Starting phenix.real_space_refine on Thu Feb 13 16:04:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vh0_43230/02_2025/8vh0_43230.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vh0_43230/02_2025/8vh0_43230.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vh0_43230/02_2025/8vh0_43230.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vh0_43230/02_2025/8vh0_43230.map" model { file = "/net/cci-nas-00/data/ceres_data/8vh0_43230/02_2025/8vh0_43230.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vh0_43230/02_2025/8vh0_43230.cif" } resolution = 2.3 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= -0.001 sd= 0.205 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: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 V 2 8.30 5 S 14 5.16 5 C 5796 2.51 5 N 1522 2.21 5 O 1800 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9136 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4559 Classifications: {'peptide': 590} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 36, 'TRANS': 552} Chain: "B" Number of atoms: 4559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4559 Classifications: {'peptide': 590} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 36, 'TRANS': 552} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 5 Unusual residues: {' CA': 1, 'VO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 5 Unusual residues: {' CA': 1, 'VO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 7.03, per 1000 atoms: 0.77 Number of scatterers: 9136 At special positions: 0 Unit cell: (106.09, 96.82, 98.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) V 2 22.97 Ca 2 19.99 S 14 16.00 O 1800 8.00 N 1522 7.00 C 5796 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.72 Conformation dependent library (CDL) restraints added in 1.2 seconds 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2176 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 12 sheets defined 51.5% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 10 through 29 Processing helix chain 'A' and resid 38 through 43 removed outlier: 3.997A pdb=" N TYR A 43 " --> pdb=" O GLU A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 removed outlier: 3.875A pdb=" N PHE A 77 " --> pdb=" O ASP A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 94 Processing helix chain 'A' and resid 112 through 118 Processing helix chain 'A' and resid 129 through 133 Processing helix chain 'A' and resid 154 through 170 Processing helix chain 'A' and resid 174 through 178 Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 183 through 196 Processing helix chain 'A' and resid 197 through 202 Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 240 through 245 removed outlier: 3.625A pdb=" N ILE A 244 " --> pdb=" O SER A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 268 Processing helix chain 'A' and resid 296 through 305 Processing helix chain 'A' and resid 324 through 335 removed outlier: 3.725A pdb=" N PHE A 334 " --> pdb=" O THR A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 351 Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 377 through 402 removed outlier: 3.526A pdb=" N THR A 386 " --> pdb=" O LEU A 382 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ALA A 389 " --> pdb=" O VAL A 385 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N THR A 390 " --> pdb=" O THR A 386 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG A 391 " --> pdb=" O GLU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 426 Proline residue: A 423 - end of helix Processing helix chain 'A' and resid 430 through 432 No H-bonds generated for 'chain 'A' and resid 430 through 432' Processing helix chain 'A' and resid 433 through 440 Processing helix chain 'A' and resid 440 through 459 Processing helix chain 'A' and resid 485 through 502 Processing helix chain 'A' and resid 532 through 550 Processing helix chain 'A' and resid 554 through 578 removed outlier: 3.813A pdb=" N LEU A 578 " --> pdb=" O GLU A 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 29 Processing helix chain 'B' and resid 38 through 43 removed outlier: 3.927A pdb=" N TYR B 43 " --> pdb=" O GLU B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 87 removed outlier: 3.744A pdb=" N PHE B 77 " --> pdb=" O ASP B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 94 Processing helix chain 'B' and resid 112 through 118 Processing helix chain 'B' and resid 129 through 133 Processing helix chain 'B' and resid 154 through 170 Processing helix chain 'B' and resid 174 through 178 Processing helix chain 'B' and resid 180 through 182 No H-bonds generated for 'chain 'B' and resid 180 through 182' Processing helix chain 'B' and resid 183 through 196 Processing helix chain 'B' and resid 197 through 202 Processing helix chain 'B' and resid 209 through 