Starting phenix.real_space_refine on Thu Oct 10 11:01:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wx4_37900/10_2024/8wx4_37900.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wx4_37900/10_2024/8wx4_37900.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wx4_37900/10_2024/8wx4_37900.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wx4_37900/10_2024/8wx4_37900.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wx4_37900/10_2024/8wx4_37900.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wx4_37900/10_2024/8wx4_37900.cif" } resolution = 3.12 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= 0.002 sd= 0.089 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: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 4966 2.51 5 N 1224 2.21 5 O 1282 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 7512 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3738 Classifications: {'peptide': 486} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 465} Chain breaks: 2 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Classifications: {'peptide': 1} Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Restraints were copied for chains: B Time building chain proxies: 6.38, per 1000 atoms: 0.85 Number of scatterers: 7512 At special positions: 0 Unit cell: (83.415, 120.765, 82.17, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 1282 8.00 N 1224 7.00 C 4966 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 68 " - pdb=" SG CYS B 141 " distance=2.03 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 153 " 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 Time building additional restraints: 1.98 Conformation dependent library (CDL) restraints added in 1.2 seconds 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1796 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 2 sheets defined 75.6% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'B' and resid 33 through 55 removed outlier: 3.539A pdb=" N CYS B 37 " --> pdb=" O ARG B 33 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL B 40 " --> pdb=" O ALA B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 63 Processing helix chain 'B' and resid 70 through 99 removed outlier: 3.559A pdb=" N LEU B 78 " --> pdb=" O ALA B 74 " (cutoff:3.500A) Proline residue: B 90 - end of helix Processing helix chain 'B' and resid 103 through 118 removed outlier: 3.603A pdb=" N LEU B 118 " --> pdb=" O LEU B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 125 Processing helix chain 'B' and resid 125 through 133 removed outlier: 4.188A pdb=" N ALA B 130 " --> pdb=" O PRO B 126 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ALA B 131 " --> pdb=" O ALA B 127 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N CYS B 133 " --> pdb=" O ARG B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 181 removed outlier: 3.572A pdb=" N ASN B 174 " --> pdb=" O THR B 170 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N THR B 176 " --> pdb=" O LYS B 172 " (cutoff:3.500A) Proline residue: B 177 - end of helix Processing helix chain 'B' and resid 182 through 186 removed outlier: 5.436A pdb=" N ASP B 185 " --> pdb=" O GLN B 182 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG B 186 " --> pdb=" O VAL B 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 182 through 186' Processing helix chain 'B' and resid 187 through 220 removed outlier: 4.778A pdb=" N ILE B 207 " --> pdb=" O ASN B 203 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ALA B 214 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N TYR B 215 " --> pdb=" O GLY B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 244 removed outlier: 3.514A pdb=" N GLY B 225 " --> pdb=" O SER B 221 " (cutoff:3.500A) Proline residue: B 229 - end of helix Processing helix chain 'B' and resid 312 through 320 removed outlier: 3.652A pdb=" N LEU B 318 " --> pdb=" O ASP B 314 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS B 320 " --> pdb=" O LYS B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 347 Proline residue: B 330 - end of helix removed outlier: 3.728A pdb=" N VAL B 343 " --> pdb=" O GLN B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 372 removed outlier: 4.205A pdb=" N LEU B 369 " --> pdb=" O PRO B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 