e-01 1.96e+02 angle pdb=" C12 ZEA A 701 " pdb=" C13 ZEA A 701 " pdb=" C15 ZEA A 701 " ideal model delta sigma weight residual 125.58 167.55 -41.97 3.00e+00 1.11e-01 1.96e+02 angle pdb=" C12 ZEA B 701 " pdb=" C13 ZEA B 701 " pdb=" C14 ZEA B 701 " ideal model delta sigma weight residual 121.92 87.91 34.01 3.00e+00 1.11e-01 1.28e+02 angle pdb=" C12 ZEA A 701 " pdb=" C13 ZEA A 701 " pdb=" C14 ZEA A 701 " ideal model delta sigma weight residual 121.92 87.94 33.98 3.00e+00 1.11e-01 1.28e+02 angle pdb=" C14 ZEA A 701 " pdb=" C13 ZEA A 701 " pdb=" C15 ZEA A 701 " ideal model delta sigma weight residual 112.50 79.62 32.88 3.00e+00 1.11e-01 1.20e+02 ... (remaining 29917 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.94: 7404 24.94 - 49.87: 339 49.87 - 74.80: 132 74.80 - 99.74: 4 99.74 - 124.67: 3 Dihedral angle restraints: 7882 sinusoidal: 4248 harmonic: 3634 Sorted by residual: dihedral pdb=" CB CYS A 78 " pdb=" SG CYS A 78 " pdb=" SG CYS A 123 " pdb=" CB CYS A 123 " ideal model delta sinusoidal sigma weight residual -86.00 -145.94 59.94 1 1.00e+01 1.00e-02 4.79e+01 dihedral pdb=" CB CYS B 78 " pdb=" SG CYS B 78 " pdb=" SG CYS B 123 " pdb=" CB CYS B 123 " ideal model delta sinusoidal sigma weight residual -86.00 -144.84 58.84 1 1.00e+01 1.00e-02 4.63e+01 dihedral pdb=" CA VAL A 484 " pdb=" C VAL A 484 " pdb=" N GLY A 485 " pdb=" CA GLY A 485 " ideal model delta harmonic sigma weight residual 180.00 150.51 29.49 0 5.00e+00 4.00e-02 3.48e+01 ... (remaining 7879 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1137 0.053 - 0.105: 191 0.105 - 0.158: 27 0.158 - 0.210: 0 0.210 - 0.263: 1 Chirality restraints: 1356 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN B 270 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA ILE A 362 " pdb=" N ILE A 362 " pdb=" C ILE A 362 " pdb=" CB ILE A 362 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.90e-01 chirality pdb=" CB THR B 250 " pdb=" CA THR B 250 " pdb=" OG1 THR B 250 " pdb=" CG2 THR B 250 " both_signs ideal model delta sigma weight residual False 2.55 2.42 0.13 2.00e-01 2.50e+01 4.38e-01 ... (remaining 1353 not shown) Planarity restraints: 2434 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 486 " -0.043 5.00e-02 4.00e+02 6.49e-02 6.74e+00 pdb=" N PRO A 487 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 487 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 487 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 486 " -0.043 5.00e-02 4.00e+02 6.46e-02 6.68e+00 pdb=" N PRO B 487 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 487 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 487 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 340 " 0.043 5.00e-02 4.00e+02 6.32e-02 6.39e+00 pdb=" N PRO A 341 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 341 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 341 " 0.035 5.00e-02 4.00e+02 ... (remaining 2431 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.19: 766 2.19 - 2.79: 32112 2.79 - 3.39: 45274 3.39 - 4.00: 56801 4.00 - 4.60: 89965 Nonbonded interactions: 224918 Sorted by model distance: nonbonded pdb=" O LEU A 519 " pdb=" HG1 THR A 523 " model vdw 1.583 2.450 nonbonded pdb=" O LEU B 519 " pdb=" HG1 THR B 523 " model vdw 1.584 2.450 nonbonded pdb=" HG SER A 268 " pdb=" OD1 ASN A 270 " model vdw 1.608 2.450 nonbonded pdb=" O SER B 88 " pdb="HD21 ASN A 270 " model vdw 1.630 2.450 nonbonded pdb=" O PHE B 332 " pdb=" HG1 THR B 338 " model vdw 1.633 2.450 ... (remaining 224913 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.190 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: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 35.980 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.130 8340 Z= 0.213 Angle : 1.070 41.971 11362 Z= 0.456 Chirality : 0.040 0.263 1356 Planarity : 0.005 0.065 1400 Dihedral : 14.040 124.675 2938 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.89 (0.26), residues: 1076 helix: 1.65 (0.21), residues: 642 sheet: None (None), residues: 0 loop : -1.07 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 482 HIS 0.003 0.001 HIS A 360 PHE 0.010 0.001 PHE A 189 TYR 0.013 0.001 TYR B 309 ARG 0.017 0.001 ARG B 23 Details of bonding type rmsd link_NAG-ASN : bond 0.00177 ( 2) link_NAG-ASN : angle 1.42070 ( 6) link_BETA1-4 : bond 0.00262 ( 2) link_BETA1-4 : angle 1.54546 ( 6) hydrogen bonds : bond 0.13654 ( 509) hydrogen bonds : angle 5.56263 ( 1458) SS BOND : bond 0.00223 ( 8) SS BOND : angle 0.74306 ( 16) covalent geometry : bond 0.00430 ( 8328) covalent geometry : angle 1.07007 (11334) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 1.243 Fit side-chains REVERT: B 390 ASP cc_start: 0.7078 (m-30) cc_final: 0.6821 (m-30) REVERT: B 