Starting phenix.real_space_refine on Sat Apr 6 05:14:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x2l_38016/04_2024/8x2l_38016_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x2l_38016/04_2024/8x2l_38016.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x2l_38016/04_2024/8x2l_38016.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x2l_38016/04_2024/8x2l_38016.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x2l_38016/04_2024/8x2l_38016_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x2l_38016/04_2024/8x2l_38016_updated.pdb" } resolution = 2.99 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= 0.011 sd= 0.067 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: 7 Type Number sf(0) Gaussians Fe 2 7.16 5 P 2 5.49 5 Mg 1 5.21 5 S 34 5.16 5 C 4639 2.51 5 N 1168 2.21 5 O 1253 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 7099 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1030 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 128} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 4108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4108 Classifications: {'peptide': 525} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 502} Chain breaks: 3 Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 172 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 2, 'ASN:plan1': 5, 'HIS:plan': 1, 'GLU:plan': 8, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 105 Chain: "H" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 935 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 113} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "L" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 103} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 169 Unusual residues: {' MG': 1, 'FAD': 1, 'HEM': 2, 'NAG': 2} Classifications: {'undetermined': 6, 'water': 1} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.04, per 1000 atoms: 0.57 Number of scatterers: 7099 At special positions: 0 Unit cell: (72.988, 84.296, 152.144, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 2 26.01 S 34 16.00 P 2 15.00 Mg 1 11.99 O 1253 8.00 N 1168 7.00 C 4639 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 244 " - pdb=" SG CYS B 257 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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=3, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG B 604 " - " ASN B 132 " " NAG B 605 " - " ASN B 240 " " NAG C 1 " - " ASN B 149 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.21 Conformation dependent library (CDL) restraints added in 1.2 seconds 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1644 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 31 helices and 10 sheets defined 43.2% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'A' and resid 6 through 30 removed outlier: 3.555A pdb=" N ALA A 16 " --> pdb=" O GLU A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 54 Processing helix chain 'A' and resid 70 through 79 Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 87 through 103 Proline residue: A 100 - end of helix removed outlier: 4.762A pdb=" N PHE A 103 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 127 removed outlier: 4.353A pdb=" N LEU A 109 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N GLY A 110 " --> pdb=" O ALA A 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 31 removed outlier: 3.718A pdb=" N LEU B 25 " --> pdb=" O LEU B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 45 removed outlier: 5.017A pdb=" N TYR B 41 " --> pdb=" O LYS B 38 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR B 42 " --> pdb=" O PHE B 39 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU B 45 " --> pdb=" O THR B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 51 through 70 Proline residue: B 56 - end of helix removed outlier: 3.595A pdb=" N MET B 65 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU B 68 " --> pdb=" O CYS B 64 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU B 69 " --> pdb=" O MET B 65 " (cutoff:3.500A) Proline residue: B 70 - end of helix Processing helix chain 'B' and resid 73 through 82 Processing helix chain 'B' and resid 89 through 94 Processing helix chain 'B' and