387 Proline residue: B 382 - end of helix Processing helix chain 'B' and resid 387 through 395 Processing helix chain 'B' and resid 400 through 430 removed outlier: 3.683A pdb=" N ARG B 404 " --> pdb=" O SER B 400 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN B 428 " --> pdb=" O SER B 424 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU B 429 " --> pdb=" O LYS B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 453 Processing helix chain 'B' and resid 454 through 479 removed outlier: 3.661A pdb=" N ILE B 461 " --> pdb=" O GLN B 457 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ILE B 470 " --> pdb=" O ILE B 466 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ALA B 471 " --> pdb=" O PHE B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 510 Processing helix chain 'B' and resid 531 through 559 removed outlier: 3.609A pdb=" N TYR B 535 " --> pdb=" O TYR B 531 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL B 555 " --> pdb=" O LEU B 551 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS B 556 " --> pdb=" O ILE B 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 55 removed outlier: 3.539A pdb=" N CYS A 37 " --> pdb=" O ARG A 33 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL A 40 " --> pdb=" O ALA A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 63 Processing helix chain 'A' and resid 70 through 99 removed outlier: 3.559A pdb=" N LEU A 78 " --> pdb=" O ALA A 74 " (cutoff:3.500A) Proline residue: A 90 - end of helix Processing helix chain 'A' and resid 103 through 118 removed outlier: 3.603A pdb=" N LEU A 118 " --> pdb=" O LEU A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 125 Processing helix chain 'A' and resid 125 through 133 removed outlier: 4.188A pdb=" N ALA A 130 " --> pdb=" O PRO A 126 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ALA A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N CYS A 133 " --> pdb=" O ARG A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 181 removed outlier: 3.572A pdb=" N ASN A 174 " --> pdb=" O THR A 170 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N THR A 176 " --> pdb=" O LYS A 172 " (cutoff:3.500A) Proline residue: A 177 - end of helix Processing helix chain 'A' and resid 182 through 186 removed outlier: 5.435A pdb=" N ASP A 185 " --> pdb=" O GLN A 182 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG A 186 " --> pdb=" O VAL A 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 182 through 186' Processing helix chain 'A' and resid 187 through 220 removed outlier: 4.778A pdb=" N ILE A 207 " --> pdb=" O ASN A 203 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ALA A 214 " --> pdb=" O LEU A 210 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N TYR A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 244 removed outlier: 3.514A pdb=" N GLY A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) Proline residue: A 229 - end of helix Processing helix chain 'A' and resid 312 through 320 removed outlier: 3.652A pdb=" N LEU A 318 " --> pdb=" O ASP A 314 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS A 320 " --> pdb=" O LYS A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 347 Proline residue: A 330 - end of helix removed outlier: 3.728A pdb=" N VAL A 343 " --> pdb=" O GLN A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 372 removed outlier: 4.205A pdb=" N LEU A 369 " --> pdb=" O PRO A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 387 Proline residue: A 382 - end of helix Processing helix chain 'A' and resid 387 through 395 Processing helix chain 'A' and resid 400 through 430 removed outlier: 3.683A pdb=" N ARG A 404 " --> pdb=" O SER A 400 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN A 428 " --> pdb=" O SER A 424 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU A 429 " --> pdb=" O LYS A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 453 Processing helix chain 'A' and resid 454 through 479 removed outlier: 3.661A pdb=" N ILE A 461 " --> pdb=" O GLN A 457 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ILE A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ALA A 471 " --> pdb=" O PHE A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 510 Processing helix chain 'A' and resid 531 through 559 removed outlier: 3.609A pdb=" N TYR A 535 " --> pdb=" O TYR A 531 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL A 555 " --> pdb=" O LEU A 551 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS A 556 " --> pdb=" O ILE A 552 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 434 through 438 Processing sheet with id=AA2, first strand: chain 'A' and resid 434 through 438 504 hydrogen bonds defined for protein. 