216 Processing helix chain 'B' and resid 240 through 245 removed outlier: 3.629A pdb=" N ILE B 244 " --> pdb=" O SER B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 269 Processing helix chain 'B' and resid 296 through 305 Processing helix chain 'B' and resid 324 through 335 removed outlier: 3.759A pdb=" N PHE B 334 " --> pdb=" O THR B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 351 Processing helix chain 'B' and resid 364 through 369 Processing helix chain 'B' and resid 377 through 402 removed outlier: 3.592A pdb=" N THR B 386 " --> pdb=" O LEU B 382 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ALA B 389 " --> pdb=" O VAL B 385 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N THR B 390 " --> pdb=" O THR B 386 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG B 391 " --> pdb=" O GLU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 422 Processing helix chain 'B' and resid 423 through 426 Processing helix chain 'B' and resid 430 through 432 No H-bonds generated for 'chain 'B' and resid 430 through 432' Processing helix chain 'B' and resid 433 through 440 Processing helix chain 'B' and resid 440 through 459 Processing helix chain 'B' and resid 485 through 502 Processing helix chain 'B' and resid 532 through 549 Processing helix chain 'B' and resid 554 through 578 removed outlier: 3.653A pdb=" N LEU B 578 " --> pdb=" O GLU B 574 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 254 through 255 Processing sheet with id=AA2, first strand: chain 'A' and resid 272 through 275 removed outlier: 3.600A pdb=" N THR A 279 " --> pdb=" O SER B 281 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR B 279 " --> pdb=" O SER A 281 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 272 through 275 removed outlier: 3.600A pdb=" N THR A 279 " --> pdb=" O SER B 281 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR B 279 " --> pdb=" O SER A 281 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N GLN B 282 " --> pdb=" O ARG B 320 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ARG B 320 " --> pdb=" O GLN B 282 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL B 284 " --> pdb=" O GLY B 318 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N GLY B 318 " --> pdb=" O VAL B 284 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ILE B 286 " --> pdb=" O GLU B 316 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 284 through 287 removed outlier: 6.750A pdb=" N VAL A 284 " --> pdb=" O GLY A 318 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N GLY A 318 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ILE A 286 " --> pdb=" O GLU A 316 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 370 through 371 Processing sheet with id=AA6, first strand: chain 'A' and resid 507 through 508 removed outlier: 4.327A pdb=" N LEU A 530 " --> pdb=" O ILE A 508 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 512 through 514 Processing sheet with id=AA8, first strand: chain 'A' and resid 586 through 589 Processing sheet with id=AA9, first strand: chain 'B' and resid 254 through 255 Processing sheet with id=AB1, first strand: chain 'B' and resid 507 through 508 removed outlier: 4.410A pdb=" N LEU B 530 " --> pdb=" O ILE B 508 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 512 through 514 Processing sheet with id=AB3, first strand: chain 'B' and resid 586 through 589 423 hydrogen bonds defined for protein. 1206 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: 2.73 Time building geometry restraints manager: 3.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 1639 1.27 - 1.41: 2201 1.41 - 1.54: 5340 1.54 - 1.67: 120 1.67 - 1.80: 24 Bond restraints: 9324 Sorted by residual: bond pdb=" O1 VO4 B 602 " pdb=" V VO4 B 602 " ideal model delta sigma weight residual 1.910 1.550 0.360 2.00e-02 2.50e+03 3.24e+02 bond pdb=" O1 VO4 A 602 " pdb=" V VO4 A 602 " ideal model delta sigma weight residual 1.910 1.550 0.360 2.00e-02 2.50e+03 3.24e+02 bond pdb=" O2 VO4 B 602 " pdb=" V VO4 B 602 " ideal model delta sigma weight residual 1.910 1.570 0.340 2.00e-02 2.50e+03 2.90e+02 bond pdb=" O3 VO4 A 602 " pdb=" V VO4 A 602 " ideal model delta sigma weight residual 1.910 1.570 0.340 2.00e-02 2.50e+03 2.89e+02 bond pdb=" O3 VO4 B 602 " pdb=" V VO4 B 602 " ideal model delta sigma weight residual 1.910 1.600 0.310 2.00e-02 2.50e+03 2.41e+02 ... (remaining 9319 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.94: 12587 2.94 - 5.87: 80 5.87 - 8.81: 3 8.81 - 11.75: 1 11.75 - 14.68: 3 Bond angle restraints: 12674 Sorted by residual: angle pdb=" CA TYR B 341 " pdb=" C TYR B 341 " pdb=" O TYR B 341 " ideal model delta sigma weight residual 119.41 126.37 -6.96 1.13e+00 7.83e-01 3.80e+01 angle pdb=" O2 VO4 B 602 " pdb=" V VO4 B 602 " pdb=" O3 VO4 B 602 " ideal model delta sigma