resid 97 through 128 Processing helix chain 'B' and resid 136 through 143 Processing helix chain 'B' and resid 164 through 172 Processing helix chain 'B' and resid 174 through 193 Processing helix chain 'B' and resid 195 through 200 Processing helix chain 'B' and resid 202 through 220 removed outlier: 4.500A pdb=" N LEU B 211 " --> pdb=" O TYR B 207 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N PHE B 212 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N VAL B 213 " --> pdb=" O HIS B 209 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N ILE B 214 " --> pdb=" O HIS B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 238 Processing helix chain 'B' and resid 241 through 244 No H-bonds generated for 'chain 'B' and resid 241 through 244' Processing helix chain 'B' and resid 248 through 250 No H-bonds generated for 'chain 'B' and resid 248 through 250' Processing helix chain 'B' and resid 269 through 292 removed outlier: 5.206A pdb=" N GLY B 275 " --> pdb=" O LYS B 271 " (cutoff:3.500A) Proline residue: B 276 - end of helix Processing helix chain 'B' and resid 360 through 369 Processing helix chain 'B' and resid 398 through 400 No H-bonds generated for 'chain 'B' and resid 398 through 400' Processing helix chain 'B' and resid 410 through 429 removed outlier: 3.755A pdb=" N VAL B 413 " --> pdb=" O GLY B 410 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR B 414 " --> pdb=" O ILE B 411 " (cutoff:3.500A) Proline residue: B 415 - end of helix removed outlier: 4.065A pdb=" N ASN B 429 " --> pdb=" O LYS B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 467 Processing helix chain 'B' and resid 516 through 526 Processing helix chain 'B' and resid 540 through 553 Processing helix chain 'H' and resid 62 through 64 No H-bonds generated for 'chain 'H' and resid 62 through 64' Processing helix chain 'H' and resid 88 through 90 No H-bonds generated for 'chain 'H' and resid 88 through 90' Processing helix chain 'L' and resid 80 through 82 No H-bonds generated for 'chain 'L' and resid 80 through 82' Processing sheet with id= A, first strand: chain 'B' and resid 229 through 231 Processing sheet with id= B, first strand: chain 'B' and resid 351 through 356 removed outlier: 3.558A pdb=" N ILE B 353 " --> pdb=" O LEU B 310 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR B 307 " --> pdb=" O HIS B 303 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LYS B 313 " --> pdb=" O ILE B 297 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ILE B 297 " --> pdb=" O LYS B 313 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 338 through 341 Processing sheet with id= D, first strand: chain 'B' and resid 562 through 567 removed outlier: 7.003A pdb=" N VAL B 403 " --> pdb=" O GLY B 533 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N PHE B 535 " --> pdb=" O VAL B 403 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N MET B 405 " --> pdb=" O PHE B 535 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N CYS B 537 " --> pdb=" O MET B 405 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N VAL B 407 " --> pdb=" O CYS B 537 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LYS B 438 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N LEU B 406 " --> pdb=" O LYS B 438 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N TYR B 440 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N GLY B 408 " --> pdb=" O TYR B 440 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N TYR B 442 " --> pdb=" O GLY B 408 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'H' and resid 4 through 8 Processing sheet with id= F, first strand: chain 'H' and resid 106 through 109 removed outlier: 6.849A pdb=" N ARG H 98 " --> pdb=" O ASP H 107 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'H' and resid 45 through 47 removed outlier: 3.678A pdb=" N LYS H 45 " --> pdb=" O PHE H 41 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'L' and resid 4 through 6 removed outlier: 3.524A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.060A pdb=" N LYS L 103 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ALA L 13 " --> pdb=" O LYS L 103 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N GLU L 105 " --> pdb=" O ALA L 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'L' and resid 84 through 90 removed outlier: 6.146A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LYS L 39 " --> pdb=" O VAL L 44 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N VAL L 44 " --> pdb=" O LYS L 39 " (cutoff:3.500A) 323 hydrogen bonds defined for protein. 