Starting phenix.real_space_refine on Sat Nov 16 16:11:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zxk_60542/11_2024/8zxk_60542.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zxk_60542/11_2024/8zxk_60542.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zxk_60542/11_2024/8zxk_60542.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zxk_60542/11_2024/8zxk_60542.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zxk_60542/11_2024/8zxk_60542.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zxk_60542/11_2024/8zxk_60542.cif" } resolution = 2.76 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= 0.003 sd= 0.047 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 48 5.16 5 C 7844 2.51 5 N 1794 2.21 5 O 1967 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 11653 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 3866 Classifications: {'peptide': 495} Link IDs: {'CIS': 3, 'PTRANS': 17, 'TRANS': 474} Chain: "B" Number of atoms: 3900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3900 Classifications: {'peptide': 499} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 481} Chain: "C" Number of atoms: 3875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3875 Classifications: {'peptide': 496} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 477} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'KEN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'KEN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'KEN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.88, per 1000 atoms: 0.68 Number of scatterers: 11653 At special positions: 0 Unit cell: (111.3, 116.6, 79.5, 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 48 16.00 O 1967 8.00 N 1794 7.00 C 7844 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: 3.76 Conformation dependent library (CDL) restraints added in 1.5 seconds 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2710 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 0 sheets defined 84.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 14 through 35 removed outlier: 5.266A pdb=" N THR A 20 " --> pdb=" O PRO A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 74 removed outlier: 3.656A pdb=" N GLY A 40 " --> pdb=" O PRO A 36 " (cutoff:3.500A) Proline residue: A 44 - end of helix removed outlier: 5.741A pdb=" N TRP A 56 " --> pdb=" O SER A 52 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N PHE A 57 " --> pdb=" O ASN A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 80 removed outlier: 3.717A pdb=" N ARG A 79 " --> pdb=" O LYS A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 100 removed outlier: 3.645A pdb=" N ALA A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 113 removed outlier: 3.659A pdb=" N MET A 110 " --> pdb=" O GLY A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 123 Processing helix chain 'A' and resid 130 through 147 Processing helix chain 'A' and resid 147 through 167 removed outlier: 3.564A pdb=" N TRP A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 177 No H-bonds generated for 'chain 'A' and resid 175 through 177' Processing helix chain 'A' and resid 178 through 183 Processing helix chain 'A' and resid 190 through 226 removed outlier: 3.883A pdb=" N ILE A 194 " --> pdb=" O TRP A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 249 Processing helix chain 'A' and resid 262 through 279 Processing helix chain 'A' and resid 280 through 298 Processing helix chain 'A' and resid 298 through 304 Processing helix chain 'A' and resid 318 through 340 Proline residue: A 331 - end of helix removed outlier: 3.975A pdb=" N PHE A 336 " --> pdb=" O PHE A 332 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE A 340 " --> pdb=" O PHE A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 379 removed outlier: 4.350A pdb=" N VAL A 356 " --> pdb=" O GLY A 352 " (cutoff:3.500A) Proline residue: A 357 - end of helix removed outlier: 3.987A pdb=" N SER A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 390 removed outlier: 3.542A pdb=" N ALA A 385 " --> pdb=" O VAL A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 400 Processing helix chain 'A' and resid 404 through 437 Processing helix chain 'A' and resid 443 through 464 removed outlier: 4.172A pdb=" N ARG A 447 " --> pdb=" O PRO A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 503 Proline residue: A 480 - end of helix Processing helix chain 'B' and resid 16 through 35 Processing helix chain 'B' and resid 35 through 74 Proline residue: B 44 - end of helix removed outlier: 5.701A pdb=" N TRP B 56 " --> pdb=" O SER B 52 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N PHE B 57 " --> pdb=" O ASN B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 