Starting phenix.real_space_refine on Thu Nov 14 22:03:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g04_29644/11_2024/8g04_29644.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g04_29644/11_2024/8g04_29644.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g04_29644/11_2024/8g04_29644.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g04_29644/11_2024/8g04_29644.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g04_29644/11_2024/8g04_29644.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g04_29644/11_2024/8g04_29644.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.042 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 39 5.16 5 C 4664 2.51 5 N 1236 2.21 5 O 1375 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 7314 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1136 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 11, 'TRANS': 139} Chain: "B" Number of atoms: 3027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3027 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 34, 'TRANS': 363} Chain breaks: 5 Unresolved non-hydrogen bonds: 179 Unresolved non-hydrogen angles: 226 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 2, 'PCA:plan-2': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 3, 'TYR:plan': 1, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 141 Chain: "C" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3001 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 34, 'TRANS': 360} Chain breaks: 5 Unresolved non-hydrogen bonds: 184 Unresolved non-hydrogen angles: 231 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 2, 'PCA:plan-2': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 4, 'TYR:plan': 1, 'GLU:plan': 9, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 141 Chain: "B" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'MAN': 3, 'NAG': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'MAN': 3, 'NAG': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 4.99, per 1000 atoms: 0.68 Number of scatterers: 7314 At special positions: 0 Unit cell: (83.006, 116.424, 130.438, 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 39 16.00 O 1375 8.00 N 1236 7.00 C 4664 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 28 " - pdb=" SG CYS A 172 " distance=2.03 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 106 " distance=2.03 Simple disulfide: pdb=" SG CYS B 40 " - pdb=" SG CYS B 50 " distance=2.03 Simple disulfide: pdb=" SG CYS B 77 " - pdb=" SG CYS B 93 " distance=2.03 Simple disulfide: pdb=" SG CYS B 193 " - pdb=" SG CYS B 323 " distance=2.03 Simple disulfide: pdb=" SG CYS B 194 " - pdb=" SG CYS B 241 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 334 " - pdb=" SG CYS B 352 " distance=2.03 Simple disulfide: pdb=" SG CYS C 40 " - pdb=" SG CYS C 50 " distance=2.03 Simple disulfide: pdb=" SG CYS C 77 " - pdb=" SG CYS C 93 " distance=2.03 Simple disulfide: pdb=" SG CYS C 193 " - pdb=" SG CYS C 323 " distance=2.03 Simple disulfide: pdb=" SG CYS C 194 " - pdb=" SG CYS C 241 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 334 " - pdb=" SG CYS C 352 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=6, symmetry=0 Links applied NAG-ASN " NAG B1001 " - " ASN B 117 " " NAG B1002 " - " ASN B 298 " " NAG B1003 " - " ASN B 358 " " NAG C1001 " - " ASN C 117 " " NAG C1002 " - " ASN C 298 " " NAG C1003 " - " ASN C 358 " Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.78 Conformation dependent library (CDL) restraints added in 1.1 seconds 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1756 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 19 sheets defined 18.1% alpha, 31.8% 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 25 through 28 Processing helix chain 'A' and resid 29 through 48 removed outlier: 4.057A pdb=" N LEU A 33 " --> pdb=" O ASP A 29 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER A 48 " --> pdb=" O HIS A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 75 removed outlier: 3.758A pdb=" N THR A 74 " --> pdb=" O GLY A 70 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 100 removed outlier: 3.599A pdb=" N GLY A 100 " --> pdb=" O MET A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 130 removed outlier: 3.615A pdb=" N SER A 109 " --> pdb=" O