weight residual 109.47 124.16 -14.68 3.00e+00 1.11e-01 2.40e+01 angle pdb=" C TYR B 341 " pdb=" CA TYR B 341 " pdb=" CB TYR B 341 " ideal model delta sigma weight residual 109.24 117.47 -8.23 1.75e+00 3.27e-01 2.21e+01 angle pdb=" O1 VO4 A 602 " pdb=" V VO4 A 602 " pdb=" O3 VO4 A 602 " ideal model delta sigma weight residual 109.47 123.05 -13.58 3.00e+00 1.11e-01 2.05e+01 angle pdb=" O1 VO4 B 602 " pdb=" V VO4 B 602 " pdb=" O2 VO4 B 602 " ideal model delta sigma weight residual 109.47 122.46 -12.99 3.00e+00 1.11e-01 1.88e+01 ... (remaining 12669 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 4859 17.94 - 35.87: 542 35.87 - 53.81: 146 53.81 - 71.74: 27 71.74 - 89.68: 18 Dihedral angle restraints: 5592 sinusoidal: 2212 harmonic: 3380 Sorted by residual: dihedral pdb=" CA ALA B 145 " pdb=" C ALA B 145 " pdb=" N MET B 146 " pdb=" CA MET B 146 " ideal model delta harmonic sigma weight residual 180.00 162.99 17.01 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" C ILE B 545 " pdb=" N ILE B 545 " pdb=" CA ILE B 545 " pdb=" CB ILE B 545 " ideal model delta harmonic sigma weight residual -122.00 -130.47 8.47 0 2.50e+00 1.60e-01 1.15e+01 dihedral pdb=" CB GLU A 566 " pdb=" CG GLU A 566 " pdb=" CD GLU A 566 " pdb=" OE1 GLU A 566 " ideal model delta sinusoidal sigma weight residual 0.00 89.68 -89.68 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 5589 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1035 0.043 - 0.085: 280 0.085 - 0.128: 79 0.128 - 0.170: 6 0.170 - 0.213: 4 Chirality restraints: 1404 Sorted by residual: chirality pdb=" CB THR A 412 " pdb=" CA THR A 412 " pdb=" OG1 THR A 412 " pdb=" CG2 THR A 412 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA TYR B 341 " pdb=" N TYR B 341 " pdb=" C TYR B 341 " pdb=" CB TYR B 341 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA LEU B 564 " pdb=" N LEU B 564 " pdb=" C LEU B 564 " pdb=" CB LEU B 564 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.84e-01 ... (remaining 1401 not shown) Planarity restraints: 1704 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 341 " 0.022 2.00e-02 2.50e+03 4.61e-02 2.13e+01 pdb=" C TYR A 341 " -0.080 2.00e-02 2.50e+03 pdb=" O TYR A 341 " 0.032 2.00e-02 2.50e+03 pdb=" N LEU A 342 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 340 " 0.022 2.00e-02 2.50e+03 4.32e-02 1.87e+01 pdb=" C ALA A 340 " -0.075 2.00e-02 2.50e+03 pdb=" O ALA A 340 " 0.027 2.00e-02 2.50e+03 pdb=" N TYR A 341 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 340 " -0.018 2.00e-02 2.50e+03 3.54e-02 1.26e+01 pdb=" C ALA B 340 " 0.061 2.00e-02 2.50e+03 pdb=" O ALA B 340 " -0.023 2.00e-02 2.50e+03 pdb=" N TYR B 341 " -0.021 2.00e-02 2.50e+03 ... (remaining 1701 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 857 2.74 - 3.28: 10355 3.28 - 3.82: 19168 3.82 - 4.36: 23516 4.36 - 4.90: 35694 Nonbonded interactions: 89590 Sorted by model distance: nonbonded pdb=" OG1 THR B 412 " pdb=" OH TYR B 554 " model vdw 2.196 3.040 nonbonded pdb=" O LEU A 166 " pdb=" OH TYR A 186 " model vdw 2.199 3.040 nonbonded pdb=" O LEU B 166 " pdb=" OH TYR B 186 " model vdw 2.204 3.040 nonbonded pdb=" N GLY A 138 " pdb=" OE1 GLU A 575 " model vdw 2.209 3.120 nonbonded pdb=" O THR A 330 " pdb=" OG SER B 277 " model vdw 2.214 3.040 ... (remaining 89585 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' } 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: 18.130 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 23.480 Find NCS groups from input model: 0.310 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:11.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 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 : 0.010 0.360 9324 Z= 0.746 Angle : 0.651 14.684 12674 Z= 0.353 Chirality : 0.043 0.213 1404 Planarity : 0.004 0.046 1704 Dihedral : 17.125 89.678 3416 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 18.26 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.06 % Favored : 96.77 % Rotamer: Outliers : 2.37 % Allowed : 19.34 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: 0.83 (0.24), residues: 1176 helix: 0.74 (0.22), residues: 532 sheet: None (None), residues: 0 loop : 0.56 (0.26), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 331 HIS 0.006 0.001 HIS A 480 PHE 0.014 0.002 PHE B 479 TYR 0.030 0.003 TYR A 341 ARG 0.008 0.001 ARG B 283 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 90 LYS cc_start: 0.7914 (tmmt) cc_final: 0.7418 (ttmp) REVERT: B 541 ASP cc_start: 0.7245 (OUTLIER) cc_final: 0.6994 (t70) outliers start: 23 outliers final: 12 residues processed: 130 average time/residue: 1.0948 time to fit residues: 154.2723 Evaluate side-chains 113 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 450 SER Chi-restraints excluded: chain B residue 541 ASP Chi-restraints excluded: chain B residue 