897 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: 2.12 Time building geometry restraints manager: 3.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.39: 2962 1.39 - 1.56: 4282 1.56 - 1.74: 4 1.74 - 1.91: 48 1.91 - 2.08: 8 Bond restraints: 7304 Sorted by residual: bond pdb=" C5X FAD B 601 " pdb=" C9A FAD B 601 " ideal model delta sigma weight residual 1.412 1.499 -0.087 2.00e-02 2.50e+03 1.88e+01 bond pdb=" C4A FAD B 601 " pdb=" C5A FAD B 601 " ideal model delta sigma weight residual 1.386 1.471 -0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" C5A FAD B 601 " pdb=" C6A FAD B 601 " ideal model delta sigma weight residual 1.407 1.479 -0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" C7 FAD B 601 " pdb=" C8 FAD B 601 " ideal model delta sigma weight residual 1.420 1.491 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" C4X FAD B 601 " pdb=" N5 FAD B 601 " ideal model delta sigma weight residual 1.288 1.349 -0.061 2.00e-02 2.50e+03 9.45e+00 ... (remaining 7299 not shown) Histogram of bond angle deviations from ideal: 87.50 - 105.10: 122 105.10 - 122.71: 8997 122.71 - 140.32: 856 140.32 - 157.93: 0 157.93 - 175.54: 4 Bond angle restraints: 9979 Sorted by residual: angle pdb=" P FAD B 601 " pdb=" O3P FAD B 601 " pdb=" PA FAD B 601 " ideal model delta sigma weight residual 130.34 120.89 9.45 3.00e+00 1.11e-01 9.93e+00 angle pdb=" C2A FAD B 601 " pdb=" N3A FAD B 601 " pdb=" C4A FAD B 601 " ideal model delta sigma weight residual 111.66 120.72 -9.06 3.00e+00 1.11e-01 9.12e+00 angle pdb=" C MET B 65 " pdb=" N LEU B 66 " pdb=" CA LEU B 66 " ideal model delta sigma weight residual 121.18 116.07 5.11 1.98e+00 2.55e-01 6.67e+00 angle pdb=" C5A FAD B 601 " pdb=" C4A FAD B 601 " pdb=" N3A FAD B 601 " ideal model delta sigma weight residual 126.50 119.07 7.43 3.00e+00 1.11e-01 6.14e+00 angle pdb=" C ASN B 430 " pdb=" N ALA B 431 " pdb=" CA ALA B 431 " ideal model delta sigma weight residual 121.54 126.02 -4.48 1.91e+00 2.74e-01 5.51e+00 ... (remaining 9974 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.31: 4163 31.31 - 62.61: 72 62.61 - 93.92: 15 93.92 - 125.23: 4 125.23 - 156.53: 1 Dihedral angle restraints: 4255 sinusoidal: 1694 harmonic: 2561 Sorted by residual: dihedral pdb=" O5' FAD B 601 " pdb=" O3P FAD B 601 " pdb=" P FAD B 601 " pdb=" PA FAD B 601 " ideal model delta sinusoidal sigma weight residual 298.23 141.70 156.53 1 3.00e+01 1.11e-03 2.05e+01 dihedral pdb=" CA LEU B 335 " pdb=" C LEU B 335 " pdb=" N GLU B 336 " pdb=" CA GLU B 336 " ideal model delta harmonic sigma weight residual -180.00 -157.93 -22.07 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA ASP B 388 " pdb=" C ASP B 388 " pdb=" N GLY B 389 " pdb=" CA GLY B 389 " ideal model delta harmonic sigma weight residual 180.00 159.17 20.83 0 5.00e+00 4.00e-02 1.73e+01 ... (remaining 4252 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 904 0.054 - 0.107: 171 0.107 - 0.161: 41 0.161 - 0.214: 0 0.214 - 0.268: 2 Chirality restraints: 1118 Sorted by residual: chirality pdb=" C1 BMA C 3 " pdb=" O4 NAG C 2 " pdb=" C2 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.34 -0.06 2.00e-02 2.50e+03 9.23e+00 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.46 0.06 2.00e-02 2.50e+03 7.96e+00 chirality pdb=" C3B FAD B 601 " pdb=" C2B FAD B 601 " pdb=" C4B FAD B 601 " pdb=" O3B FAD B 601 " both_signs ideal model delta sigma weight residual False -2.72 -2.45 -0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 1115 not shown) Planarity restraints: 1212 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 20 " 0.015 2.00e-02 2.50e+03 3.05e-02 9.31e+00 pdb=" C GLY B 20 " -0.053 2.00e-02 2.50e+03 pdb=" O GLY B 20 " 0.020 2.00e-02 2.50e+03 pdb=" N LEU B 21 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 36 " -0.043 5.00e-02 4.00e+02 6.49e-02 6.74e+00 pdb=" N PRO B 37 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 