1506 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: 2.25 Time building geometry restraints manager: 2.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1140 1.30 - 1.43: 2074 1.43 - 1.55: 4422 1.55 - 1.68: 0 1.68 - 1.81: 60 Bond restraints: 7696 Sorted by residual: bond pdb=" C TYR B 52 " pdb=" O TYR B 52 " ideal model delta sigma weight residual 1.236 1.178 0.058 1.31e-02 5.83e+03 1.94e+01 bond pdb=" C TYR A 52 " pdb=" O TYR A 52 " ideal model delta sigma weight residual 1.236 1.178 0.058 1.31e-02 5.83e+03 1.94e+01 bond pdb=" C ASN A 203 " pdb=" O ASN A 203 " ideal model delta sigma weight residual 1.235 1.168 0.067 1.59e-02 3.96e+03 1.77e+01 bond pdb=" C ASN B 203 " pdb=" O ASN B 203 " ideal model delta sigma weight residual 1.235 1.168 0.067 1.59e-02 3.96e+03 1.76e+01 bond pdb=" C TYR A 335 " pdb=" O TYR A 335 " ideal model delta sigma weight residual 1.236 1.186 0.050 1.26e-02 6.30e+03 1.60e+01 ... (remaining 7691 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.34: 10368 3.34 - 6.68: 92 6.68 - 10.01: 2 10.01 - 13.35: 0 13.35 - 16.69: 2 Bond angle restraints: 10464 Sorted by residual: angle pdb=" N LEU B 204 " pdb=" CA LEU B 204 " pdb=" C LEU B 204 " ideal model delta sigma weight residual 113.18 96.49 16.69 1.33e+00 5.65e-01 1.57e+02 angle pdb=" N LEU A 204 " pdb=" CA LEU A 204 " pdb=" C LEU A 204 " ideal model delta sigma weight residual 113.18 96.50 16.68 1.33e+00 5.65e-01 1.57e+02 angle pdb=" CA ILE A 202 " pdb=" C ILE A 202 " pdb=" O ILE A 202 " ideal model delta sigma weight residual 121.27 115.46 5.81 1.04e+00 9.25e-01 3.13e+01 angle pdb=" CA ILE B 202 " pdb=" C ILE B 202 " pdb=" O ILE B 202 " ideal model delta sigma weight residual 121.27 115.49 5.78 1.04e+00 9.25e-01 3.09e+01 angle pdb=" O VAL B 334 " pdb=" C VAL B 334 " pdb=" N TYR B 335 " ideal model delta sigma weight residual 121.91 116.73 5.18 9.80e-01 1.04e+00 2.79e+01 ... (remaining 10459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.38: 3951 16.38 - 32.76: 384 32.76 - 49.14: 98 49.14 - 65.52: 24 65.52 - 81.90: 5 Dihedral angle restraints: 4462 sinusoidal: 1668 harmonic: 2794 Sorted by residual: dihedral pdb=" SG CYS B 133 " pdb=" CB CYS B 153 " pdb=" SG CYS B 153 " pdb=" CA CYS B 153 " ideal model delta sinusoidal sigma weight residual -73.00 0.31 -73.31 1 2.00e+01 2.50e-03 1.71e+01 dihedral pdb=" CA ASP A 373 " pdb=" CB ASP A 373 " pdb=" CG ASP A 373 " pdb=" OD1 ASP A 373 " ideal model delta sinusoidal sigma weight residual -30.00 -86.15 56.15 1 2.00e+01 2.50e-03 1.06e+01 dihedral pdb=" CA ASP B 373 " pdb=" CB ASP B 373 " pdb=" CG ASP B 373 " pdb=" OD1 ASP B 373 " ideal model delta sinusoidal sigma weight residual -30.00 -86.13 56.13 1 2.00e+01 2.50e-03 1.06e+01 ... (remaining 4459 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 974 0.041 - 0.082: 192 0.082 - 0.123: 50 0.123 - 0.164: 8 0.164 - 0.205: 4 Chirality restraints: 1228 Sorted by residual: chirality pdb=" CA ILE A 202 " pdb=" N ILE A 202 " pdb=" C ILE A 202 " pdb=" CB ILE A 202 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA ILE B 202 " pdb=" N ILE B 202 " pdb=" C ILE B 202 " pdb=" CB ILE B 202 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CB ILE B 202 " pdb=" CA ILE B 202 " pdb=" CG1 ILE B 202 " pdb=" CG2 ILE B 202 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.71e-01 ... (remaining 1225 not shown) Planarity restraints: 1288 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 464 " -0.017 2.00e-02 2.50e+03 3.41e-02 1.16e+01 pdb=" C SER A 464 " 0.059 2.00e-02 2.50e+03 pdb=" O SER A 464 " -0.021 2.00e-02 2.50e+03 pdb=" N GLU A 465 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 464 " 0.017 2.00e-02 2.50e+03 3.40e-02 1.16e+01 pdb=" C SER B 464 " -0.059 2.00e-02 2.50e+03 pdb=" O SER B 464 " 0.021 2.00e-02 2.50e+03 pdb=" N GLU B 465 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 203 " -0.014 2.00e-02 