444 GLU cc_start: 0.6848 (mp0) cc_final: 0.6634 (mp0) REVERT: A 390 ASP cc_start: 0.7144 (m-30) cc_final: 0.6882 (m-30) REVERT: A 444 GLU cc_start: 0.6869 (mp0) cc_final: 0.6630 (mp0) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.2850 time to fit residues: 59.3098 Evaluate side-chains 108 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 1.808 ------------------------------------------------------------------------------- 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: 0.7980 chunk 81 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 0.2980 chunk 55 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.123147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.100217 restraints weight = 39667.508| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.48 r_work: 0.3253 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.0970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8340 Z= 0.132 Angle : 0.998 37.416 11362 Z= 0.405 Chirality : 0.039 0.208 1356 Planarity : 0.005 0.065 1400 Dihedral : 8.553 110.924 1236 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.35 % Allowed : 6.29 % Favored : 93.36 % 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: 1.17 (0.26), residues: 1076 helix: 1.82 (0.20), residues: 652 sheet: None (None), residues: 0 loop : -0.90 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 482 HIS 0.004 0.001 HIS B 360 PHE 0.012 0.001 PHE B 46 TYR 0.010 0.001 TYR B 524 ARG 0.004 0.000 ARG A 23 Details of bonding type rmsd link_NAG-ASN : bond 0.00468 ( 2) link_NAG-ASN : angle 1.67164 ( 6) link_BETA1-4 : bond 0.00338 ( 2) link_BETA1-4 : angle 2.53256 ( 6) hydrogen bonds : bond 0.05766 ( 509) hydrogen bonds : angle 4.63676 ( 1458) SS BOND : bond 0.00119 ( 8) SS BOND : angle 0.77983 ( 16) covalent geometry : bond 0.00277 ( 8328) covalent geometry : angle 0.99589 (11334) *********************** 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 117 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 114 time to evaluate : 1.231 Fit side-chains REVERT: B 390 ASP cc_start: 0.7560 (m-30) cc_final: 0.7269 (m-30) REVERT: B 444 GLU cc_start: 0.7492 (mp0) cc_final: 0.7215 (mp0) REVERT: A 390 ASP cc_start: 0.7563 (m-30) cc_final: 0.7283 (m-30) outliers start: 3 outliers final: 2 residues processed: 115 average time/residue: 0.2984 time to fit residues: 53.5109 Evaluate side-chains 109 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 107 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain A residue 335 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 21 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.119420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.096405 restraints weight = 39569.348| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.46 r_work: 0.3205 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8340 Z= 0.219 Angle : 1.032 37.651 11362 Z= 0.431 Chirality : 0.042 0.209 1356 Planarity : 0.006 0.070 1400 Dihedral : 8.366 103.386 1236 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.02 % Favored : 94.89 % Rotamer: Outliers : 1.52 % Allowed : 8.39 % Favored : 90.09 % 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: 0.73 (0.25), residues: 1076 helix: 1.57 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -1.24 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 543 HIS 0.004 0.002 HIS B 350 PHE 0.018 0.002 PHE B 189 TYR 0.009 0.001 TYR B 524 ARG 0.002 0.000 ARG B 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00409 ( 2) link_NAG-ASN : angle 1.97236 ( 6) link_BETA1-4 : bond 0.00265 ( 2) link_BETA1-4 : angle 2.48009 ( 6) hydrogen bonds : bond 0.06530 ( 509) hydrogen bonds : angle 4.68561 ( 1458) SS BOND : bond 0.00273 ( 8) SS BOND : angle 1.46385 ( 16) covalent geometry : bond 0.00490 ( 8328) covalent geometry : angle 1.02955 (11334) *********************** 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 114 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 1.205 Fit side-chains REVERT: B 390 ASP cc_start: 0.7630 (m-30) cc_final: 0.7390 (m-30) REVERT: A 86 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7685 (mm) outliers start: 13 outliers final: 10 residues processed: 108 average time/residue: 0.3264 time to fit residues: 53.2511 Evaluate side-chains 110 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 551 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 46 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 39 optimal weight: 0.0670 chunk 103 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 overall best weight: 1.9524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.119618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.097050 restraints weight = 