37 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 37 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B 329 " 0.038 5.00e-02 4.00e+02 5.84e-02 5.45e+00 pdb=" N PRO B 330 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO B 330 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 330 " 0.032 5.00e-02 4.00e+02 ... (remaining 1209 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 97 2.66 - 3.22: 6927 3.22 - 3.78: 11745 3.78 - 4.34: 16509 4.34 - 4.90: 26359 Nonbonded interactions: 61637 Sorted by model distance: nonbonded pdb=" NE2 HIS B 222 " pdb="FE HEM B 602 " model vdw 2.102 3.080 nonbonded pdb=" OE1 GLU A 53 " pdb=" OH TYR A 121 " model vdw 2.106 2.440 nonbonded pdb=" CE1 HIS B 209 " pdb="FE HEM B 603 " model vdw 2.194 2.576 nonbonded pdb=" O TYR L 50 " pdb=" OG1 THR L 51 " model vdw 2.220 2.440 nonbonded pdb=" OH TYR B 207 " pdb=" OE2 GLU B 336 " model vdw 2.228 2.440 ... (remaining 61632 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 2.450 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: 0.010 Extract box with map and model: 7.130 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 24.590 Find NCS groups from input model: 0.200 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:15.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 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 : 0.006 0.087 7304 Z= 0.376 Angle : 0.798 9.455 9979 Z= 0.385 Chirality : 0.046 0.268 1118 Planarity : 0.006 0.065 1209 Dihedral : 13.826 156.533 2602 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.14 % Allowed : 1.12 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -0.31 (0.28), residues: 871 helix: 0.31 (0.26), residues: 367 sheet: -0.56 (0.34), residues: 199 loop : -0.35 (0.36), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 18 HIS 0.010 0.002 HIS B 209 PHE 0.020 0.002 PHE B 62 TYR 0.014 0.002 TYR B 201 ARG 0.005 0.001 ARG B 43 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 180 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 416 PHE cc_start: 0.7890 (m-80) cc_final: 0.7604 (m-80) outliers start: 1 outliers final: 0 residues processed: 181 average time/residue: 1.0789 time to fit residues: 206.7833 Evaluate side-chains 115 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 40 optimal weight: 0.2980 chunk 50 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 ASN B 265 ASN B 293 GLN B 527 HIS B 566 ASN H 5 GLN L 6 GLN L 55 HIS L 90 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7304 Z= 0.283 Angle : 0.672 14.380 9979 Z= 0.314 Chirality : 0.044 0.197 1118 Planarity : 0.005 0.056 1209 Dihedral : 9.662 155.835 1118 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.78 % Allowed : 12.46 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -0.06 (0.28), residues: 871 helix: 0.57 (0.26), residues: 371 sheet: -0.51 (0.34), residues: 201 loop : -0.22 (0.38), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 424 HIS 0.006 0.001 HIS B 111 PHE 0.026 0.002 PHE B 62 TYR 0.018 0.002 TYR A 88 ARG 0.005 0.001 ARG B 159 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 138 time to evaluate : 0.850 Fit side-chains revert: symmetry clash REVERT: B 349 ASP cc_start: 0.7221 (OUTLIER) cc_final: 0.7005 (m-30) REVERT: B 402 GLU cc_start: 0.6306 (OUTLIER) cc_final: 0.5853 (tp30) outliers start: 27 outliers final: 11 residues processed: 151 average time/residue: 0.9849 time to fit residues: 159.1924 Evaluate side-chains 132 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 119 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 349 ASP Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 58 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 43 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 78 optimal weight: 4.9990 chunk 84 optimal weight: 0.5980 chunk 69 optimal weight: 0.0980 chunk 77 optimal weight: 0.1980 chunk 26 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 ASN ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 7304 Z= 0.229 Angle : 0.615 12.977 9979 Z= 0.283 Chirality : 0.042 0.196 1118 Planarity : 0.005 0.049 1209 Dihedral : 8.495 157.750 1118 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.64 % Allowed : 15.69 