2.50e+03 2.86e-02 8.17e+00 pdb=" C ASN B 203 " 0.049 2.00e-02 2.50e+03 pdb=" O ASN B 203 " -0.018 2.00e-02 2.50e+03 pdb=" N LEU B 204 " -0.017 2.00e-02 2.50e+03 ... (remaining 1285 not shown) Histogram of nonbonded interaction distances: 1.34 - 2.05: 4 2.05 - 2.76: 1346 2.76 - 3.47: 10464 3.47 - 4.19: 17954 4.19 - 4.90: 32226 Nonbonded interactions: 61994 Sorted by model distance: nonbonded pdb=" C LYS B 701 " pdb=" N LEU B 702 " model vdw 1.335 3.350 nonbonded pdb=" C LYS A 701 " pdb=" N LEU A 702 " model vdw 1.336 3.350 nonbonded pdb=" SG CYS A 68 " pdb=" SG CYS A 141 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS A 133 " pdb=" SG CYS A 153 " model vdw 2.032 3.760 nonbonded pdb=" O LYS B 701 " pdb=" N LEU B 702 " model vdw 2.250 3.120 ... (remaining 61989 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: 0.00 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: 0.470 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: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.080 Process input model: 22.390 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 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 0.067 7696 Z= 0.244 Angle : 0.706 16.688 10464 Z= 0.458 Chirality : 0.037 0.205 1228 Planarity : 0.004 0.034 1288 Dihedral : 14.158 81.900 2660 Min Nonbonded Distance : 1.335 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.53 % Allowed : 4.59 % Favored : 93.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.64 (0.25), residues: 960 helix: -0.58 (0.18), residues: 706 sheet: None (None), residues: 0 loop : -2.22 (0.37), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 453 HIS 0.003 0.001 HIS A 521 PHE 0.008 0.001 PHE A 492 TYR 0.021 0.001 TYR A 335 ARG 0.002 0.000 ARG A 137 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 112 time to evaluate : 0.845 Fit side-chains REVERT: B 433 LYS cc_start: 0.8027 (ttpt) cc_final: 0.7707 (tttt) REVERT: A 433 LYS cc_start: 0.7952 (ttpt) cc_final: 0.7654 (tttt) REVERT: B 701 LYS cc_start: 0.8113 (OUTLIER) cc_final: 0.7815 (mmtm) REVERT: A 701 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7828 (mmtm) outliers start: 12 outliers final: 6 residues processed: 122 average time/residue: 0.1659 time to fit residues: 28.6929 Evaluate side-chains 89 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 81 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 373 ASP Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain B residue 701 LYS Chi-restraints excluded: chain A residue 701 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 40 optimal weight: 0.2980 chunk 24 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 56 optimal weight: 0.0170 chunk 87 optimal weight: 0.8980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 ASN ** B 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 HIS A 196 ASN ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 395 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7696 Z= 0.203 Angle : 0.529 6.760 10464 Z= 0.270 Chirality : 0.040 0.248 1228 Planarity : 0.004 0.025 1288 Dihedral : 6.532 58.460 1054 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.42 % Allowed : 9.57 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.00 (0.28), residues: 960 helix: 0.72 (0.20), residues: 718 sheet: None (None), residues: 0 loop : -2.11 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 94 HIS 0.002 0.000 HIS A 559 PHE 0.012 0.001 PHE A 120 TYR 0.013 0.001 TYR A 113 ARG 0.003 0.000 ARG B 186 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 69 time to evaluate : 0.862 Fit side-chains REVERT: B 226 TYR cc_start: 0.8259 (OUTLIER) cc_final: 0.7815 (m-80) REVERT: B 433 LYS cc_start: 0.8090 (ttpt) cc_final: 0.7764 (tttt) REVERT: B 489 MET cc_start: 0.8318 (mmt) cc_final: 0.7930 (tpp) REVERT: A 226 TYR cc_start: 0.8261 (OUTLIER) cc_final: 0.7753 (m-80) REVERT: A 433 LYS cc_start: 0.8020 (ttpt) cc_final: 0.7711 (tttt) REVERT: A 489 MET cc_start: 0.8311 (mmt) cc_final: 0.7946 (tpp) outliers start: 19 outliers final: 10 residues processed: 88 average time/residue: 0.2201 time to fit residues: 26.0972 Evaluate side-chains 75 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 63 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 226 TYR Chi-restraints excluded: chain B residue 373 