80 removed outlier: 4.011A pdb=" N ARG B 79 " --> pdb=" O LYS B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 101 Processing helix chain 'B' and resid 106 through 123 removed outlier: 5.372A pdb=" N ILE B 114 " --> pdb=" O MET B 110 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ALA B 115 " --> pdb=" O PHE B 111 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU B 116 " --> pdb=" O PHE B 112 " (cutoff:3.500A) Proline residue: B 117 - end of helix Processing helix chain 'B' and resid 130 through 147 Processing helix chain 'B' and resid 147 through 167 removed outlier: 3.614A pdb=" N TRP B 151 " --> pdb=" O GLY B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 177 No H-bonds generated for 'chain 'B' and resid 175 through 177' Processing helix chain 'B' and resid 178 through 183 Processing helix chain 'B' and resid 190 through 226 removed outlier: 3.720A pdb=" N ILE B 194 " --> pdb=" O TRP B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 251 removed outlier: 3.741A pdb=" N THR B 246 " --> pdb=" O ILE B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 279 removed outlier: 3.754A pdb=" N LYS B 258 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 298 Processing helix chain 'B' and resid 298 through 304 Processing helix chain 'B' and resid 313 through 317 Processing helix chain 'B' and resid 318 through 340 Proline residue: B 331 - end of helix removed outlier: 3.874A pdb=" N PHE B 336 " --> pdb=" O PHE B 332 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE B 340 " --> pdb=" O PHE B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 379 removed outlier: 4.364A pdb=" N VAL B 356 " --> pdb=" O GLY B 352 " (cutoff:3.500A) Proline residue: B 357 - end of helix removed outlier: 3.956A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY B 379 " --> pdb=" O THR B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 390 Processing helix chain 'B' and resid 393 through 400 Processing helix chain 'B' and resid 404 through 437 Processing helix chain 'B' and resid 443 through 464 removed outlier: 3.942A pdb=" N ARG B 447 " --> pdb=" O PRO B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 503 Proline residue: B 480 - end of helix removed outlier: 4.008A pdb=" N VAL B 483 " --> pdb=" O LEU B 479 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR B 490 " --> pdb=" O LEU B 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 35 removed outlier: 3.535A pdb=" N ILE C 19 " --> pdb=" O PRO C 15 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR C 20 " --> pdb=" O PRO C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 74 removed outlier: 3.580A pdb=" N VAL C 41 " --> pdb=" O GLU C 37 " (cutoff:3.500A) Proline residue: C 44 - end of helix removed outlier: 5.694A pdb=" N TRP C 56 " --> pdb=" O SER C 52 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N PHE C 57 " --> pdb=" O ASN C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 80 removed outlier: 3.859A pdb=" N ARG C 79 " --> pdb=" O LYS C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 101 Processing helix chain 'C' and resid 106 through 113 Processing helix chain 'C' and resid 114 through 123 Processing helix chain 'C' and resid 130 through 147 Processing helix chain 'C' and resid 147 through 167 removed outlier: 3.586A pdb=" N TRP C 151 " --> pdb=" O GLY C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 186 removed outlier: 3.526A pdb=" N PHE C 178 " --> pdb=" O ARG C 175 " (cutoff:3.500A) Proline residue: C 180 - end of helix removed outlier: 4.859A pdb=" N GLY C 183 " --> pdb=" O PRO C 180 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N GLU C 184 " --> pdb=" O PHE C 181 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ILE C 186 " --> pdb=" O GLY C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 226 Processing helix chain 'C' and resid 230 through 251 removed outlier: 3.979A pdb=" N SER C 248 " --> pdb=" O ILE C 244 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL C 249 " --> pdb=" O ALA C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 279 removed outlier: 3.856A pdb=" N ASN C 262 " --> pdb=" O LYS C 258 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET C 265 " --> pdb=" O SER C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 298 Processing helix chain 'C' and resid 298 through 304 Processing helix chain 'C' and resid 318 through 340 Proline residue: C 331 - end of helix removed outlier: 4.244A pdb=" N SER C 335 " --> pdb=" O PRO C 331 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE C 340 " --> pdb=" O PHE C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 378 removed outlier: 4.481A pdb=" N VAL C 356 " --> pdb=" O GLY C 352 " (cutoff:3.500A) Proline residue: C 357 - end of helix removed outlier: 3.977A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 390 Processing helix chain 'C' and resid 393 through 400 Processing helix chain 'C' and resid 404 through 437 Processing helix chain 'C' and resid 443 through 464 removed outlier: 3.861A pdb=" N ARG C 447 " --> pdb=" O PRO C 443 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 503 Proline residue: C 480 - end of helix 916 hydrogen bonds defined for protein. 