THR A 105 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU A 128 " --> pdb=" O ALA A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 158 removed outlier: 4.270A pdb=" N ILE A 148 " --> pdb=" O ASP A 144 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE A 149 " --> pdb=" O PRO A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 167 Processing helix chain 'A' and resid 168 through 171 removed outlier: 3.814A pdb=" N LEU A 171 " --> pdb=" O GLY A 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 168 through 171' Processing helix chain 'B' and resid 27 through 31 Processing helix chain 'B' and resid 128 through 130 No H-bonds generated for 'chain 'B' and resid 128 through 130' Processing helix chain 'B' and resid 158 through 162 Processing helix chain 'B' and resid 189 through 193 Processing helix chain 'B' and resid 283 through 288 removed outlier: 3.801A pdb=" N ALA B 286 " --> pdb=" O ASP B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 388 No H-bonds generated for 'chain 'B' and resid 386 through 388' Processing helix chain 'C' and resid 27 through 31 Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 128 through 130 No H-bonds generated for 'chain 'C' and resid 128 through 130' Processing helix chain 'C' and resid 158 through 163 removed outlier: 5.348A pdb=" N ASP C 163 " --> pdb=" O GLU C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 288 Processing helix chain 'C' and resid 386 through 388 No H-bonds generated for 'chain 'C' and resid 386 through 388' Processing helix chain 'C' and resid 414 through 418 removed outlier: 4.099A pdb=" N ALA C 417 " --> pdb=" O SER C 414 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA C 418 " --> pdb=" O SER C 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 414 through 418' Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 62 Processing sheet with id=AA2, first strand: chain 'B' and resid 39 through 41 removed outlier: 3.550A pdb=" N THR B 49 " --> pdb=" O PHE B 41 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 75 through 77 removed outlier: 4.562A pdb=" N LEU B 65 " --> pdb=" O CYS B 77 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR B 121 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ASN B 113 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N THR B 119 " --> pdb=" O ASN B 113 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 139 through 143 removed outlier: 3.576A pdb=" N TRP B 154 " --> pdb=" O GLY B 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 183 through 187 removed outlier: 4.564A pdb=" N TYR B 167 " --> pdb=" O LEU B 187 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 292 through 294 removed outlier: 3.774A pdb=" N PHE B 292 " --> pdb=" O THR B 300 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR B 300 " --> pdb=" O PHE B 292 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN B 298 " --> pdb=" O LEU B 294 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 332 through 333 removed outlier: 3.696A pdb=" N SER B 310 " --> pdb=" O THR B 369 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N THR B 374 " --> pdb=" O THR B 370 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 332 through 333 removed outlier: 3.696A pdb=" N SER B 310 " --> pdb=" O THR B 369 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE B 362 " --> pdb=" O PHE B 383 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 396 through 399 Processing sheet with id=AB1, first strand: chain 'B' and resid 436 through 438 removed outlier: 3.654A pdb=" N LYS B 436 " --> pdb=" O TYR B 427 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N THR B 428 " --> pdb=" O ARG B 458 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ALA B 463 " --> pdb=" O TRP B 474 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N TRP B 474 " --> pdb=" O ALA B 463 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU B 465 " --> pdb=" O GLY B 472 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 39 through 41 removed outlier: 3.535A pdb=" N THR C 49 " --> pdb=" O PHE C 41 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 75 through 76 Processing sheet with id=AB4, first strand: chain 'C' and resid 138 through 143 removed outlier: 4.697A pdb=" N ILE C 138 " --> pdb=" O GLU C 155 