ASP Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 483 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 59 optimal weight: 7.9990 chunk 24 optimal weight: 0.0970 chunk 87 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 86 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 203 ASN B 219 ASN A 203 ASN A 219 ASN A 337 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7696 Z= 0.204 Angle : 0.523 6.611 10464 Z= 0.264 Chirality : 0.040 0.248 1228 Planarity : 0.003 0.027 1288 Dihedral : 4.994 44.949 1044 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.30 % Allowed : 11.99 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.49 (0.28), residues: 960 helix: 1.14 (0.20), residues: 718 sheet: None (None), residues: 0 loop : -2.15 (0.37), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 94 HIS 0.003 0.001 HIS A 559 PHE 0.012 0.001 PHE B 194 TYR 0.016 0.001 TYR B 113 ARG 0.007 0.001 ARG A 394 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 81 time to evaluate : 0.757 Fit side-chains REVERT: B 133 CYS cc_start: 0.5521 (OUTLIER) cc_final: 0.5304 (p) REVERT: B 168 VAL cc_start: 0.8628 (t) cc_final: 0.8418 (t) REVERT: B 186 ARG cc_start: 0.7415 (mtt90) cc_final: 0.6772 (mtm110) REVERT: B 226 TYR cc_start: 0.8385 (OUTLIER) cc_final: 0.7683 (m-10) REVERT: B 253 ASP cc_start: 0.6810 (p0) cc_final: 0.6444 (p0) REVERT: B 373 ASP cc_start: 0.7958 (OUTLIER) cc_final: 0.7739 (p0) REVERT: B 433 LYS cc_start: 0.8074 (ttpt) cc_final: 0.7724 (tttt) REVERT: B 489 MET cc_start: 0.8488 (mmt) cc_final: 0.7929 (mmt) REVERT: A 226 TYR cc_start: 0.8363 (OUTLIER) cc_final: 0.7826 (m-80) REVERT: A 253 ASP cc_start: 0.6933 (p0) cc_final: 0.6568 (p0) REVERT: A 433 LYS cc_start: 0.8018 (ttpt) cc_final: 0.7685 (tttt) REVERT: A 489 MET cc_start: 0.8490 (mmt) cc_final: 0.8024 (mmt) outliers start: 18 outliers final: 9 residues processed: 97 average time/residue: 0.2327 time to fit residues: 30.0229 Evaluate side-chains 76 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 63 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 226 TYR Chi-restraints excluded: chain B residue 373 ASP Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 483 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 92 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 7696 Z= 0.223 Angle : 0.547 9.923 10464 Z= 0.269 Chirality : 0.041 0.265 1228 Planarity : 0.003 0.024 1288 Dihedral : 4.656 43.358 1044 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.04 % Allowed : 13.52 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.70 (0.28), residues: 960 helix: 1.33 (0.20), residues: 710 sheet: None (None), residues: 0 loop : -2.08 (0.36), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 94 HIS 0.003 0.001 HIS B 395 PHE 0.012 0.001 PHE A 194 TYR 0.009 0.001 TYR A 113 ARG 0.005 0.000 ARG B 186 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 63 time to evaluate : 0.831 Fit side-chains REVERT: B 133 CYS cc_start: 0.5444 (OUTLIER) cc_final: 0.5238 (p) REVERT: B 168 VAL cc_start: 0.8806 (t) cc_final: 0.8550 (t) REVERT: B 226 TYR cc_start: 0.8486 (OUTLIER) cc_final: 0.7862 (m-80) REVERT: B 253 ASP cc_start: 0.7198 (OUTLIER) cc_final: 0.6712 (p0) REVERT: B 260 MET cc_start: 0.4647 (mmm) cc_final: 0.4427 (mmm) REVERT: B 433 LYS cc_start: 0.8086 (ttpt) cc_final: 0.7789 (tttt) REVERT: B 489 MET cc_start: 0.8550 (mmt) cc_final: 0.7960 (mmt) REVERT: A 226 TYR cc_start: 0.8473 (OUTLIER) cc_final: 0.7843 (m-80) REVERT: A 253 ASP cc_start: 0.7229 (OUTLIER) cc_final: 0.6731 (p0) REVERT: A 260 MET cc_start: 0.4682 (mmm) cc_final: 0.4438 (mmm) REVERT: A 433 LYS cc_start: 0.8071 (ttpt) cc_final: 0.7792 (tttt) REVERT: A 489 MET cc_start: 0.8549 (mmt) cc_final: 0.7961 (mmt) outliers start: 16 outliers final: 8 residues processed: 75 average time/residue: 0.2131 time to fit residues: 21.7305 Evaluate side-chains 70 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 57 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 226 TYR Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 483 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 23 optimal weight: 0.4980 chunk 31 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 7696 Z= 0.335 Angle : 0.597 6.804 10464 Z= 0.300 Chirality : 0.043 0.219 1228 Planarity : 0.004 0.027 1288 