2718 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: 3.73 Time building geometry restraints manager: 3.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3400 1.34 - 1.46: 2567 1.46 - 1.57: 5950 1.57 - 1.69: 0 1.69 - 1.81: 90 Bond restraints: 12007 Sorted by residual: bond pdb=" C PRO C 15 " pdb=" N PRO C 16 " ideal model delta sigma weight residual 1.337 1.357 -0.020 1.24e-02 6.50e+03 2.48e+00 bond pdb=" C LEU B 479 " pdb=" N PRO B 480 " ideal model delta sigma weight residual 1.337 1.353 -0.016 1.24e-02 6.50e+03 1.71e+00 bond pdb=" CB ILE A 186 " pdb=" CG1 ILE A 186 " ideal model delta sigma weight residual 1.530 1.556 -0.026 2.00e-02 2.50e+03 1.68e+00 bond pdb=" NE1 KEN C 601 " pdb=" CC1 KEN C 601 " ideal model delta sigma weight residual 1.445 1.469 -0.024 2.00e-02 2.50e+03 1.46e+00 bond pdb=" NE1 KEN A 601 " pdb=" CA1 KEN A 601 " ideal model delta sigma weight residual 1.446 1.470 -0.024 2.00e-02 2.50e+03 1.45e+00 ... (remaining 12002 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 16219 2.28 - 4.56: 130 4.56 - 6.84: 28 6.84 - 9.12: 2 9.12 - 11.40: 2 Bond angle restraints: 16381 Sorted by residual: angle pdb=" C GLU A 441 " pdb=" N SER A 442 " pdb=" CA SER A 442 " ideal model delta sigma weight residual 121.70 133.10 -11.40 1.80e+00 3.09e-01 4.01e+01 angle pdb=" C LYS A 255 " pdb=" N GLY A 256 " pdb=" CA GLY A 256 " ideal model delta sigma weight residual 121.70 131.54 -9.84 1.80e+00 3.09e-01 2.99e+01 angle pdb=" CB ILE A 186 " pdb=" CG1 ILE A 186 " pdb=" CD1 ILE A 186 " ideal model delta sigma weight residual 113.80 122.02 -8.22 2.10e+00 2.27e-01 1.53e+01 angle pdb=" N ILE B 186 " pdb=" CA ILE B 186 " pdb=" C ILE B 186 " ideal model delta sigma weight residual 106.21 110.27 -4.06 1.07e+00 8.73e-01 1.44e+01 angle pdb=" CA TRP B 329 " pdb=" CB TRP B 329 " pdb=" CG TRP B 329 " ideal model delta sigma weight residual 113.60 120.20 -6.60 1.90e+00 2.77e-01 1.21e+01 ... (remaining 16376 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 5795 17.80 - 35.59: 705 35.59 - 53.39: 158 53.39 - 71.18: 24 71.18 - 88.98: 12 Dihedral angle restraints: 6694 sinusoidal: 2464 harmonic: 4230 Sorted by residual: dihedral pdb=" CA THR B 103 " pdb=" C THR B 103 " pdb=" N GLY B 104 " pdb=" CA GLY B 104 " ideal model delta harmonic sigma weight residual 180.00 161.90 18.10 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CB GLU A 37 " pdb=" CG GLU A 37 " pdb=" CD GLU A 37 " pdb=" OE1 GLU A 37 " ideal model delta sinusoidal sigma weight residual 0.00 88.98 -88.98 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CA TRP C 323 " pdb=" CB TRP C 323 " pdb=" CG TRP C 323 " pdb=" CD1 TRP C 323 " ideal model delta sinusoidal sigma weight residual 90.00 159.01 -69.01 2 2.00e+01 2.50e-03 1.05e+01 ... (remaining 6691 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1270 0.034 - 0.068: 460 0.068 - 0.101: 135 0.101 - 0.135: 20 0.135 - 0.169: 4 Chirality restraints: 1889 Sorted by residual: chirality pdb=" CG LEU C 23 " pdb=" CB LEU C 23 " pdb=" CD1 LEU C 23 " pdb=" CD2 LEU C 23 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.14e-01 chirality pdb=" CB ILE A 186 " pdb=" CA ILE A 186 " pdb=" CG1 ILE A 186 " pdb=" CG2 ILE A 186 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.98e-01 chirality pdb=" CA LEU C 23 " pdb=" N LEU C 23 " pdb=" C LEU C 23 " pdb=" CB LEU C 23 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.95e-01 ... (remaining 1886 not shown) Planarity restraints: 1975 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 14 " 0.036 5.00e-02 4.00e+02 5.53e-02 4.90e+00 pdb=" N PRO A 15 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 15 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 15 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 366 " -0.011 2.00e-02 2.50e+03 2.12e-02 4.51e+00 pdb=" C ASN A 366 " 0.037 2.00e-02 2.50e+03 pdb=" O ASN A 366 " -0.014 2.00e-02 2.50e+03 pdb=" N VAL A 367 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 366 " 0.010 2.00e-02 2.50e+03 1.94e-02 3.77e+00 pdb=" C ASN C 366 " -0.034 2.00e-02 2.50e+03 pdb=" O ASN C 366 " 0.013 2.00e-02 2.50e+03 pdb=" N VAL C 367 " 0.011 2.00e-02 2.50e+03 ... (remaining 1972 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 