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 0.18 (0.28), residues: 871 helix: 0.83 (0.27), residues: 371 sheet: -0.29 (0.35), residues: 193 loop : -0.28 (0.36), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 206 HIS 0.005 0.001 HIS B 111 PHE 0.017 0.001 PHE B 13 TYR 0.013 0.001 TYR L 71 ARG 0.010 0.001 ARG B 531 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 128 time to evaluate : 0.786 Fit side-chains revert: symmetry clash REVERT: A 85 ARG cc_start: 0.7429 (OUTLIER) cc_final: 0.7092 (ttp80) REVERT: B 164 GLU cc_start: 0.6608 (OUTLIER) cc_final: 0.6025 (tm-30) REVERT: B 402 GLU cc_start: 0.6377 (OUTLIER) cc_final: 0.5916 (tp30) outliers start: 26 outliers final: 14 residues processed: 143 average time/residue: 0.9058 time to fit residues: 138.8175 Evaluate side-chains 132 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 115 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 58 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 0.6980 chunk 58 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 37 optimal weight: 0.0570 chunk 52 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 ASN ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 GLN B 527 HIS B 566 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 7304 Z= 0.291 Angle : 0.634 13.846 9979 Z= 0.291 Chirality : 0.042 0.189 1118 Planarity : 0.004 0.040 1209 Dihedral : 8.395 163.613 1118 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 5.74 % Allowed : 14.85 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 0.21 (0.28), residues: 871 helix: 0.85 (0.27), residues: 370 sheet: -0.21 (0.36), residues: 193 loop : -0.32 (0.37), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 337 HIS 0.007 0.001 HIS B 115 PHE 0.015 0.002 PHE B 62 TYR 0.017 0.002 TYR L 71 ARG 0.004 0.001 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 123 time to evaluate : 0.811 Fit side-chains revert: symmetry clash REVERT: A 85 ARG cc_start: 0.7434 (OUTLIER) cc_final: 0.7113 (ttp80) REVERT: B 164 GLU cc_start: 0.6607 (OUTLIER) cc_final: 0.6050 (tm-30) REVERT: B 402 GLU cc_start: 0.6307 (OUTLIER) cc_final: 0.5866 (tp30) REVERT: H 84 ASN cc_start: 0.7410 (OUTLIER) cc_final: 0.6905 (m-40) REVERT: H 111 GLN cc_start: 0.6952 (OUTLIER) cc_final: 0.6187 (pm20) outliers start: 41 outliers final: 16 residues processed: 145 average time/residue: 0.9181 time to fit residues: 142.8219 Evaluate side-chains 136 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 115 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain H residue 111 GLN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 58 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 69 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 42 optimal weight: 0.3980 chunk 74 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 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 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 HIS ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 ASN B 459 GLN B 527 HIS B 566 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 7304 Z= 0.283 Angle : 0.644 13.595 9979 Z= 0.292 Chirality : 0.043 0.191 1118 Planarity : 0.004 0.040 1209 Dihedral : 8.479 165.469 1118 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 4.76 % Allowed : 16.53 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 0.24 (0.28), residues: 871 helix: 0.89 (0.26), residues: 372 sheet: -0.14 (0.36), residues: 193 loop : -0.37 (0.37), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 337 HIS 0.007 0.001 HIS B 115 PHE 0.013 0.002 PHE B 62 TYR 0.022 0.002 TYR L 71 ARG 0.008 0.001 ARG B 531 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 125 time to evaluate : 0.811 Fit side-chains revert: symmetry clash REVERT: A 85 ARG cc_start: 0.7487 (OUTLIER) cc_final: 0.7160 (ttp80) REVERT: B 164 GLU cc_start: 0.6533 (OUTLIER) cc_final: 0.6004 (tm-30) REVERT: B 356 ARG cc_start: 0.7773 (OUTLIER) cc_final: 0.6782 (mtt180) REVERT: B 402 GLU cc_start: 0.6232 (OUTLIER) cc_final: 0.5835 (tp30) outliers start: 34 outliers final: 20 residues processed: 144 average time/residue: 1.0191 time to fit residues: 157.3060 Evaluate side-chains 142 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 118 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 349 ASP Chi-restraints excluded: chain B residue 356 ARG Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 63 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 0.4980 chunk 74 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 83 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 43 optimal weight: 0.0870 chunk 80 optimal weight: 0.