Dihedral : 4.556 39.384 1040 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.81 % Allowed : 13.39 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.51 (0.28), residues: 960 helix: 1.16 (0.20), residues: 710 sheet: None (None), residues: 0 loop : -2.04 (0.36), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 94 HIS 0.003 0.001 HIS A 395 PHE 0.014 0.002 PHE B 194 TYR 0.013 0.002 TYR B 113 ARG 0.004 0.001 ARG B 186 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 53 time to evaluate : 0.826 Fit side-chains REVERT: B 117 MET cc_start: 0.8508 (mmt) cc_final: 0.8280 (mmt) REVERT: B 133 CYS cc_start: 0.5892 (OUTLIER) cc_final: 0.5617 (p) REVERT: B 176 THR cc_start: 0.8534 (OUTLIER) cc_final: 0.8255 (p) REVERT: B 186 ARG cc_start: 0.7307 (mtt90) cc_final: 0.7020 (mtt-85) REVERT: B 226 TYR cc_start: 0.8732 (OUTLIER) cc_final: 0.7966 (m-80) REVERT: B 253 ASP cc_start: 0.7606 (OUTLIER) cc_final: 0.7137 (p0) REVERT: B 260 MET cc_start: 0.4717 (mmm) cc_final: 0.4490 (mmm) REVERT: B 489 MET cc_start: 0.8651 (mmt) cc_final: 0.8076 (mmt) REVERT: A 176 THR cc_start: 0.8534 (OUTLIER) cc_final: 0.8254 (p) REVERT: A 226 TYR cc_start: 0.8726 (OUTLIER) cc_final: 0.7969 (m-80) REVERT: A 253 ASP cc_start: 0.7597 (OUTLIER) cc_final: 0.7130 (p0) REVERT: A 260 MET cc_start: 0.4741 (mmm) cc_final: 0.4485 (mmm) REVERT: A 489 MET cc_start: 0.8648 (mmt) cc_final: 0.8070 (mmt) outliers start: 22 outliers final: 13 residues processed: 71 average time/residue: 0.2147 time to fit residues: 20.8324 Evaluate side-chains 69 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 49 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 226 TYR Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 521 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 0.3980 chunk 18 optimal weight: 0.5980 chunk 54 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 92 optimal weight: 0.3980 chunk 77 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 89 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7696 Z= 0.171 Angle : 0.504 6.822 10464 Z= 0.252 Chirality : 0.039 0.189 1228 Planarity : 0.003 0.025 1288 Dihedral : 4.337 38.444 1040 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.04 % Allowed : 14.03 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.05 (0.28), residues: 960 helix: 1.57 (0.20), residues: 710 sheet: None (None), residues: 0 loop : -1.91 (0.37), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 94 HIS 0.001 0.000 HIS B 559 PHE 0.009 0.001 PHE A 194 TYR 0.006 0.001 TYR A 52 ARG 0.004 0.000 ARG B 186 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 55 time to evaluate : 0.793 Fit side-chains REVERT: B 133 CYS cc_start: 0.5629 (OUTLIER) cc_final: 0.5196 (p) REVERT: B 168 VAL cc_start: 0.8811 (t) cc_final: 0.8544 (t) REVERT: B 186 ARG cc_start: 0.7283 (mtt90) cc_final: 0.6823 (mtm110) REVERT: B 226 TYR cc_start: 0.8610 (OUTLIER) cc_final: 0.7781 (m-80) REVERT: B 253 ASP cc_start: 0.7414 (OUTLIER) cc_final: 0.6971 (p0) REVERT: A 226 TYR cc_start: 0.8600 (OUTLIER) cc_final: 0.7783 (m-80) REVERT: A 253 ASP cc_start: 0.7406 (OUTLIER) cc_final: 0.6977 (p0) outliers start: 16 outliers final: 10 residues processed: 68 average time/residue: 0.1696 time to fit residues: 16.8294 Evaluate side-chains 69 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 54 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 226 TYR Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 521 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 9.9990 chunk 52 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 92 optimal weight: 9.9990 chunk 57 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 7696 Z= 0.226 Angle : 0.514 6.664 10464 Z= 0.259 Chirality : 0.040 0.181 1228 Planarity : 0.003 0.026 1288 Dihedral : 4.325 38.179 1040 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.30 % Allowed : 14.16 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.07 (0.28), residues: 960 helix: 1.58 (0.20), residues: 710 sheet: None (None), residues: 0 loop : -1.87 (0.37), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 94 HIS 0.002 0.000 HIS B 395 PHE 0.011 0.001 PHE B 194 TYR 0.008 0.001 TYR A 52 ARG 0.003 0.000 ARG B 186 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 56 time to evaluate : 0.811 Fit side-chains