339 2.72 - 3.26: 12099 3.26 - 3.81: 20987 3.81 - 4.35: 24860 4.35 - 4.90: 43652 Nonbonded interactions: 101937 Sorted by model distance: nonbonded pdb=" O SER C 341 " pdb=" OG SER C 341 " model vdw 2.171 3.040 nonbonded pdb=" O PHE A 299 " pdb=" OG SER A 303 " model vdw 2.206 3.040 nonbonded pdb=" O PHE C 299 " pdb=" OG SER C 303 " model vdw 2.220 3.040 nonbonded pdb=" O LEU C 177 " pdb=" OG SER C 491 " model vdw 2.231 3.040 nonbonded pdb=" OE1 GLN B 47 " pdb=" OG1 THR B 472 " model vdw 2.246 3.040 ... (remaining 101932 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' and (resid 10 through 504 or resid 601)) selection = (chain 'C' and (resid 10 through 504 or resid 601)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.920 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: 0.120 Check model and map are aligned: 0.000 Set scattering table: 0.100 Process input model: 29.120 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.050 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:15.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 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 : 0.003 0.037 12007 Z= 0.188 Angle : 0.543 11.395 16381 Z= 0.299 Chirality : 0.038 0.169 1889 Planarity : 0.004 0.055 1975 Dihedral : 16.405 88.978 3984 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.16 % Allowed : 24.98 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.48 (0.22), residues: 1484 helix: 2.15 (0.15), residues: 1167 sheet: None (None), residues: 0 loop : -0.25 (0.37), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 329 HIS 0.002 0.001 HIS C 192 PHE 0.022 0.002 PHE B 417 TYR 0.008 0.001 TYR A 295 ARG 0.003 0.000 ARG A 344 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 145 time to evaluate : 1.273 Fit side-chains REVERT: B 19 ILE cc_start: 0.7971 (mm) cc_final: 0.7745 (mp) REVERT: B 105 MET cc_start: 0.2930 (mmm) cc_final: 0.2617 (mpp) REVERT: C 93 LYS cc_start: 0.4598 (pttp) cc_final: 0.4094 (ptpt) outliers start: 2 outliers final: 0 residues processed: 147 average time/residue: 0.9828 time to fit residues: 162.0264 Evaluate side-chains 139 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 115 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 133 optimal weight: 0.1980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 446 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.0583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12007 Z= 0.203 Angle : 0.520 6.858 16381 Z= 0.284 Chirality : 0.039 0.148 1889 Planarity : 0.004 0.049 1975 Dihedral : 3.993 17.528 1547 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 4.07 % Allowed : 21.16 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.61 (0.22), residues: 1484 helix: 2.19 (0.15), residues: 1178 sheet: None (None), residues: 0 loop : -0.06 (0.38), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 329 HIS 0.003 0.001 HIS C 374 PHE 0.024 0.002 PHE C 122 TYR 0.008 0.001 TYR A 295 ARG 0.003 0.000 ARG C 168 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 145 time to evaluate : 1.431 Fit side-chains REVERT: A 93 LYS cc_start: 0.5832 (OUTLIER) cc_final: 0.5268 (ttpt) REVERT: A 181 PHE cc_start: 0.7394 (m-10) cc_final: 0.7135 (m-10) REVERT: A 184 GLU cc_start: 0.6932 (OUTLIER) cc_final: 0.6494 (mm-30) REVERT: B 19 ILE cc_start: 0.7905 (mm) cc_final: 0.7663 (mp) REVERT: B 93 LYS cc_start: 0.5282 (OUTLIER) cc_final: 0.5029 (ttpt) REVERT: C 93 LYS cc_start: 0.4668 (pttp) cc_final: 0.4141 (ptpt) REVERT: C 301 ASP cc_start: 0.7257 (t0) cc_final: 0.6976 (t0) outliers start: 50 outliers final: 16 residues processed: 182 average time/residue: 0.8453 time to fit residues: 175.5312 Evaluate side-chains 153 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain C residue 323 TRP Chi-restraints excluded: chain C residue 330 SER Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 488 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 74 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 36 optimal weight: 0.4980 chunk 133 optimal weight: 1.9990 chunk 144 optimal weight: 0.9980 chunk 119 optimal weight: 3.9990 chunk 132 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.0687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12007 Z= 0.211 Angle : 0.524 7.079 16381 Z= 0.284 Chirality : 0.039 0.147 1889 Planarity : 0.004 0.046 1975 Dihedral : 4.012 18.117 1547 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 4.39 % Allowed : 20.83 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.22), residues: 1484 helix: 2.17 (0.15), residues: 1176 sheet: None (None), residues: 0 loop : -0.15 (0.38), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 329 HIS 0.002 0.001 HIS C 187 PHE 0.023 0.002 PHE