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 HIS ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 HIS B 566 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7304 Z= 0.240 Angle : 0.633 12.837 9979 Z= 0.285 Chirality : 0.041 0.169 1118 Planarity : 0.004 0.053 1209 Dihedral : 8.461 166.261 1118 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 5.18 % Allowed : 17.79 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 0.30 (0.29), residues: 871 helix: 0.93 (0.27), residues: 373 sheet: -0.11 (0.37), residues: 193 loop : -0.34 (0.37), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 337 HIS 0.006 0.001 HIS B 115 PHE 0.022 0.002 PHE B 13 TYR 0.031 0.002 TYR L 50 ARG 0.003 0.000 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 123 time to evaluate : 0.875 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7104 (OUTLIER) cc_final: 0.6305 (mmt180) REVERT: A 65 MET cc_start: 0.5150 (mtm) cc_final: 0.4944 (mtm) REVERT: A 85 ARG cc_start: 0.7449 (OUTLIER) cc_final: 0.7133 (ttp80) REVERT: B 164 GLU cc_start: 0.6498 (OUTLIER) cc_final: 0.5973 (tm-30) REVERT: B 356 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.6907 (mtt180) REVERT: B 402 GLU cc_start: 0.6203 (OUTLIER) cc_final: 0.5805 (tp30) REVERT: H 84 ASN cc_start: 0.7311 (OUTLIER) cc_final: 0.6788 (m-40) REVERT: H 106 MET cc_start: 0.8127 (OUTLIER) cc_final: 0.7898 (mtt) REVERT: H 111 GLN cc_start: 0.7028 (OUTLIER) cc_final: 0.6268 (pm20) outliers start: 37 outliers final: 21 residues processed: 139 average time/residue: 0.9590 time to fit residues: 142.5131 Evaluate side-chains 143 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 114 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain B residue 65 MET Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 349 ASP Chi-restraints excluded: chain B residue 356 ARG Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain H residue 106 MET Chi-restraints excluded: chain H residue 111 GLN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 77 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 50 optimal weight: 0.5980 chunk 38 optimal weight: 0.0870 chunk 33 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 HIS ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 HIS B 553 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7304 Z= 0.260 Angle : 0.626 13.132 9979 Z= 0.285 Chirality : 0.042 0.207 1118 Planarity : 0.004 0.044 1209 Dihedral : 8.457 166.806 1118 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 5.32 % Allowed : 18.35 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 0.28 (0.29), residues: 871 helix: 0.96 (0.27), residues: 373 sheet: -0.15 (0.37), residues: 196 loop : -0.37 (0.37), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 337 HIS 0.006 0.001 HIS B 115 PHE 0.020 0.002 PHE B 13 TYR 0.026 0.002 TYR L 71 ARG 0.007 0.000 ARG B 531 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 123 time to evaluate : 0.788 Fit side-chains REVERT: A 32 ARG cc_start: 0.7155 (OUTLIER) cc_final: 0.6314 (mmt180) REVERT: A 85 ARG cc_start: 0.7461 (OUTLIER) cc_final: 0.7160 (ttp80) REVERT: B 103 MET cc_start: 0.7928 (OUTLIER) cc_final: 0.7543 (mtm) REVERT: B 164 GLU cc_start: 0.6471 (OUTLIER) cc_final: 0.5977 (tm-30) REVERT: B 356 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.6911 (mtt180) REVERT: B 363 GLU cc_start: 0.6535 (tm-30) cc_final: 0.6250 (tm-30) REVERT: B 402 GLU cc_start: 0.6223 (OUTLIER) cc_final: 0.5824 (tp30) REVERT: H 49 MET cc_start: 0.8437 (mtp) cc_final: 0.8133 (mtp) REVERT: H 84 ASN cc_start: 0.7331 (OUTLIER) cc_final: 0.6809 (m-40) REVERT: H 111 GLN cc_start: 0.7037 (OUTLIER) cc_final: 0.6283 (pm20) outliers start: 38 outliers final: 21 residues processed: 139 average time/residue: 0.9632 time to fit residues: 143.5351 Evaluate side-chains 143 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 