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU C 155 " --> pdb=" O ILE C 138 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N MET C 142 " --> pdb=" O GLN C 151 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 183 through 186 Processing sheet with id=AB6, first strand: chain 'C' and resid 290 through 294 removed outlier: 4.096A pdb=" N ASN C 298 " --> pdb=" O LEU C 294 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 332 through 333 removed outlier: 3.930A pdb=" N SER C 310 " --> pdb=" O THR C 369 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 332 through 333 removed outlier: 3.930A pdb=" N SER C 310 " --> pdb=" O THR C 369 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE C 383 " --> pdb=" O ILE C 362 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 397 through 399 removed outlier: 3.590A pdb=" N ARG C 399 " --> pdb=" O GLU C 407 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU C 407 " --> pdb=" O ARG C 399 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 425 through 428 295 hydrogen bonds defined for protein. 744 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: 2.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2349 1.34 - 1.46: 1813 1.46 - 1.58: 3316 1.58 - 1.70: 0 1.70 - 1.82: 46 Bond restraints: 7524 Sorted by residual: bond pdb=" N PCA B 26 " pdb=" CD PCA B 26 " ideal model delta sigma weight residual 1.345 1.464 -0.119 2.00e-02 2.50e+03 3.56e+01 bond pdb=" N PCA C 26 " pdb=" CD PCA C 26 " ideal model delta sigma weight residual 1.345 1.463 -0.118 2.00e-02 2.50e+03 3.51e+01 bond pdb=" CG TRP B 474 " pdb=" CD1 TRP B 474 " ideal model delta sigma weight residual 1.365 1.477 -0.112 2.50e-02 1.60e+03 2.01e+01 bond pdb=" CG TRP B 272 " pdb=" CD1 TRP B 272 " ideal model delta sigma weight residual 1.365 1.476 -0.111 2.50e-02 1.60e+03 1.98e+01 bond pdb=" CG TRP C 272 " pdb=" CD1 TRP C 272 " ideal model delta sigma weight residual 1.365 1.476 -0.111 2.50e-02 1.60e+03 1.97e+01 ... (remaining 7519 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 10078 2.25 - 4.50: 204 4.50 - 6.75: 6 6.75 - 9.00: 3 9.00 - 11.25: 2 Bond angle restraints: 10293 Sorted by residual: angle pdb=" CD2 TRP C 269 " pdb=" CE2 TRP C 269 " pdb=" CZ2 TRP C 269 " ideal model delta sigma weight residual 122.40 118.01 4.39 1.00e+00 1.00e+00 1.92e+01 angle pdb=" CD2 TRP B 269 " pdb=" CE2 TRP B 269 " pdb=" CZ2 TRP B 269 " ideal model delta sigma weight residual 122.40 118.04 4.36 1.00e+00 1.00e+00 1.90e+01 angle pdb=" CD2 TRP C 272 " pdb=" CE2 TRP C 272 " pdb=" CZ2 TRP C 272 " ideal model delta sigma weight residual 122.40 118.12 4.28 1.00e+00 1.00e+00 1.84e+01 angle pdb=" CD2 TRP C 474 " pdb=" CE2 TRP C 474 " pdb=" CZ2 TRP C 474 " ideal model delta sigma weight residual 122.40 118.15 4.25 1.00e+00 1.00e+00 1.80e+01 angle pdb=" O PCA C 26 " pdb=" C PCA C 26 " pdb=" N ASP C 27 " ideal model delta sigma weight residual 123.00 116.24 6.76 1.60e+00 3.91e-01 1.79e+01 ... (remaining 10288 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.86: 4250 14.86 - 29.72: 264 29.72 - 44.57: 84 44.57 - 59.43: 24 59.43 - 74.29: 3 Dihedral angle restraints: 4625 sinusoidal: 1912 harmonic: 2713 Sorted by residual: dihedral pdb=" CA PHE B 383 " pdb=" C PHE B 383 " pdb=" N TRP B 384 " pdb=" CA TRP B 384 " ideal model delta harmonic sigma weight residual 180.00 160.02 19.98 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" SG CYS C 193 " pdb=" CB CYS C 323 " pdb=" SG CYS C 323 " pdb=" CA CYS C 323 " ideal model delta sinusoidal sigma weight residual 79.00 22.61 56.39 1 2.00e+01 2.50e-03 1.07e+01 dihedral pdb=" N CYS B 352 " pdb=" CA CYS B 352 " pdb=" CB CYS B 352 " pdb=" SG CYS B 352 " ideal model delta sinusoidal sigma weight residual 60.00 116.92 -56.92 3 1.50e+01 4.44e-03 9.42e+00 ... (remaining 4622 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 745 0.028 - 0.055: 277 0.055 - 0.083: 75 0.083 - 0.110: 63 0.110 - 0.138: 7 Chirality restraints: 1167 Sorted by residual: chirality pdb=" CA PRO C 70 " pdb=" N PRO C 70 " pdb=" C PRO C 70 " pdb=" CB PRO C 70 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.75e-01 chirality pdb=" CA ILE B 330 " pdb=" N ILE B 330 " pdb=" C ILE B 330 " pdb=" CB ILE B 330 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.99e-01 chirality