REVERT: B 117 MET cc_start: 0.8330 (mmt) cc_final: 0.7932 (mmt) REVERT: B 133 CYS cc_start: 0.5732 (OUTLIER) cc_final: 0.5292 (p) REVERT: B 168 VAL cc_start: 0.8824 (t) cc_final: 0.8564 (t) REVERT: B 186 ARG cc_start: 0.7251 (mtt90) cc_final: 0.6802 (mtm110) REVERT: B 226 TYR cc_start: 0.8666 (OUTLIER) cc_final: 0.7787 (m-80) REVERT: B 253 ASP cc_start: 0.7481 (OUTLIER) cc_final: 0.7028 (p0) REVERT: B 489 MET cc_start: 0.8541 (mmt) cc_final: 0.7958 (mmt) REVERT: A 207 ILE cc_start: 0.8245 (mm) cc_final: 0.8041 (mt) REVERT: A 226 TYR cc_start: 0.8660 (OUTLIER) cc_final: 0.7805 (m-80) REVERT: A 253 ASP cc_start: 0.7462 (OUTLIER) cc_final: 0.7032 (p0) REVERT: A 489 MET cc_start: 0.8511 (mmt) cc_final: 0.7912 (mmt) outliers start: 18 outliers final: 11 residues processed: 70 average time/residue: 0.1715 time to fit residues: 17.4754 Evaluate side-chains 72 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 56 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 226 TYR Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 521 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 0.0270 chunk 18 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 58 optimal weight: 9.9990 chunk 63 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 88 optimal weight: 0.0870 chunk 80 optimal weight: 0.5980 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7696 Z= 0.170 Angle : 0.485 6.457 10464 Z= 0.244 Chirality : 0.039 0.174 1228 Planarity : 0.003 0.025 1288 Dihedral : 4.218 37.424 1040 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.17 % Allowed : 14.92 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.34 (0.28), residues: 960 helix: 1.78 (0.20), residues: 710 sheet: None (None), residues: 0 loop : -1.82 (0.37), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 94 HIS 0.001 0.000 HIS B 560 PHE 0.009 0.001 PHE A 194 TYR 0.006 0.001 TYR A 52 ARG 0.003 0.000 ARG B 186 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 58 time to evaluate : 0.835 Fit side-chains REVERT: B 133 CYS cc_start: 0.5690 (OUTLIER) cc_final: 0.5250 (p) REVERT: B 168 VAL cc_start: 0.8833 (t) cc_final: 0.8577 (t) REVERT: B 186 ARG cc_start: 0.7167 (mtt90) cc_final: 0.6772 (mtm110) REVERT: B 207 ILE cc_start: 0.8215 (mm) cc_final: 0.8004 (mt) REVERT: B 226 TYR cc_start: 0.8593 (OUTLIER) cc_final: 0.7698 (m-80) REVERT: B 253 ASP cc_start: 0.7407 (OUTLIER) cc_final: 0.6980 (p0) REVERT: B 341 THR cc_start: 0.8138 (p) cc_final: 0.7774 (p) REVERT: A 117 MET cc_start: 0.8121 (mmt) cc_final: 0.7362 (mmm) REVERT: A 226 TYR cc_start: 0.8584 (OUTLIER) cc_final: 0.7713 (m-80) REVERT: A 253 ASP cc_start: 0.7403 (OUTLIER) cc_final: 0.6991 (p0) REVERT: A 341 THR cc_start: 0.8134 (p) cc_final: 0.7764 (p) outliers start: 17 outliers final: 12 residues processed: 71 average time/residue: 0.1743 time to fit residues: 17.9349 Evaluate side-chains 73 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 56 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 226 TYR Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 521 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 1.9990 chunk 88 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 77 optimal weight: 4.9990 chunk 81 optimal weight: 0.6980 chunk 85 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 91 optimal weight: 0.3980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 ASN A 196 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7696 Z= 0.199 Angle : 0.501 6.581 10464 Z= 0.252 Chirality : 0.040 0.269 1228 Planarity : 0.003 0.026 1288 Dihedral : 4.214 37.133 1040 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.42 % Allowed : 14.92 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.31 (0.28), residues: 960 helix: 1.76 (0.20), residues: 710 sheet: None (None), residues: 0 loop : -1.82 (0.37), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 94 HIS 0.001 0.000 HIS B 395 PHE 0.010 0.001 PHE A 194 TYR 0.007 0.001 TYR A 52 ARG 0.003 0.000 ARG B 186 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 60 time to evaluate : 0.864 Fit side-chains REVERT: B 133 CYS cc_start: 0.5671 (OUTLIER) cc_final: 0.5267 (p) REVERT: B 168 VAL cc_start: 0.8848 (t) cc_final: 0.8598 (t) REVERT: B 186 ARG cc_start: 0.7161 (mtt90) cc_final: 0.6797 (mtm110) REVERT: B 226 TYR cc_start: 