39950.200| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.45 r_work: 0.3206 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 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 0.031 8340 Z= 0.145 Angle : 0.996 36.859 11362 Z= 0.403 Chirality : 0.040 0.213 1356 Planarity : 0.005 0.067 1400 Dihedral : 7.984 97.725 1236 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.05 % Allowed : 9.67 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.04 (0.26), residues: 1076 helix: 1.79 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -1.05 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 482 HIS 0.002 0.001 HIS A 350 PHE 0.013 0.001 PHE B 189 TYR 0.009 0.001 TYR B 181 ARG 0.001 0.000 ARG B 204 Details of bonding type rmsd link_NAG-ASN : bond 0.00462 ( 2) link_NAG-ASN : angle 1.89783 ( 6) link_BETA1-4 : bond 0.00244 ( 2) link_BETA1-4 : angle 2.50129 ( 6) hydrogen bonds : bond 0.05687 ( 509) hydrogen bonds : angle 4.43785 ( 1458) SS BOND : bond 0.00199 ( 8) SS BOND : angle 1.03336 ( 16) covalent geometry : bond 0.00313 ( 8328) covalent geometry : angle 0.99417 (11334) *********************** 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 112 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 1.135 Fit side-chains REVERT: B 390 ASP cc_start: 0.7548 (m-30) cc_final: 0.7323 (m-30) outliers start: 9 outliers final: 7 residues processed: 109 average time/residue: 0.3172 time to fit residues: 53.1815 Evaluate side-chains 109 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 102 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 551 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 1 optimal weight: 7.9990 chunk 9 optimal weight: 0.0870 chunk 68 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.119712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.097135 restraints weight = 40509.576| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.48 r_work: 0.3207 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8340 Z= 0.140 Angle : 0.991 36.776 11362 Z= 0.397 Chirality : 0.039 0.210 1356 Planarity : 0.005 0.067 1400 Dihedral : 7.713 92.104 1236 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 1.05 % Allowed : 10.61 % Favored : 88.34 % 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: 1.18 (0.26), residues: 1076 helix: 1.91 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -1.01 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 482 HIS 0.002 0.001 HIS A 350 PHE 0.017 0.001 PHE B 555 TYR 0.009 0.001 TYR A 181 ARG 0.001 0.000 ARG B 204 Details of bonding type rmsd link_NAG-ASN : bond 0.00371 ( 2) link_NAG-ASN : angle 1.77130 ( 6) link_BETA1-4 : bond 0.00477 ( 2) link_BETA1-4 : angle 2.62963 ( 6) hydrogen bonds : bond 0.05408 ( 509) hydrogen bonds : angle 4.33100 ( 1458) SS BOND : bond 0.00199 ( 8) SS BOND : angle 1.01354 ( 16) covalent geometry : bond 0.00304 ( 8328) covalent geometry : angle 0.98864 (11334) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 1.260 Fit side-chains REVERT: B 390 ASP cc_start: 0.7545 (m-30) cc_final: 0.7321 (m-30) REVERT: B 524 TYR cc_start: 0.8817 (OUTLIER) cc_final: 0.8026 (m-80) outliers start: 9 outliers final: 8 residues processed: 110 average time/residue: 0.3183 time to fit residues: 53.6768 Evaluate side-chains 112 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 524 TYR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 551 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 20 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 49 optimal weight: 0.4980 chunk 8 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.120781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.098649 restraints weight = 39777.428| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.43 r_work: 0.3230 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8340 Z= 0.116 Angle : 0.981 36.515 11362 Z= 0.388 Chirality : 0.039 0.205 1356 Planarity : 0.005 0.066 1400 Dihedral : 7.337 84.638 1236 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.28 % Allowed : 10.96 % Favored : 87.76 % 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: 1.40 (0.27), residues: 1076 helix: 2.07 (0.21), residues: 646 sheet: None (None), residues: 0 loop : -0.89 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 482 HIS 0.002 0.001 HIS A 289 PHE 0.014 0.001 PHE A 555 TYR 0.008 0.001 TYR A 181 ARG 0.001 0.000 ARG B 204 Details of bonding type rmsd link_NAG-ASN : bond 0.00377 ( 2) link_NAG-ASN : angle 1.63214 ( 6) link_BETA1-4 : bond 0.00325 ( 2) link_BETA1-4 : angle 2.76795 ( 6) hydrogen bonds : bond 0.04955 ( 509) hydrogen bonds : angle 4.17057 ( 1458) SS BOND : bond 0.00175 ( 8) SS BOND : angle 0.85405 ( 16) covalent geometry : bond 0.00246 ( 8328) covalent geometry : angle 0.97928 (11334) *********************** 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 113 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 1.943 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 390 ASP cc_start: 0.7536 (m-30) cc_final: 0.7295 (m-30) REVERT: B 524 TYR cc_start: 0.8827 (OUTLIER) cc_final: 0.8144 (m-80) outliers start: 11 outliers final: 9 residues processed: 109 average time/residue: 0.3505 time to fit residues: 59.3571 Evaluate side-chains 112 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 309 TYR Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 524 TYR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 551 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 25 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.117884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.095638 restraints weight = 40105.405| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.43 r_work: 0.3184 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8340 Z= 0.195 Angle : 1.015 36.695 11362 Z= 0.414 Chirality : 0.041 0.209 1356 Planarity : 0.005 0.067 1400 Dihedral : 7.355 77.849 1236 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 1.40 % Allowed : 11.89 % Favored : 86.71 % 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: 1.09 (0.26), residues: 1076 helix: 1.87 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -1.10 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 543 HIS 0.003 0.001 HIS A 350 PHE 0.024 0.002 PHE A 555 TYR 0.009 0.001 TYR A 181 ARG 0.001 0.000 ARG A 204 Details of bonding type rmsd link_NAG-ASN : bond 0.00428 ( 2) link_NAG-ASN : angle 1.76771 ( 6) link_BETA1-4 : bond 0.00133 ( 2) link_BETA1-4 : angle 3.03063 ( 6) hydrogen bonds : bond 0.05839 ( 509) hydrogen bonds : angle 4.36814 ( 1458) SS BOND : bond 0.00231 ( 8) SS BOND : angle 1.29743 ( 16) covalent geometry : bond 0.00439 ( 8328) covalent geometry : angle 1.01146 (11334) *********************** 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 115 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 1.474 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 524 TYR cc_start: 0.8874 (OUTLIER) cc_final: 0.8029 (m-80) outliers start: 12 outliers final: 11 residues processed: 110 average time/residue: 0.3571 time to fit residues: 57.9021 Evaluate side-chains 112 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 524 TYR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 48 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 54 optimal weight: 9.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.118507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.096756 restraints weight = 39947.780| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.40 r_work: 0.3207 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8340 Z= 0.127 Angle : 0.991 36.552 11362 Z= 0.394 Chirality : 0.039 0.206 1356 Planarity : 0.005 0.067 1400 Dihedral : 6.851 69.434 1236 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 1.63 % Allowed : 12.35 % Favored : 86.01 % 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: 1.33 (0.26), residues: 1076 helix: 2.03 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -0.95 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 482 HIS 0.002 0.001 HIS A 289 PHE 0.012 0.001 PHE A 189 TYR 0.008 0.001 TYR A 181 ARG 0.004 0.000 ARG A 103 Details of bonding type rmsd link_NAG-ASN : bond 0.00368 ( 2) link_NAG-ASN : angle 1.69643 ( 6) link_BETA1-4 : bond 0.00216 ( 2) link_BETA1-4 : angle 3.36729 ( 6) hydrogen bonds : bond 0.05195 ( 509) hydrogen bonds : angle 4.18046 ( 1458) SS BOND : bond 0.00164 ( 8) SS BOND : angle 0.94620 ( 16) covalent geometry : bond 0.00274 ( 8328) covalent geometry : angle 0.98765 (11334) *********************** 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 116 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 524 TYR cc_start: 0.8846 (OUTLIER) cc_final: 0.8144 (m-80) REVERT: A 236 GLN cc_start: 0.6670 (mp10) cc_final: 0.6462 (mp10) outliers start: 14 outliers final: 13 residues processed: 111 average time/residue: 0.3545 time to fit residues: 57.6958 Evaluate side-chains 116 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 309 TYR Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 524 TYR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 2 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.120966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.099034 restraints weight = 39738.471| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.42 r_work: 0.3242 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8340 Z= 0.105 Angle : 0.978 36.520 11362 Z= 0.383 Chirality : 0.038 0.196 1356 Planarity : 0.005 0.066 1400 Dihedral : 5.865 53.700 