114 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain B residue 65 MET Chi-restraints excluded: chain B residue 103 MET Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 349 ASP Chi-restraints excluded: chain B residue 356 ARG Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 47 GLU Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain H residue 111 GLN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 77 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 75 optimal weight: 0.3980 chunk 79 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 77 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 HIS ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 ASN B 527 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 7304 Z= 0.279 Angle : 0.628 13.488 9979 Z= 0.290 Chirality : 0.042 0.200 1118 Planarity : 0.004 0.042 1209 Dihedral : 8.509 167.821 1118 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 4.76 % Allowed : 19.33 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 0.23 (0.29), residues: 871 helix: 0.88 (0.27), residues: 373 sheet: -0.16 (0.37), residues: 196 loop : -0.37 (0.37), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 337 HIS 0.007 0.001 HIS B 115 PHE 0.021 0.002 PHE H 60 TYR 0.030 0.002 TYR L 71 ARG 0.005 0.001 ARG B 531 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 120 time to evaluate : 0.835 Fit side-chains REVERT: A 32 ARG cc_start: 0.7260 (OUTLIER) cc_final: 0.6583 (mmt180) REVERT: A 85 ARG cc_start: 0.7475 (OUTLIER) cc_final: 0.7155 (ttp80) REVERT: B 164 GLU cc_start: 0.6471 (OUTLIER) cc_final: 0.5976 (tm-30) REVERT: B 197 ILE cc_start: 0.8459 (mm) cc_final: 0.8074 (mm) REVERT: B 356 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.6857 (mtt180) REVERT: B 363 GLU cc_start: 0.6512 (tm-30) cc_final: 0.6226 (tm-30) REVERT: B 402 GLU cc_start: 0.6273 (OUTLIER) cc_final: 0.5765 (tp30) REVERT: H 84 ASN cc_start: 0.7400 (OUTLIER) cc_final: 0.6918 (m-40) REVERT: H 111 GLN cc_start: 0.7088 (OUTLIER) cc_final: 0.6317 (pm20) outliers start: 34 outliers final: 20 residues processed: 135 average time/residue: 0.9704 time to fit residues: 139.8449 Evaluate side-chains 141 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 114 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain B residue 65 MET Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 349 ASP Chi-restraints excluded: chain B residue 356 ARG Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 47 GLU Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain H residue 111 GLN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 77 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 79 optimal weight: 0.5980 chunk 46 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 69 optimal weight: 0.5980 chunk 73 optimal weight: 0.5980 chunk 76 optimal weight: 0.0020 chunk 50 optimal weight: 0.0980 chunk 81 optimal weight: 0.0670 chunk 49 optimal weight: 0.6980 overall best weight: 0.2726 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 HIS ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7304 Z= 0.192 Angle : 0.606 11.416 9979 Z= 0.279 Chirality : 0.041 0.166 1118 Planarity : 0.004 0.040 1209 Dihedral : 8.439 167.747 1118 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.62 % Allowed : 20.17 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 0.39 (0.29), residues: 871 helix: 0.98 (0.27), residues: 371 sheet: -0.10 (0.38), residues: 196 loop : -0.21 (0.38), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP B 337 HIS 0.005 0.001 HIS B 111 PHE 0.018 0.001 PHE B 13 TYR 0.026 0.001 TYR L 71 ARG 0.003 0.000 ARG B 199 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 117 time to evaluate : 0.695 Fit side-chains REVERT: A 85 ARG cc_start: 0.7401 (OUTLIER) cc_final: 0.7162 (ttp80) REVERT: B 103 MET cc_start: 0.7905 (OUTLIER) cc_final: 0.7605 (mtm) REVERT: B 265 ASN cc_start: 0.7583 (m110) cc_final: 0.7377 (m110) REVERT: B 356 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.6856 (mtt180) REVERT: B 363 GLU cc_start: 0.6585 (tm-30) cc_final: 0.6312 (tm-30) REVERT: B 402 GLU cc_start: 0.6208 (OUTLIER) cc_final: 0.5689 (tp30) REVERT: H 49 MET cc_start: 0.8277 (mtp) cc_final: 