0.8637 (OUTLIER) cc_final: 0.7799 (m-80) REVERT: B 253 ASP cc_start: 0.7439 (OUTLIER) cc_final: 0.7005 (p0) REVERT: B 341 THR cc_start: 0.8203 (p) cc_final: 0.7833 (p) REVERT: B 489 MET cc_start: 0.8419 (mmt) cc_final: 0.7984 (tpp) REVERT: A 226 TYR cc_start: 0.8640 (OUTLIER) cc_final: 0.7696 (m-80) REVERT: A 253 ASP cc_start: 0.7600 (OUTLIER) cc_final: 0.7167 (p0) REVERT: A 341 THR cc_start: 0.8192 (p) cc_final: 0.7816 (p) REVERT: A 489 MET cc_start: 0.8413 (mmt) cc_final: 0.7979 (tpp) outliers start: 19 outliers final: 13 residues processed: 75 average time/residue: 0.1752 time to fit residues: 19.1177 Evaluate side-chains 77 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 59 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 226 TYR Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 521 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 95 optimal weight: 0.5980 chunk 88 optimal weight: 0.0970 chunk 76 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 58 optimal weight: 10.0000 chunk 46 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 81 optimal weight: 0.5980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7696 Z= 0.190 Angle : 0.496 6.519 10464 Z= 0.250 Chirality : 0.040 0.269 1228 Planarity : 0.003 0.026 1288 Dihedral : 4.174 36.638 1040 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.30 % Allowed : 15.05 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.35 (0.28), residues: 960 helix: 1.79 (0.20), residues: 710 sheet: None (None), residues: 0 loop : -1.82 (0.37), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 94 HIS 0.001 0.000 HIS B 395 PHE 0.009 0.001 PHE A 194 TYR 0.007 0.001 TYR A 52 ARG 0.003 0.000 ARG B 186 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 60 time to evaluate : 0.824 Fit side-chains REVERT: B 133 CYS cc_start: 0.5851 (OUTLIER) cc_final: 0.5455 (p) REVERT: B 168 VAL cc_start: 0.8846 (t) cc_final: 0.8588 (t) REVERT: B 186 ARG cc_start: 0.7177 (mtt90) cc_final: 0.6840 (mtm110) REVERT: B 226 TYR cc_start: 0.8622 (OUTLIER) cc_final: 0.7711 (m-80) REVERT: B 253 ASP cc_start: 0.7432 (OUTLIER) cc_final: 0.7023 (p0) REVERT: B 341 THR cc_start: 0.8185 (p) cc_final: 0.7816 (p) REVERT: B 489 MET cc_start: 0.8466 (mmt) cc_final: 0.8069 (tpp) REVERT: B 518 MET cc_start: 0.5786 (mmm) cc_final: 0.5568 (mmm) REVERT: A 117 MET cc_start: 0.8172 (mmt) cc_final: 0.7474 (mmm) REVERT: A 226 TYR cc_start: 0.8612 (OUTLIER) cc_final: 0.7718 (m-80) REVERT: A 253 ASP cc_start: 0.7671 (OUTLIER) cc_final: 0.7194 (p0) REVERT: A 341 THR cc_start: 0.8180 (p) cc_final: 0.7807 (p) REVERT: A 489 MET cc_start: 0.8461 (mmt) cc_final: 0.8064 (tpp) REVERT: A 518 MET cc_start: 0.5768 (mmm) cc_final: 0.5551 (mmm) outliers start: 18 outliers final: 11 residues processed: 74 average time/residue: 0.1670 time to fit residues: 18.1218 Evaluate side-chains 75 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 59 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 226 TYR Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 483 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 11 optimal weight: 0.2980 chunk 21 optimal weight: 0.4980 chunk 76 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 66 optimal weight: 0.0770 chunk 4 optimal weight: 5.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- 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 = 0.3480 r_free = 0.3480 target = 0.137446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.101889 restraints weight = 7917.249| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 1.60 r_work: 0.2931 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7696 Z= 0.171 Angle : 0.488 6.499 10464 Z= 0.246 Chirality : 0.040 0.255 1228 Planarity : 0.003 0.025 1288 Dihedral : 4.145 36.283 1040 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.04 % Allowed : 15.69 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.43 (0.28), residues: 960 helix: 1.86 (0.20), residues: 710 sheet: None (None), residues: 0 loop : -1.81 (0.37), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 94 HIS 0.001 0.000 HIS B 395 PHE 0.009 0.001 PHE A 194 TYR 0.006 0.001 TYR A 52 ARG 0.003 0.000 ARG B 186 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1696.85 seconds wall clock time: 31 minutes 43.01 seconds (1903.01 seconds total)