B 122 TYR 0.009 0.001 TYR C 490 ARG 0.002 0.000 ARG C 168 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 140 time to evaluate : 1.388 Fit side-chains REVERT: A 93 LYS cc_start: 0.5829 (OUTLIER) cc_final: 0.5274 (ttpt) REVERT: A 181 PHE cc_start: 0.7397 (m-10) cc_final: 0.7106 (m-10) REVERT: A 184 GLU cc_start: 0.6957 (OUTLIER) cc_final: 0.6454 (mm-30) REVERT: A 265 MET cc_start: 0.7725 (mmp) cc_final: 0.7324 (ttp) REVERT: A 329 TRP cc_start: 0.6835 (OUTLIER) cc_final: 0.6405 (t60) REVERT: B 19 ILE cc_start: 0.7914 (mm) cc_final: 0.7672 (mp) REVERT: B 93 LYS cc_start: 0.5284 (OUTLIER) cc_final: 0.5002 (ttpt) REVERT: C 93 LYS cc_start: 0.4660 (pttp) cc_final: 0.4136 (ptpt) REVERT: C 126 ARG cc_start: 0.8960 (OUTLIER) cc_final: 0.7895 (mtm180) REVERT: C 301 ASP cc_start: 0.7305 (t0) cc_final: 0.7092 (t0) outliers start: 54 outliers final: 25 residues processed: 178 average time/residue: 0.8496 time to fit residues: 170.0834 Evaluate side-chains 167 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 137 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 323 TRP Chi-restraints excluded: chain A residue 329 TRP Chi-restraints excluded: chain A residue 404 PHE Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain B residue 13 ILE Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 323 TRP Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 126 ARG Chi-restraints excluded: chain C residue 323 TRP Chi-restraints excluded: chain C residue 330 SER Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 488 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 132 optimal weight: 0.8980 chunk 100 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 134 optimal weight: 0.0770 chunk 142 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 127 optimal weight: 0.7980 chunk 38 optimal weight: 0.2980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 ASN ** C 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.0788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12007 Z= 0.175 Angle : 0.505 7.790 16381 Z= 0.274 Chirality : 0.038 0.144 1889 Planarity : 0.004 0.045 1975 Dihedral : 3.922 16.017 1547 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 4.96 % Allowed : 21.07 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.68 (0.22), residues: 1484 helix: 2.28 (0.15), residues: 1174 sheet: None (None), residues: 0 loop : -0.18 (0.38), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 329 HIS 0.002 0.001 HIS A 192 PHE 0.023 0.002 PHE B 417 TYR 0.008 0.001 TYR A 295 ARG 0.002 0.000 ARG C 168 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 141 time to evaluate : 1.181 Fit side-chains REVERT: A 93 LYS cc_start: 0.5786 (OUTLIER) cc_final: 0.5196 (ttpt) REVERT: A 265 MET cc_start: 0.7729 (mmp) cc_final: 0.7350 (tmm) REVERT: B 19 ILE cc_start: 0.7841 (mm) cc_final: 0.7609 (mp) REVERT: B 93 LYS cc_start: 0.5242 (OUTLIER) cc_final: 0.4969 (ttpt) REVERT: C 93 LYS cc_start: 0.4579 (pttp) cc_final: 0.4139 (ptpt) REVERT: C 126 ARG cc_start: 0.8956 (OUTLIER) cc_final: 0.7926 (mtm180) outliers start: 61 outliers final: 31 residues processed: 189 average time/residue: 0.8144 time to fit residues: 174.4776 Evaluate side-chains 171 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 137 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 323 TRP Chi-restraints excluded: chain A residue 404 PHE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain B residue 13 ILE Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 323 TRP Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 126 ARG Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 392 SER Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 488 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 118 optimal weight: 0.9990 chunk 80 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 58 optimal weight: 5.9990 chunk 121 optimal weight: 0.9990 chunk 98 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 454 GLN C 123 ASN C 140 GLN ** C 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.0850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12007 Z= 0.212 Angle : 0.530 8.911 16381 Z= 0.285 Chirality : 0.039 0.156 1889 Planarity : 0.004 0.044 1975 Dihedral : 3.985 16.641 1547 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 4.88 % Allowed : 21.40 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.60 (0.22), residues: 1484 helix: 2.20 (0.15), residues: 1175 sheet: None (None), residues: 0 loop : -0.14 (0.39), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 329 HIS 0.002 0.001 HIS C 374 PHE 0.023 0.002 PHE B 122 TYR 0.009 0.001 TYR C 490 ARG 0.003 0.000 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 142 time to evaluate : 