pdb=" CA ILE C 139 " pdb=" N ILE C 139 " pdb=" C ILE C 139 " pdb=" CB ILE C 139 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.83e-01 ... (remaining 1164 not shown) Planarity restraints: 1320 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PCA C 26 " 0.048 2.00e-02 2.50e+03 9.22e-02 8.50e+01 pdb=" C PCA C 26 " -0.159 2.00e-02 2.50e+03 pdb=" O PCA C 26 " 0.060 2.00e-02 2.50e+03 pdb=" N ASP C 27 " 0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PCA B 26 " 0.037 2.00e-02 2.50e+03 7.26e-02 5.28e+01 pdb=" C PCA B 26 " -0.126 2.00e-02 2.50e+03 pdb=" O PCA B 26 " 0.047 2.00e-02 2.50e+03 pdb=" N ASP B 27 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 103 " 0.025 5.00e-02 4.00e+02 3.78e-02 2.28e+00 pdb=" N PRO A 104 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 104 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 104 " 0.021 5.00e-02 4.00e+02 ... (remaining 1317 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1101 2.76 - 3.30: 6778 3.30 - 3.83: 11606 3.83 - 4.37: 12670 4.37 - 4.90: 22748 Nonbonded interactions: 54903 Sorted by model distance: nonbonded pdb=" ND1 HIS C 412 " pdb=" OH TYR C 423 " model vdw 2.229 3.120 nonbonded pdb=" O SER B 318 " pdb=" OG SER B 360 " model vdw 2.236 3.040 nonbonded pdb=" OE1 GLU C 156 " pdb=" OH TYR C 167 " model vdw 2.275 3.040 nonbonded pdb=" NE2 GLN C 302 " pdb=" O SER C 350 " model vdw 2.280 3.120 nonbonded pdb=" O SER C 318 " pdb=" OG SER C 360 " model vdw 2.308 3.040 ... (remaining 54898 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 'B' and (resid 26 through 148 or (resid 149 and (name N or name CA or nam \ e C or name O or name CB )) or resid 150 through 173 or (resid 174 through 175 a \ nd (name N or name CA or name C or name O or name CB )) or resid 176 or (resid 1 \ 77 through 178 and (name N or name CA or name C or name O or name CB )) or resid \ 179 or (resid 180 and (name N or name CA or name C or name O or name CB )) or r \ esid 181 through 246 or (resid 247 and (name N or name CA or name C or name O or \ name CB )) or resid 248 through 294 or (resid 295 and (name N or name CA or nam \ e C or name O or name CB )) or resid 296 through 325 or (resid 326 through 327 a \ nd (name N or name CA or name C or name O or name CB )) or resid 328 through 329 \ or (resid 330 and (name N or name CA or name C or name O or name CB )) or resid \ 331 through 400 or resid 405 through 428 or (resid 435 through 437 and (name N \ or name CA or name C or name O or name CB )) or resid 438 through 450 or (resid \ 456 through 458 and (name N or name CA or name C or name O or name CB )) or resi \ d 459 through 482 or resid 1001 through 1006)) selection = (chain 'C' and (resid 26 through 85 or (resid 86 and (name N or name CA or name \ C or name O or name CB )) or resid 87 through 97 or (resid 98 and (name N or nam \ e CA or name C or name O or name CB )) or resid 99 through 145 or (resid 146 and \ (name N or name CA or name C or name O or name CB )) or resid 147 through 326 o \ r (resid 327 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 28 through 334 or (resid 335 and (name N or name CA or name C or name O or name \ CB )) or resid 336 through 337 or (resid 348 through 349 and (name N or name CA \ or name C or name O or name CB )) or resid 350 through 397 or (resid 398 through \ 405 and (name N or name CA or name C or name O or name CB )) or resid 406 throu \ gh 482 or resid 1001 through 1006)) } 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: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.270 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 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 : 0.005 0.119 7524 Z= 0.334 Angle : 0.661 11.245 10293 Z= 0.355 Chirality : 0.037 0.138 1167 Planarity : 0.005 0.092 1314 Dihedral : 11.250 74.289 2827 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.28 % Allowed : 5.64 % Favored : 92.