557 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 GLN ** A 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 ASN B 127 ASN ** B 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 576 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.135674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.121007 restraints weight = 10213.660| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.29 r_work: 0.3397 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 9324 Z= 0.334 Angle : 0.580 5.582 12674 Z= 0.309 Chirality : 0.042 0.146 1404 Planarity : 0.004 0.038 1704 Dihedral : 6.448 73.960 1283 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.15 % Favored : 96.77 % Rotamer: Outliers : 4.42 % Allowed : 16.56 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: 0.92 (0.24), residues: 1176 helix: 0.78 (0.22), residues: 530 sheet: None (None), residues: 0 loop : 0.65 (0.26), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 331 HIS 0.010 0.002 HIS B 553 PHE 0.018 0.002 PHE B 479 TYR 0.024 0.003 TYR A 341 ARG 0.006 0.001 ARG A 405 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 102 time to evaluate : 1.048 Fit side-chains revert: symmetry clash REVERT: A 172 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8215 (mp0) REVERT: A 439 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.6979 (mt-10) REVERT: A 448 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7578 (tt0) REVERT: B 13 LYS cc_start: 0.7754 (mmtm) cc_final: 0.7403 (tppt) REVERT: B 90 LYS cc_start: 0.7736 (tmmt) cc_final: 0.6846 (ttmp) REVERT: B 173 ILE cc_start: 0.8264 (OUTLIER) cc_final: 0.7968 (mt) REVERT: B 252 SER cc_start: 0.8008 (OUTLIER) cc_final: 0.7751 (t) REVERT: B 272 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7264 (mp0) REVERT: B 438 GLU cc_start: 0.7496 (mt-10) cc_final: 0.7242 (mm-30) REVERT: B 558 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.6809 (mp10) outliers start: 43 outliers final: 10 residues processed: 136 average time/residue: 1.1395 time to fit residues: 167.4293 Evaluate side-chains 111 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 341 TYR Chi-restraints excluded: chain B residue 453 LYS Chi-restraints excluded: chain B residue 558 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 58 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 20 optimal weight: 0.2980 chunk 26 optimal weight: 0.9980 chunk 105 optimal weight: 0.5980 chunk 11 optimal weight: 0.3980 chunk 92 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 chunk 19 optimal weight: 0.1980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN A 370 GLN ** B 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.141604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.127320 restraints weight = 10334.684| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.30 r_work: 0.3475 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3367 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9324 Z= 0.194 Angle : 0.497 5.207 12674 Z= 0.265 Chirality : 0.039 0.135 1404 Planarity : 0.004 0.038 1704 Dihedral : 5.659 76.307 1267 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.38 % Favored : 97.45 % Rotamer: Outliers : 4.42 % Allowed : 16.98 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: 0.96 (0.24), residues: 1176 helix: 0.87 (0.22), residues: 532 sheet: None (None), residues: 0 loop : 0.61 (0.26), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 331 HIS 0.006 0.001 HIS B 480 PHE 0.012 0.001 PHE B 479 TYR 0.022 0.002 TYR A 341 ARG 0.005 0.000 ARG B 283 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 106 time to evaluate : 1.110 Fit side-chains revert: symmetry clash REVERT: A 90 LYS cc_start: 0.7826 (OUTLIER) cc_final: 0.7444 (ttpt) REVERT: A 144 ILE cc_start: 0.8291 (OUTLIER) cc_final: 0.8084 (pp) REVERT: A 172 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8087 (mp0) REVERT: A 448 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7655 (tt0) REVERT: B 13 LYS cc_start: 0.7721 (mmtm) cc_final: 0.6982 (mtmt) REVERT: B 90 LYS cc_start: 0.7670 (tmmt) cc_final: 0.6742 (ttmp) REVERT: B 96 THR cc_start: 0.8823 (OUTLIER) cc_final: 0.8560 (p) REVERT: B 137 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.6970 (mt-10) REVERT: B 252 SER cc_start: 0.7863 (OUTLIER) cc_final: 0.7621 (t) REVERT: B 438 GLU cc_start: 0.7463 (mt-10) cc_final: 0.7217 (mm-30) REVERT: B 558 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.8026 (mm-40) REVERT: B 574 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7410 (mt-10) outliers start: 43 outliers final: 4 residues processed: 142 average time/residue: 1.1452 time to fit residues: 175.7201 Evaluate side-chains 108 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 558 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 9 