1.292 Fit side-chains revert: symmetry clash REVERT: A 93 LYS cc_start: 0.5783 (OUTLIER) cc_final: 0.5196 (ttpt) REVERT: A 265 MET cc_start: 0.7756 (mmp) cc_final: 0.7401 (ttt) REVERT: B 19 ILE cc_start: 0.7880 (mm) cc_final: 0.7646 (mp) REVERT: B 93 LYS cc_start: 0.5254 (OUTLIER) cc_final: 0.4971 (ttpt) REVERT: C 93 LYS cc_start: 0.4611 (pttp) cc_final: 0.4168 (ptpt) REVERT: C 126 ARG cc_start: 0.8964 (OUTLIER) cc_final: 0.7889 (mtm180) outliers start: 60 outliers final: 37 residues processed: 190 average time/residue: 0.7942 time to fit residues: 171.3349 Evaluate side-chains 177 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 137 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 323 TRP Chi-restraints excluded: chain A residue 404 PHE Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain B residue 13 ILE Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 323 TRP Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 126 ARG Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 250 PHE Chi-restraints excluded: chain C residue 323 TRP Chi-restraints excluded: chain C residue 330 SER Chi-restraints excluded: chain C residue 392 SER Chi-restraints excluded: chain C residue 404 PHE Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 488 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 47 optimal weight: 0.5980 chunk 127 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 118 optimal weight: 0.6980 chunk 65 optimal weight: 4.9990 chunk 11 optimal weight: 0.0470 chunk 74 optimal weight: 7.9990 chunk 137 optimal weight: 0.8980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 123 ASN ** C 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.0889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12007 Z= 0.179 Angle : 0.515 9.758 16381 Z= 0.277 Chirality : 0.038 0.154 1889 Planarity : 0.004 0.043 1975 Dihedral : 3.927 16.515 1547 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 5.53 % Allowed : 20.83 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.71 (0.22), residues: 1484 helix: 2.29 (0.15), residues: 1176 sheet: None (None), residues: 0 loop : -0.16 (0.39), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 329 HIS 0.002 0.001 HIS C 120 PHE 0.025 0.002 PHE B 417 TYR 0.008 0.001 TYR A 295 ARG 0.003 0.000 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 145 time to evaluate : 1.170 Fit side-chains REVERT: A 93 LYS cc_start: 0.5768 (OUTLIER) cc_final: 0.5184 (ttpt) REVERT: A 265 MET cc_start: 0.7747 (mmp) cc_final: 0.7419 (ttt) REVERT: B 19 ILE cc_start: 0.7880 (mm) cc_final: 0.7554 (mp) REVERT: B 93 LYS cc_start: 0.5217 (OUTLIER) cc_final: 0.4930 (ttpt) REVERT: B 123 ASN cc_start: 0.8181 (t0) cc_final: 0.7975 (t0) REVERT: C 35 PHE cc_start: 0.7188 (m-10) cc_final: 0.6863 (m-10) REVERT: C 93 LYS cc_start: 0.4588 (pttp) cc_final: 0.4153 (ptpt) REVERT: C 126 ARG cc_start: 0.8967 (OUTLIER) cc_final: 0.7882 (mtm180) REVERT: C 258 LYS cc_start: 0.5421 (OUTLIER) cc_final: 0.4943 (mmtt) outliers start: 68 outliers final: 37 residues processed: 196 average time/residue: 0.7607 time to fit residues: 169.7342 Evaluate side-chains 181 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 140 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 323 TRP Chi-restraints excluded: chain A residue 404 PHE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain B residue 13 ILE Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 323 TRP Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 126 ARG Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 250 PHE Chi-restraints excluded: chain C residue 258 LYS Chi-restraints excluded: chain C residue 330 SER Chi-restraints excluded: chain C residue 392 SER Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 488 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 16 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 chunk 103 optimal weight: 0.6980 chunk 80 optimal weight: 0.8980 chunk 119 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 141 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 123 ASN ** C 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.0921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12007 Z= 0.214 Angle : 0.533 10.875 16381 Z= 0.287 Chirality : 0.039 0.169 1889 Planarity : 0.004 0.043 1975 Dihedral : 3.972 15.732 1547 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 5.13 % Allowed : 21.97 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.59 (0.22), residues: 1484 helix: 2.20 (0.15), residues: 1175 sheet: None (None), residues: 0 loop : -0.17 (0.39), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 329 HIS 0.002 0.001 HIS C 374 PHE 0.024 0.002 PHE A 417 TYR 0.009 0.001 TYR C 490 ARG 0.004 