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.29), residues: 916 helix: 2.74 (0.55), residues: 105 sheet: 0.61 (0.28), residues: 364 loop : -0.59 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 272 HIS 0.002 0.000 HIS C 376 PHE 0.007 0.001 PHE A 162 TYR 0.006 0.001 TYR C 423 ARG 0.002 0.000 ARG C 464 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 144 ASP cc_start: 0.8820 (p0) cc_final: 0.8501 (p0) REVERT: B 49 THR cc_start: 0.8591 (OUTLIER) cc_final: 0.8220 (t) REVERT: B 140 LYS cc_start: 0.8682 (mmtm) cc_final: 0.8464 (mmtm) REVERT: B 315 PHE cc_start: 0.7963 (p90) cc_final: 0.7559 (p90) REVERT: B 424 GLN cc_start: 0.7737 (pt0) cc_final: 0.7440 (pt0) REVERT: C 421 THR cc_start: 0.8513 (m) cc_final: 0.8301 (p) outliers start: 17 outliers final: 7 residues processed: 127 average time/residue: 0.1966 time to fit residues: 34.5790 Evaluate side-chains 95 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 105 PHE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 352 CYS Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 302 GLN Chi-restraints excluded: chain C residue 368 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 72 optimal weight: 0.5980 chunk 28 optimal weight: 0.3980 chunk 44 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 302 GLN B 304 GLN C 64 GLN C 151 GLN C 302 GLN C 306 GLN ** C 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7524 Z= 0.245 Angle : 0.630 13.193 10293 Z= 0.305 Chirality : 0.039 0.145 1167 Planarity : 0.005 0.050 1314 Dihedral : 6.412 58.641 1258 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.36 % Allowed : 9.26 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.29), residues: 916 helix: 2.60 (0.54), residues: 105 sheet: 0.57 (0.26), residues: 386 loop : -0.49 (0.32), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 410 HIS 0.003 0.001 HIS C 412 PHE 0.021 0.001 PHE C 354 TYR 0.017 0.001 TYR C 470 ARG 0.005 0.000 ARG C 319 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 91 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 THR cc_start: 0.8667 (OUTLIER) cc_final: 0.8369 (t) REVERT: B 287 LEU cc_start: 0.7193 (pt) cc_final: 0.6818 (tt) REVERT: B 315 PHE cc_start: 0.7976 (p90) cc_final: 0.7756 (p90) REVERT: B 328 TYR cc_start: 0.7595 (m-10) cc_final: 0.7358 (m-10) REVERT: B 477 TRP cc_start: 0.7419 (m100) cc_final: 0.6772 (m100) outliers start: 25 outliers final: 13 residues processed: 113 average time/residue: 0.1640 time to fit residues: 26.4684 Evaluate side-chains 95 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 352 CYS Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 352 CYS Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 368 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 46 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 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 312 GLN ** C 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7524 Z= 0.260 Angle : 0.627 13.002 10293 Z= 0.302 Chirality : 0.039 0.189 1167 Planarity : 0.005 0.049 1314 Dihedral : 5.732 53.574 1253 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.49 % Allowed : 10.60 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.29), residues: 916 helix: 2.57 (0.53), residues: 105 sheet: 0.48 (0.26), residues: 387 loop : -0.50 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 272 HIS 0.002 0.001 HIS B 317 PHE 0.017 0.001 PHE C 354 TYR 0.014 0.001 TYR B 316 ARG 0.002 0.000 ARG C 319 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 49 THR cc_start: 0.8719 (OUTLIER) cc_final: 0.8433 (t) REVERT: B 287 LEU cc_start: 0.7137 (pt) cc_final: 0.6824 (tt) REVERT: B 302 GLN cc_start: 0.8352 (tm-30) cc_final: 0.7914 (tm-30) REVERT: B 315 PHE cc_start: 0.8049 (p90) cc_final: 0.7767 (p90) REVERT: B 477 TRP cc_start: 0.7377 (m100) cc_final: 0.6699 (m100) REVERT: C 302 GLN cc_start: 0.6463 (OUTLIER) cc_final: 0.6158 (tm-30) REVERT: C 304 GLN cc_start: 0.8728 (OUTLIER) cc_final: 0.8517 (pm20) REVERT: C 470 TYR cc_start: 0.8085 (m-80) cc_final: 0.7777 (m-80) outliers start: 26 outliers final: 18 residues processed: 116 average time/residue: 0.1715 time to fit residues: 28.0757 Evaluate side-chains 108 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 352 CYS Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 302 GLN Chi-restraints excluded: chain C residue 304 GLN Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 464 ARG Chi-restraints excluded: chain C residue 469 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 83 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 chunk 9 optimal weight: 0.6980 chunk 40 optimal weight: 0.0030 chunk 56 