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 chunk 110 optimal weight: 8.9990 chunk 18 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 114 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN A 370 GLN B 264 ASN B 576 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.135957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.121317 restraints weight = 10260.809| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.32 r_work: 0.3396 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 9324 Z= 0.329 Angle : 0.563 7.209 12674 Z= 0.296 Chirality : 0.042 0.144 1404 Planarity : 0.004 0.038 1704 Dihedral : 5.691 74.577 1266 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.64 % Favored : 97.19 % Rotamer: Outliers : 4.63 % Allowed : 17.49 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: 0.91 (0.24), residues: 1176 helix: 0.79 (0.22), residues: 530 sheet: None (None), residues: 0 loop : 0.62 (0.25), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 331 HIS 0.007 0.002 HIS B 480 PHE 0.016 0.002 PHE B 479 TYR 0.029 0.003 TYR B 341 ARG 0.004 0.001 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 102 time to evaluate : 1.077 Fit side-chains revert: symmetry clash REVERT: A 144 ILE cc_start: 0.8333 (OUTLIER) cc_final: 0.8130 (pp) REVERT: A 172 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8172 (mp0) REVERT: A 448 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7566 (tt0) REVERT: A 479 PHE cc_start: 0.8830 (OUTLIER) cc_final: 0.8211 (t80) REVERT: B 13 LYS cc_start: 0.7743 (mmtm) cc_final: 0.7320 (tppt) REVERT: B 252 SER cc_start: 0.7975 (OUTLIER) cc_final: 0.7681 (t) REVERT: B 438 GLU cc_start: 0.7411 (mt-10) cc_final: 0.7115 (mm-30) REVERT: B 506 ILE cc_start: 0.8337 (OUTLIER) cc_final: 0.8094 (mp) REVERT: B 558 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.8202 (mm-40) REVERT: B 574 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7417 (mt-10) outliers start: 45 outliers final: 12 residues processed: 143 average time/residue: 1.0407 time to fit residues: 161.5228 Evaluate side-chains 112 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 479 PHE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 264 ASN Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 558 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 103 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 104 optimal weight: 0.7980 chunk 72 optimal weight: 5.9990 chunk 71 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN A 370 GLN ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 ASN B 576 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.137734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.123511 restraints weight = 10338.053| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.28 r_work: 0.3427 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 9324 Z= 0.256 Angle : 0.529 6.631 12674 Z= 0.280 Chirality : 0.040 0.138 1404 Planarity : 0.004 0.037 1704 Dihedral : 5.633 74.924 1266 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.64 % Favored : 97.19 % Rotamer: Outliers : 4.01 % Allowed : 18.42 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: 0.87 (0.24), residues: 1176 helix: 0.78 (0.22), residues: 532 sheet: None (None), residues: 0 loop : 0.58 (0.26), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 125 HIS 0.006 0.001 HIS A 480 PHE 0.015 0.001 PHE B 479 TYR 0.029 0.003 TYR B 341 ARG 0.004 0.000 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 100 time to evaluate : 1.083 Fit side-chains revert: symmetry clash REVERT: A 90 LYS cc_start: 0.7834 (OUTLIER) cc_final: 0.7606 (ttpt) REVERT: A 172 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.8068 (mp0) REVERT: A 182 LYS cc_start: 0.8074 (OUTLIER) cc_final: 0.7794 (ptpt) REVERT: A 356 ASP cc_start: 0.8106 (OUTLIER) cc_final: 0.7634 (t70) REVERT: A 448 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7598 (tt0) REVERT: A 479 PHE cc_start: 0.8755 (OUTLIER) cc_final: 0.8177 (t80) REVERT: B 13 LYS cc_start: 0.7806 (mmtm) cc_final: 0.7025 (mtmt) REVERT: B 90 LYS cc_start: 0.7704 (tmmt) cc_final: 0.6777 (ttmp) REVERT: B 252 SER cc_start: 0.7963 (OUTLIER) cc_final: 0.7707 (t) REVERT: B 438 GLU cc_start: 0.7462 (mt-10) cc_final: 0.7224 (mm-30) REVERT: B 479 PHE cc_start: 0.8751 (OUTLIER) cc_final: 0.8483 (m-80) REVERT: B 506 ILE cc_start: 0.8257 (OUTLIER) cc_final: 0.8053 (mp) REVERT: B 523 LYS cc_start: 0.7843 (tptm) cc_final: 0.7595 (tppp) REVERT: B 558 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.8081 (mm-40) REVERT: B 574 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7376 (mt-10) outliers start: 39 outliers final: 9 residues processed: 135 average time/residue: 1.0996 time to fit residues: 161.1175 Evaluate side-chains 117 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 356 