1236 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.52 % Allowed : 12.59 % Favored : 85.90 % 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: 1.65 (0.27), residues: 1076 helix: 2.29 (0.21), residues: 646 sheet: None (None), residues: 0 loop : -0.80 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 482 HIS 0.001 0.000 HIS B 289 PHE 0.014 0.001 PHE A 466 TYR 0.008 0.001 TYR A 181 ARG 0.005 0.000 ARG A 103 Details of bonding type rmsd link_NAG-ASN : bond 0.00284 ( 2) link_NAG-ASN : angle 1.69861 ( 6) link_BETA1-4 : bond 0.00254 ( 2) link_BETA1-4 : angle 4.28682 ( 6) hydrogen bonds : bond 0.04492 ( 509) hydrogen bonds : angle 3.97936 ( 1458) SS BOND : bond 0.00158 ( 8) SS BOND : angle 0.68012 ( 16) covalent geometry : bond 0.00218 ( 8328) covalent geometry : angle 0.97334 (11334) *********************** 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 116 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 524 TYR cc_start: 0.8816 (OUTLIER) cc_final: 0.8219 (m-80) REVERT: A 234 ASN cc_start: 0.8772 (t0) cc_final: 0.8512 (t0) REVERT: A 524 TYR cc_start: 0.8827 (OUTLIER) cc_final: 0.7931 (m-80) outliers start: 13 outliers final: 10 residues processed: 113 average time/residue: 0.3807 time to fit residues: 63.5148 Evaluate side-chains 112 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 309 TYR Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 524 TYR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 524 TYR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 83 optimal weight: 3.9990 chunk 18 optimal weight: 0.0040 chunk 16 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.119086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.097198 restraints weight = 40240.901| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.42 r_work: 0.3214 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8340 Z= 0.134 Angle : 0.986 36.558 11362 Z= 0.391 Chirality : 0.039 0.205 1356 Planarity : 0.005 0.067 1400 Dihedral : 5.715 54.676 1236 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 1.28 % Allowed : 13.29 % Favored : 85.43 % 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: 1.58 (0.26), residues: 1076 helix: 2.25 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -0.88 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 482 HIS 0.002 0.001 HIS B 289 PHE 0.020 0.001 PHE A 555 TYR 0.009 0.001 TYR A 181 ARG 0.002 0.000 ARG A 103 Details of bonding type rmsd link_NAG-ASN : bond 0.00344 ( 2) link_NAG-ASN : angle 2.10909 ( 6) link_BETA1-4 : bond 0.00341 ( 2) link_BETA1-4 : angle 4.27811 ( 6) hydrogen bonds : bond 0.04921 ( 509) hydrogen bonds : angle 4.05357 ( 1458) SS BOND : bond 0.00195 ( 8) SS BOND : angle 0.95803 ( 16) covalent geometry : bond 0.00294 ( 8328) covalent geometry : angle 0.98009 (11334) ********************** 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 114 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 524 TYR cc_start: 0.8830 (OUTLIER) cc_final: 0.8176 (m-80) outliers start: 11 outliers final: 10 residues processed: 111 average time/residue: 0.3304 time to fit residues: 54.6032 Evaluate side-chains 113 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 309 TYR Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 524 TYR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 85 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 80 optimal weight: 0.0980 chunk 9 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.119992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.098131 restraints weight = 40096.736| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.43 r_work: 0.3228 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8340 Z= 0.113 Angle : 0.973 36.530 11362 Z= 0.383 Chirality : 0.038 0.213 1356 Planarity : 0.005 0.066 1400 Dihedral : 5.593 53.981 1236 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 1.63 % Allowed : 12.94 % Favored : 85.43 % 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: 2.32 (0.21), residues: 646 sheet: None (None), residues: 0 loop : -0.81 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 482 HIS 0.002 0.001 HIS A 289 PHE 0.024 0.001 PHE A 555 TYR 0.008 0.001 TYR A 181 ARG 0.001 0.000 ARG B 204 Details of bonding type rmsd link_NAG-ASN : bond 0.00388 ( 2) link_NAG-ASN : angle 2.17268 ( 6) link_BETA1-4 : bond 0.00154 ( 2) link_BETA1-4 : angle 3.62048 ( 6) hydrogen bonds : bond 0.04658 ( 509) hydrogen bonds : angle 3.98062 ( 1458) SS BOND : bond 0.00149 ( 8) SS BOND : angle 0.78531 ( 16) covalent geometry : bond 0.00241 ( 8328) covalent geometry : angle 0.96933 (11334) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7704.35 seconds wall clock time: 131 minutes 22.19 seconds (7882.19 seconds total)