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 89 optimal weight: 0.4980 chunk 44 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 424 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7524 Z= 0.204 Angle : 0.620 12.358 10293 Z= 0.295 Chirality : 0.041 0.446 1167 Planarity : 0.004 0.050 1314 Dihedral : 6.078 59.588 1253 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 4.03 % Allowed : 12.08 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.28), residues: 916 helix: 2.60 (0.53), residues: 105 sheet: 0.59 (0.26), residues: 381 loop : -0.55 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 477 HIS 0.005 0.001 HIS C 412 PHE 0.014 0.001 PHE C 354 TYR 0.015 0.001 TYR B 328 ARG 0.002 0.000 ARG C 462 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 97 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 THR cc_start: 0.8703 (OUTLIER) cc_final: 0.8441 (t) REVERT: B 140 LYS cc_start: 0.8696 (mmtm) cc_final: 0.8366 (mmtm) REVERT: B 287 LEU cc_start: 0.7082 (pt) cc_final: 0.6778 (tt) REVERT: B 302 GLN cc_start: 0.8404 (tm-30) cc_final: 0.7915 (tm-30) REVERT: B 315 PHE cc_start: 0.7986 (p90) cc_final: 0.7755 (p90) REVERT: B 477 TRP cc_start: 0.7294 (m100) cc_final: 0.6584 (m100) REVERT: C 56 GLU cc_start: 0.8301 (mp0) cc_final: 0.8101 (mp0) REVERT: C 99 GLU cc_start: 0.8517 (tt0) cc_final: 0.8307 (mt-10) REVERT: C 279 ASP cc_start: 0.8659 (m-30) cc_final: 0.8386 (m-30) REVERT: C 302 GLN cc_start: 0.6461 (OUTLIER) cc_final: 0.6165 (tm-30) REVERT: C 304 GLN cc_start: 0.8720 (OUTLIER) cc_final: 0.8499 (pm20) outliers start: 30 outliers final: 20 residues processed: 124 average time/residue: 0.1608 time to fit residues: 28.1973 Evaluate side-chains 110 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 87 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 352 CYS Chi-restraints excluded: chain B residue 353 HIS Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 302 GLN Chi-restraints excluded: chain C residue 304 GLN Chi-restraints excluded: chain C residue 352 CYS Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 464 ARG Chi-restraints excluded: chain C residue 469 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 74 optimal weight: 0.0870 chunk 51 optimal weight: 9.9990 chunk 1 optimal weight: 0.9980 chunk 66 optimal weight: 0.3980 chunk 37 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 80 optimal weight: 9.9990 chunk 22 optimal weight: 0.3980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 424 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7524 Z= 0.204 Angle : 0.621 12.003 10293 Z= 0.294 Chirality : 0.043 0.638 1167 Planarity : 0.004 0.052 1314 Dihedral : 5.754 53.548 1253 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.62 % Allowed : 13.15 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.29), residues: 916 helix: 2.62 (0.53), residues: 105 sheet: 0.63 (0.26), residues: 377 loop : -0.52 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 477 HIS 0.002 0.000 HIS C 412 PHE 0.019 0.001 PHE C 354 TYR 0.013 0.001 TYR B 328 ARG 0.004 0.000 ARG C 319 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 90 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 49 THR cc_start: 0.8717 (OUTLIER) cc_final: 0.8460 (t) REVERT: B 140 LYS cc_start: 0.8690 (mmtm) cc_final: 0.8393 (mmtm) REVERT: B 287 LEU cc_start: 0.7101 (pt) cc_final: 0.6784 (tt) REVERT: B 302 GLN cc_start: 0.8432 (tm-30) cc_final: 0.7932 (tm-30) REVERT: B 315 PHE cc_start: 0.7948 (p90) cc_final: 0.7695 (p90) REVERT: B 477 TRP cc_start: 0.7288 (m100) cc_final: 0.6567 (m100) REVERT: C 302 GLN cc_start: 0.6476 (OUTLIER) cc_final: 0.6132 (tm-30) REVERT: C 304 GLN cc_start: 0.8701 (OUTLIER) cc_final: 0.8282 (pm20) outliers start: 27 outliers final: 17 residues processed: 115 average time/residue: 0.1779 time to fit residues: 28.9209 Evaluate side-chains 106 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 352 CYS Chi-restraints excluded: chain B residue 353 HIS Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 302 GLN Chi-restraints excluded: chain C residue 304 GLN Chi-restraints excluded: chain C residue 352 CYS Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 469 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 30 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 52 optimal