0.8008 (ptp) REVERT: H 111 GLN cc_start: 0.7042 (OUTLIER) cc_final: 0.6251 (pm20) outliers start: 33 outliers final: 18 residues processed: 133 average time/residue: 0.9528 time to fit residues: 135.3895 Evaluate side-chains 132 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 109 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain B residue 65 MET Chi-restraints excluded: chain B residue 103 MET Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 349 ASP Chi-restraints excluded: chain B residue 356 ARG Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 111 GLN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 77 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 0.4980 chunk 56 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 20 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 HIS ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 GLN B 527 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7304 Z= 0.296 Angle : 0.654 13.271 9979 Z= 0.303 Chirality : 0.043 0.232 1118 Planarity : 0.004 0.057 1209 Dihedral : 8.514 168.601 1118 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.78 % Allowed : 21.29 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 0.27 (0.29), residues: 871 helix: 0.88 (0.26), residues: 373 sheet: -0.11 (0.38), residues: 196 loop : -0.31 (0.37), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP B 337 HIS 0.007 0.002 HIS B 115 PHE 0.024 0.002 PHE H 60 TYR 0.023 0.002 TYR L 71 ARG 0.014 0.001 ARG B 199 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 110 time to evaluate : 0.865 Fit side-chains REVERT: A 85 ARG cc_start: 0.7459 (OUTLIER) cc_final: 0.7144 (ttp80) REVERT: B 103 MET cc_start: 0.7939 (OUTLIER) cc_final: 0.7637 (mtm) REVERT: B 319 MET cc_start: 0.7432 (ppp) cc_final: 0.7198 (ptm) REVERT: B 356 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.6888 (mtt180) REVERT: B 363 GLU cc_start: 0.6592 (tm-30) cc_final: 0.6320 (tm-30) REVERT: B 402 GLU cc_start: 0.6220 (OUTLIER) cc_final: 0.5681 (tp30) REVERT: H 84 ASN cc_start: 0.7295 (OUTLIER) cc_final: 0.6770 (m-40) REVERT: H 111 GLN cc_start: 0.7167 (OUTLIER) cc_final: 0.6379 (pm20) outliers start: 27 outliers final: 19 residues processed: 122 average time/residue: 1.0987 time to fit residues: 143.9924 Evaluate side-chains 129 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 104 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain B residue 65 MET Chi-restraints excluded: chain B residue 103 MET Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 349 ASP Chi-restraints excluded: chain B residue 356 ARG Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 47 GLU Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain H residue 111 GLN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 77 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 62 optimal weight: 0.8980 chunk 10 optimal weight: 0.2980 chunk 18 optimal weight: 0.7980 chunk 68 optimal weight: 0.4980 chunk 28 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 8 optimal weight: 0.2980 chunk 12 optimal weight: 0.7980 chunk 59 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 HIS ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 470 ASN B 527 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.118649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.101665 restraints weight = 10937.634| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.35 r_work: 0.3372 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.4057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7304 Z= 0.246 Angle : 0.635 13.023 9979 Z= 0.293 Chirality : 0.042 0.202 1118 Planarity : 0.004 0.066 1209 Dihedral : 8.549 169.631 1118 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.48 % Allowed : 20.45 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 0.32 (0.29), residues: 871 helix: 0.92 (0.26), residues: 371 sheet: -0.14 (0.37), residues: 196 loop : -0.24 (0.37), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP B 337 HIS 0.006 0.001 HIS B 115 PHE 0.017 0.002 PHE B 13 TYR 0.015 0.002 TYR L 71 ARG 0.013 0.001 ARG B 199 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3157.15 seconds wall clock time: 57 minutes 13.11 seconds (3433.11 seconds total)