ASP Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 479 PHE Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 479 PHE Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 558 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 67 optimal weight: 0.1980 chunk 13 optimal weight: 0.0060 chunk 2 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 chunk 10 optimal weight: 0.0470 chunk 5 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 overall best weight: 1.0498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN A 370 GLN ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.137260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.122743 restraints weight = 10239.498| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.32 r_work: 0.3415 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 9324 Z= 0.282 Angle : 0.535 6.375 12674 Z= 0.281 Chirality : 0.041 0.140 1404 Planarity : 0.004 0.037 1704 Dihedral : 5.646 74.116 1266 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.89 % Favored : 96.94 % Rotamer: Outliers : 4.01 % Allowed : 18.11 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: 0.88 (0.24), residues: 1176 helix: 0.78 (0.22), residues: 530 sheet: None (None), residues: 0 loop : 0.59 (0.25), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 331 HIS 0.006 0.001 HIS A 480 PHE 0.016 0.002 PHE B 479 TYR 0.031 0.003 TYR B 341 ARG 0.004 0.000 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 104 time to evaluate : 1.076 Fit side-chains revert: symmetry clash REVERT: A 172 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.8071 (mp0) REVERT: A 356 ASP cc_start: 0.8072 (OUTLIER) cc_final: 0.7590 (t70) REVERT: A 448 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7524 (tt0) REVERT: A 479 PHE cc_start: 0.8797 (OUTLIER) cc_final: 0.8169 (t80) REVERT: B 13 LYS cc_start: 0.7742 (mmtm) cc_final: 0.6901 (mtmt) REVERT: B 90 LYS cc_start: 0.7598 (tmmt) cc_final: 0.6526 (ttmp) REVERT: B 252 SER cc_start: 0.7935 (OUTLIER) cc_final: 0.7645 (t) REVERT: B 438 GLU cc_start: 0.7449 (mt-10) cc_final: 0.7136 (mm-30) REVERT: B 506 ILE cc_start: 0.8239 (OUTLIER) cc_final: 0.8008 (mp) REVERT: B 558 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.8138 (mm-40) REVERT: B 574 GLU cc_start: 0.7634 (mt-10) cc_final: 0.7409 (mt-10) outliers start: 39 outliers final: 13 residues processed: 138 average time/residue: 1.1520 time to fit residues: 171.4490 Evaluate side-chains 121 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 356 ASP Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 479 PHE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 558 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 0.7980 chunk 101 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 63 optimal weight: 0.0020 chunk 33 optimal weight: 0.6980 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN A 370 GLN ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 576 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.139926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.125908 restraints weight = 10384.197| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.28 r_work: 0.3457 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9324 Z= 0.216 Angle : 0.509 5.908 12674 Z= 0.269 Chirality : 0.039 0.135 1404 Planarity : 0.004 0.038 1704 Dihedral : 5.562 74.658 1266 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.55 % Favored : 97.28 % Rotamer: Outliers : 2.98 % Allowed : 19.65 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: 0.95 (0.24), residues: 1176 helix: 0.86 (0.22), residues: 530 sheet: None (None), residues: 0 loop : 0.60 (0.26), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 125 HIS 0.006 0.001 HIS A 480 PHE 0.015 0.001 PHE B 479 TYR 0.028 0.002 TYR B 341 ARG 0.007 0.000 ARG A 391 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 108 time to evaluate : 0.991 Fit side-chains revert: symmetry clash REVERT: A 90 LYS cc_start: 0.7833 (OUTLIER) cc_final: 0.7542 (ttpt) REVERT: A 137 GLU cc_start: 0.7685 (mt-10) cc_final: 0.7331 (mt-10) REVERT: A 172 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.8021 (mm-30) REVERT: A 356 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7716 (t70) REVERT: A 442 ASP cc_start: 0.6685 (m-30) cc_final: 0.6182 (t0) REVERT: A 448 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7640 (tt0) REVERT: A 479 PHE cc_start: 0.8677 (OUTLIER) cc_final: 0.8170 (t80) REVERT: B 13 LYS cc_start: 0.7763 (mmtm) cc_final: 0.7003 (mtmt) REVERT: B 90 LYS cc_start: 0.7661 (tmmt) cc_final: 0.6608 (ttmp) REVERT: B 252 SER cc_start: 0.7889 (OUTLIER) cc_final: 0.7629 (t) REVERT: B 438 GLU cc_start: 0.7501 (mt-10) cc_final: 0.7268 (mm-30) REVERT: B 506 ILE cc_start: 0.8063 (OUTLIER) cc_final: 0.7836 (mp) REVERT: B 558 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.7969 (mm-40) REVERT: B 574 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7350 (mt-10) outliers start: 29 outliers final: 9 residues processed: 135 average time/residue: 1.1077 time to fit residues: 161.8563 Evaluate side-chains 113 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 356 ASP Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 479 PHE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 558 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 35 optimal weight: 0.6980 chunk 110 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 104 optimal weight: 0.0470 chunk 65 optimal weight: 0.4980 chunk 79 optimal weight: 1.9990 chunk 50 optimal weight: 0.4980 chunk 10 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 GLN ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 576 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.139871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.125346 restraints weight = 10389.371| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.31 r_work: 0.3448 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 9324 Z= 0.240 Angle : 0.520 5.726 12674 Z= 0.274 Chirality : 0.040 0.146 1404 Planarity : 0.004 0.047 1704 Dihedral : 5.546 73.835 1266 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.72 % Favored : 97.11 % Rotamer: Outliers : 3.19 % Allowed : 19.44 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: 0.90 (0.24), residues: 1176 helix: 0.82 (0.22), residues: 532 sheet: None (None), residues: 0 loop : 0.58 (0.26), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 125 HIS 0.006 0.001 HIS A 480 PHE 0.016 0.001 PHE B 479 TYR 0.032 0.002 TYR B 341 ARG 0.010 0.001 ARG B 391 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 104 time to evaluate : 0.952 Fit side-chains revert: symmetry clash REVERT: A 24 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7382 (tm-30) REVERT: A 90 LYS cc_start: 0.7839 (OUTLIER) cc_final: 0.6918 (ttmt) REVERT: A 137 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7365 (mt-10) REVERT: A 172 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.8048 (mm-30) REVERT: A 356 ASP cc_start: 0.8177 (OUTLIER) cc_final: 0.7717 (t70) REVERT: A 442 ASP cc_start: 0.6668 (m-30) cc_final: 0.6174 (t0) REVERT: A 448 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7650 (tt0) REVERT: A 479 PHE cc_start: 0.8711 (OUTLIER) cc_final: 0.8206 (t80) REVERT: B 13 LYS cc_start: 0.7768 (mmtm) cc_final: 0.7000 (mtmt) REVERT: B 90 LYS cc_start: 0.7614 (tmmt) cc_final: 0.6642 (ttmp) REVERT: B 252 SER cc_start: 0.7903 (OUTLIER) cc_final: 0.7646 (t) REVERT: B 506 ILE cc_start: 0.8093 (OUTLIER) cc_final: 0.7847 (mp) REVERT: B 558 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.8003 (mm-40) REVERT: B 574 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7331 (mt-10) outliers start: 31 outliers final: 11 residues processed: 131 average time/residue: 1.1205 time to fit residues: 158.6741 Evaluate side-chains 121 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLU Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 356 ASP Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 479 PHE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 558 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 6 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 92 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 24 optimal weight: 7.9990 chunk 63 optimal weight: 0.0020 chunk 80 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 GLN ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 576 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.140205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.125807 restraints weight = 10264.168| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 1.29 r_work: 0.3454 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 9324 Z= 0.236 Angle : 0.516 5.687 12674 Z= 0.272 Chirality : 0.040 0.138 1404 Planarity : 0.004 0.037 1704 Dihedral : 5.526 73.333 1266 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.64 % Favored : 97.19 % Rotamer: Outliers : 2.88 % Allowed : 19.65 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: 0.98 (0.24), residues: 1176 helix: 0.85 (0.22), residues: 530 sheet: -0.92 (1.32), residues: 18 loop : 0.71 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 331 HIS 0.006 0.001 HIS A 480 PHE 0.019 0.001 PHE B 479 TYR 0.030 0.002 TYR B 341 ARG 0.008 0.001 ARG B 391 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 1.122 Fit side-chains revert: symmetry clash REVERT: A 90 LYS cc_start: 0.7843 (OUTLIER) cc_final: 0.6923 (ttmt) REVERT: A 172 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.8051 (mm-30) REVERT: A 219 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8069 (tp30) REVERT: A 356 ASP cc_start: 0.8165 (OUTLIER) cc_final: 0.7706 (t70) REVERT: A 442 ASP cc_start: 0.6583 (m-30) cc_final: 0.6121 (t0) REVERT: A 448 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7607 (tt0) REVERT: A 479 PHE cc_start: 0.8704 (OUTLIER) cc_final: 0.8200 (t80) REVERT: B 13 LYS cc_start: 0.7765 (mmtm) cc_final: 0.6999 (mtmt) REVERT: B 90 LYS cc_start: 0.7494 (tmmt) cc_final: 0.6593 (ttmp) REVERT: B 252 SER cc_start: 0.7902 (OUTLIER) cc_final: 0.7647 (t) REVERT: B 506 ILE cc_start: 0.8080 (OUTLIER) cc_final: 0.7834 (mp) REVERT: B 558 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.8031 (mm-40) REVERT: B 574 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7382 (mt-10) outliers start: 28 outliers final: 11 residues processed: 127 average time/residue: 1.1196 time to fit residues: 154.1591 Evaluate side-chains 119 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 356 ASP Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 479 PHE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 558 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 86 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 101 optimal weight: 0.0010 chunk 102 optimal weight: 6.9990 chunk 15 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 GLN ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 576 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.141368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.127021 restraints weight = 10299.654| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.30 r_work: 0.3470 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9324 Z= 0.220 Angle : 0.513 5.578 12674 Z= 0.270 Chirality : 0.039 0.137 1404 Planarity : 0.004 0.037 1704 Dihedral : 5.498 72.979 1266 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.38 % Favored : 97.45 % Rotamer: Outliers : 2.67 % Allowed : 19.96 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: 1.00 (0.24), residues: 1176 helix: 0.88 (0.22), residues: 530 sheet: -0.94 (1.33), residues: 18 loop : 0.72 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 125 HIS 0.006 0.001 HIS A 480 PHE 0.019 0.001 PHE B 479 TYR 0.029 0.002 TYR B 341 ARG 0.009 0.001 ARG B 391 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 1.039 Fit side-chains revert: symmetry clash REVERT: A 24 GLU cc_start: 0.7338 (tm-30) cc_final: 0.7107 (tm-30) REVERT: A 90 LYS cc_start: 0.7854 (OUTLIER) cc_final: 0.6939 (ttmt) REVERT: A 172 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7987 (mm-30) REVERT: A 219 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.8126 (tp30) REVERT: A 356 ASP cc_start: 0.8160 (OUTLIER) cc_final: 0.7702 (t70) REVERT: A 442 ASP cc_start: 0.6540 (m-30) cc_final: 0.6097 (t0) REVERT: A 448 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7648 (tt0) REVERT: B 13 LYS cc_start: 0.7742 (mmtm) cc_final: 0.6973 (mtmt) REVERT: B 90 LYS cc_start: 0.7520 (tmmt) cc_final: 0.6659 (ttmp) REVERT: B 252 SER cc_start: 0.7872 (OUTLIER) cc_final: 0.7625 (t) REVERT: B 506 ILE cc_start: 0.7996 (OUTLIER) cc_final: 0.7759 (mp) REVERT: B 558 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.8057 (mm-40) REVERT: B 574 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7458 (mt-10) outliers start: 26 outliers final: 8 residues processed: 123 average time/residue: 1.1414 time to fit residues: 151.6218 Evaluate side-chains 116 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 356 ASP Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 558 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 20 optimal weight: 0.6980 chunk 94 optimal weight: 3.9990 chunk 105 optimal weight: 0.2980 chunk 44 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 57 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 GLN ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 576 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.141033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.127069 restraints weight = 10340.261| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.27 r_work: 0.3474 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3366 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9324 Z= 0.224 Angle : 0.521 5.947 12674 Z= 0.274 Chirality : 0.040 0.138 1404 Planarity : 0.004 0.037 1704 Dihedral : 5.484 72.351 1266 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.38 % Favored : 97.45 % Rotamer: Outliers : 2.16 % Allowed : 20.88 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: 0.94 (0.24), residues: 1176 helix: 0.88 (0.22), residues: 532 sheet: None (None), residues: 0 loop : 0.57 (0.26), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 125 HIS 0.005 0.001 HIS A 480 PHE 0.018 0.001 PHE B 479 TYR 0.029 0.002 TYR B 341 ARG 0.010 0.001 ARG B 391 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6839.14 seconds wall clock time: 122 minutes 48.27 seconds (7368.27 seconds total)