weight: 9.9990 chunk 22 optimal weight: 0.6980 chunk 89 optimal weight: 9.9990 chunk 74 optimal weight: 0.8980 chunk 41 optimal weight: 6.9990 chunk 7 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7524 Z= 0.243 Angle : 0.630 11.755 10293 Z= 0.300 Chirality : 0.042 0.520 1167 Planarity : 0.005 0.092 1314 Dihedral : 5.798 53.036 1253 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.76 % Allowed : 14.09 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.29), residues: 916 helix: 2.58 (0.53), residues: 105 sheet: 0.59 (0.26), residues: 382 loop : -0.52 (0.32), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 272 HIS 0.003 0.001 HIS A 142 PHE 0.017 0.001 PHE C 354 TYR 0.016 0.001 TYR B 328 ARG 0.009 0.000 ARG C 464 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 88 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 THR cc_start: 0.8754 (OUTLIER) cc_final: 0.8497 (t) REVERT: B 140 LYS cc_start: 0.8693 (mmtm) cc_final: 0.8412 (mmtm) REVERT: B 287 LEU cc_start: 0.7112 (pt) cc_final: 0.6791 (tt) REVERT: B 302 GLN cc_start: 0.8495 (tm-30) cc_final: 0.7955 (tm-30) REVERT: B 315 PHE cc_start: 0.7958 (p90) cc_final: 0.7740 (p90) REVERT: B 477 TRP cc_start: 0.7303 (m100) cc_final: 0.6578 (m100) REVERT: C 56 GLU cc_start: 0.8323 (mp0) cc_final: 0.8012 (mp0) REVERT: C 304 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.8282 (pm20) outliers start: 28 outliers final: 20 residues processed: 113 average time/residue: 0.1536 time to fit residues: 24.8587 Evaluate side-chains 108 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 352 CYS Chi-restraints excluded: chain B residue 353 HIS Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 302 GLN Chi-restraints excluded: chain C residue 304 GLN Chi-restraints excluded: chain C residue 352 CYS Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 370 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 50 optimal weight: 10.0000 chunk 75 optimal weight: 0.3980 chunk 89 optimal weight: 0.0470 chunk 56 optimal weight: 0.7980 chunk 54 optimal weight: 0.0770 chunk 41 optimal weight: 0.0070 chunk 55 optimal weight: 0.7980 overall best weight: 0.2454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7524 Z= 0.162 Angle : 0.623 11.472 10293 Z= 0.291 Chirality : 0.041 0.463 1167 Planarity : 0.005 0.057 1314 Dihedral : 5.356 54.388 1253 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.68 % Allowed : 15.44 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.29), residues: 916 helix: 2.58 (0.54), residues: 107 sheet: 0.79 (0.26), residues: 382 loop : -0.50 (0.31), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 110 HIS 0.003 0.000 HIS C 412 PHE 0.015 0.001 PHE C 354 TYR 0.012 0.001 TYR B 328 ARG 0.006 0.000 ARG C 319 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 THR cc_start: 0.8674 (OUTLIER) cc_final: 0.8440 (t) REVERT: B 140 LYS cc_start: 0.8646 (mmtm) cc_final: 0.8429 (mmtm) REVERT: B 287 LEU cc_start: 0.7048 (pt) cc_final: 0.6736 (tt) REVERT: B 302 GLN cc_start: 0.8414 (tm-30) cc_final: 0.7912 (tm-30) REVERT: B 315 PHE cc_start: 0.7858 (p90) cc_final: 0.7638 (p90) REVERT: B 376 HIS cc_start: 0.8641 (m-70) cc_final: 0.8428 (m-70) REVERT: C 56 GLU cc_start: 0.8250 (mp0) cc_final: 0.8005 (mp0) REVERT: C 302 GLN cc_start: 0.6402 (OUTLIER) cc_final: 0.6030 (tm-30) REVERT: C 304 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.8450 (pm20) outliers start: 20 outliers final: 16 residues processed: 113 average time/residue: 0.1683 time to fit residues: 26.8791 Evaluate side-chains 107 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 352 CYS Chi-restraints excluded: chain B residue 353 HIS Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 302 GLN Chi-restraints excluded: chain C residue 304 GLN Chi-restraints excluded: chain C residue 352 CYS Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 370 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 8 optimal weight: 0.0970 chunk 70 optimal weight: 0.8980 chunk 81 optimal weight: 5.9990 chunk 85 optimal weight: 0.6980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 353 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7524 Z= 0.217 Angle : 0.628 12.629 10293 Z= 0.295 Chirality : 0.040 0.429 1167 Planarity : 0.005 0.051 1314 Dihedral : 5.325 53.222 