0.000 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 146 time to evaluate : 1.317 Fit side-chains REVERT: A 93 LYS cc_start: 0.5780 (OUTLIER) cc_final: 0.5177 (ttpt) REVERT: A 265 MET cc_start: 0.7749 (mmp) cc_final: 0.7412 (ttt) REVERT: B 93 LYS cc_start: 0.5242 (OUTLIER) cc_final: 0.4958 (ttpt) REVERT: C 93 LYS cc_start: 0.4605 (pttp) cc_final: 0.4169 (ptpt) REVERT: C 126 ARG cc_start: 0.8978 (OUTLIER) cc_final: 0.7898 (mtm180) REVERT: C 258 LYS cc_start: 0.5450 (OUTLIER) cc_final: 0.4966 (mmtt) outliers start: 63 outliers final: 39 residues processed: 194 average time/residue: 0.7871 time to fit residues: 173.4796 Evaluate side-chains 187 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 144 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 323 TRP Chi-restraints excluded: chain A residue 404 PHE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain B residue 13 ILE Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 323 TRP Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 126 ARG Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 250 PHE Chi-restraints excluded: chain C residue 258 LYS Chi-restraints excluded: chain C residue 323 TRP Chi-restraints excluded: chain C residue 330 SER Chi-restraints excluded: chain C residue 392 SER Chi-restraints excluded: chain C residue 404 PHE Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 488 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 56 optimal weight: 0.4980 chunk 84 optimal weight: 1.9990 chunk 42 optimal weight: 7.9990 chunk 27 optimal weight: 0.7980 chunk 90 optimal weight: 0.6980 chunk 96 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 111 optimal weight: 0.4980 chunk 128 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 123 ASN ** C 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.0926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12007 Z= 0.190 Angle : 0.536 11.773 16381 Z= 0.287 Chirality : 0.039 0.158 1889 Planarity : 0.004 0.043 1975 Dihedral : 3.934 15.921 1547 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 4.39 % Allowed : 22.78 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.64 (0.22), residues: 1484 helix: 2.24 (0.15), residues: 1176 sheet: None (None), residues: 0 loop : -0.16 (0.39), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 445 HIS 0.002 0.001 HIS C 374 PHE 0.030 0.002 PHE B 417 TYR 0.008 0.001 TYR A 295 ARG 0.003 0.000 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 146 time to evaluate : 1.115 Fit side-chains REVERT: A 93 LYS cc_start: 0.5771 (OUTLIER) cc_final: 0.5176 (ttpt) REVERT: A 265 MET cc_start: 0.7732 (mmp) cc_final: 0.7420 (ttt) REVERT: B 93 LYS cc_start: 0.5280 (OUTLIER) cc_final: 0.5007 (ttpt) REVERT: B 105 MET cc_start: 0.1957 (mmp) cc_final: 0.1030 (mpp) REVERT: B 123 ASN cc_start: 0.8183 (t0) cc_final: 0.7981 (t0) REVERT: C 93 LYS cc_start: 0.4497 (pttp) cc_final: 0.4082 (ptpt) REVERT: C 126 ARG cc_start: 0.8973 (OUTLIER) cc_final: 0.7889 (mtm180) outliers start: 54 outliers final: 38 residues processed: 187 average time/residue: 0.8349 time to fit residues: 176.5748 Evaluate side-chains 182 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 141 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 323 TRP Chi-restraints excluded: chain A residue 404 PHE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain B residue 13 ILE Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 323 TRP Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 126 ARG Chi-restraints excluded: chain C residue 172 MET Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 250 PHE Chi-restraints excluded: chain C residue 323 TRP Chi-restraints excluded: chain C residue 330 SER Chi-restraints excluded: chain C residue 392 SER Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 488 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 123 optimal weight: 5.9990 chunk 132 optimal weight: 0.7980 chunk 135 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 103 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 119 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 131 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 123 ASN ** C 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.0994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12007 Z= 0.203 Angle : 0.551 12.811 16381 Z= 0.292 Chirality : 0.039 0.144 1889 Planarity : 0.004 0.043 1975 Dihedral : 3.954 15.782 1547 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.66 % Allowed : 24.00 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.60 (0.22), residues: 1484 helix: 2.22 (0.15), residues: 1174 sheet: None (None), residues: 0 loop : -0.19 (0.39), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP C 445 HIS 0.002 0.001 HIS C 374 PHE 0.025 0.002 PHE A 417 TYR 0.008 0.001 TYR C 490 ARG 0.003 0.000 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 142 time to evaluate : 1.367 Fit side-chains REVERT: A 93 LYS cc_start: 0.5825 (OUTLIER) cc_final: 0.5218 (ttpt) REVERT: A 265 MET cc_start: 0.7740 (mmp) cc_final: 0.7438 (ttt) REVERT: A 365 MET cc_start: 0.8814 (mmt) cc_final: 0.8069 (mmt) REVERT: B 93 LYS cc_start: 0.5275 (OUTLIER) cc_final: 0.5010 (ttpt) REVERT: B 123 ASN cc_start: 0.8239 (t0) cc_final: 0.8032 (t0) REVERT: C 35 PHE cc_start: 0.7206 (m-10) cc_final: 0.6848 (m-10) REVERT: C 93 LYS cc_start: 0.4507 (pttp) cc_final: 0.4087 (ptpt) REVERT: C 126 ARG cc_start: 0.8975 (OUTLIER) cc_final: 0.7893 (mtm180) outliers start: 45 outliers final: 37 residues processed: 179 average time/residue: 0.8618 time to fit residues: 174.0431 Evaluate side-chains 181 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 141 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 323 TRP Chi-restraints excluded: chain A residue 404 PHE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain B residue 13 ILE Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 323 TRP Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 126 ARG Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 250 PHE Chi-restraints excluded: chain C residue 323 TRP Chi-restraints excluded: chain C residue 330 SER Chi-restraints excluded: chain C residue 392 SER Chi-restraints excluded: chain C residue 404 PHE Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 488 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 139 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 146 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 71 optimal weight: 5.9990 chunk 92 optimal weight: 9.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 ASN ** C 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 12007 Z= 0.304 Angle : 0.598 12.250 16381 Z= 0.318 Chirality : 0.042 0.156 1889 Planarity : 0.004 0.043 1975 Dihedral : 4.144 17.033 1547 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.82 % Allowed : 23.84 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.22), residues: 1484 helix: 1.95 (0.15), residues: 1181 sheet: None (None), residues: 0 loop : -0.12 (0.40), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 445 HIS 0.003 0.001 HIS C 374 PHE 0.032 0.002 PHE B 417 TYR 0.014 0.001 TYR C 490 ARG 0.004 0.000 ARG A 168 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 136 time to evaluate : 1.253 Fit side-chains REVERT: A 93 LYS cc_start: 0.5805 (OUTLIER) cc_final: 0.5233 (ttpt) REVERT: A 265 MET cc_start: 0.7788 (mmp) cc_final: 0.7398 (ttt) REVERT: B 93 LYS cc_start: 0.5278 (OUTLIER) cc_final: 0.4997 (ttpt) REVERT: C 126 ARG cc_start: 0.8995 (OUTLIER) cc_final: 0.7850 (mtm180) outliers start: 47 outliers final: 36 residues processed: 174 average time/residue: 0.8070 time to fit residues: 159.0420 Evaluate side-chains 174 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 135 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 323 TRP Chi-restraints excluded: chain A residue 404 PHE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain B residue 13 ILE Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 323 TRP Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 126 ARG Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 250 PHE Chi-restraints excluded: chain C residue 323 TRP Chi-restraints excluded: chain C residue 330 SER Chi-restraints excluded: chain C residue 392 SER Chi-restraints excluded: chain C residue 404 PHE Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 488 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 107 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 116 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.159664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.115656 restraints weight = 12266.352| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.93 r_work: 0.3003 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12007 Z= 0.205 Angle : 0.570 12.665 16381 Z= 0.301 Chirality : 0.040 0.213 1889 Planarity : 0.004 0.043 1975 Dihedral : 4.059 17.566 1547 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.17 % Allowed : 25.06 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.22), residues: 1484 helix: 2.11 (0.15), residues: 1177 sheet: None (None), residues: 0 loop : -0.18 (0.39), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C 445 HIS 0.002 0.001 HIS C 374 PHE 0.024 0.002 PHE A 417 TYR 0.008 0.001 TYR C 490 ARG 0.004 0.000 ARG A 168 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3584.31 seconds wall clock time: 66 minutes 8.28 seconds (3968.28 seconds total)