1253 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.82 % Allowed : 16.24 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.29), residues: 916 helix: 2.43 (0.53), residues: 107 sheet: 0.74 (0.26), residues: 384 loop : -0.46 (0.32), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 477 HIS 0.002 0.000 HIS A 142 PHE 0.014 0.001 PHE C 115 TYR 0.011 0.001 TYR B 328 ARG 0.005 0.000 ARG C 319 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 THR cc_start: 0.8733 (OUTLIER) cc_final: 0.8493 (t) REVERT: B 140 LYS cc_start: 0.8615 (mmtm) cc_final: 0.8392 (mmtm) REVERT: B 287 LEU cc_start: 0.7060 (pt) cc_final: 0.6747 (tt) REVERT: B 302 GLN cc_start: 0.8449 (tm-30) cc_final: 0.7930 (tm-30) REVERT: B 376 HIS cc_start: 0.8654 (m-70) cc_final: 0.8443 (m-70) REVERT: C 56 GLU cc_start: 0.8258 (mp0) cc_final: 0.8016 (mp0) REVERT: C 279 ASP cc_start: 0.8699 (m-30) cc_final: 0.8454 (m-30) REVERT: C 302 GLN cc_start: 0.6482 (OUTLIER) cc_final: 0.6084 (tm-30) REVERT: C 304 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.8475 (pm20) outliers start: 21 outliers final: 16 residues processed: 113 average time/residue: 0.1698 time to fit residues: 26.8840 Evaluate side-chains 107 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 352 CYS Chi-restraints excluded: chain B residue 353 HIS Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 302 GLN Chi-restraints excluded: chain C residue 304 GLN Chi-restraints excluded: chain C residue 352 CYS Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 370 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 chunk 65 optimal weight: 0.1980 chunk 25 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 54 optimal weight: 0.0970 chunk 88 optimal weight: 7.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7524 Z= 0.215 Angle : 0.653 13.882 10293 Z= 0.305 Chirality : 0.041 0.414 1167 Planarity : 0.005 0.052 1314 Dihedral : 5.288 53.339 1253 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.42 % Allowed : 16.38 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.29), residues: 916 helix: 2.44 (0.53), residues: 107 sheet: 0.75 (0.26), residues: 384 loop : -0.49 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 474 HIS 0.002 0.000 HIS A 142 PHE 0.014 0.001 PHE C 354 TYR 0.011 0.001 TYR B 328 ARG 0.008 0.000 ARG C 319 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 THR cc_start: 0.8712 (OUTLIER) cc_final: 0.8474 (t) REVERT: B 140 LYS cc_start: 0.8601 (mmtm) cc_final: 0.8394 (mmtm) REVERT: B 287 LEU cc_start: 0.7056 (pt) cc_final: 0.6744 (tt) REVERT: B 302 GLN cc_start: 0.8449 (tm-30) cc_final: 0.7927 (tm-30) REVERT: B 376 HIS cc_start: 0.8657 (m-70) cc_final: 0.8418 (m-70) REVERT: C 56 GLU cc_start: 0.8238 (mp0) cc_final: 0.8017 (mp0) REVERT: C 302 GLN cc_start: 0.6479 (OUTLIER) cc_final: 0.6060 (tm-30) REVERT: C 304 GLN cc_start: 0.8687 (OUTLIER) cc_final: 0.8466 (pm20) outliers start: 18 outliers final: 15 residues processed: 104 average time/residue: 0.1781 time to fit residues: 25.7965 Evaluate side-chains 106 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 352 CYS Chi-restraints excluded: chain B residue 353 HIS Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 302 GLN Chi-restraints excluded: chain C residue 304 GLN Chi-restraints excluded: chain C residue 352 CYS Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 370 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 53 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 85 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7524 Z= 0.281 Angle : 0.653 12.352 10293 Z= 0.310 Chirality : 0.041 0.409 1167 Planarity : 0.005 0.056 1314 Dihedral : 5.418 52.484 1253 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.68 % Allowed : 15.84 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.29), residues: 916 helix: 2.51 (0.53), residues: 105 sheet: 0.63 (0.26), residues: 384 loop : -0.49 (0.32), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 474 HIS 0.004 0.001 HIS B 317 PHE 0.027 0.002 PHE B 315 TYR 0.011 0.001 TYR B 328 ARG 0.004 0.000 ARG C 464 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 THR cc_start: 0.8752 (OUTLIER) cc_final: 0.8508 (t) REVERT: B 140 LYS cc_start: 0.8627 (mmtm) cc_final: 0.8411 (mmtm) REVERT: B 287 LEU cc_start: 0.7019 (pt) cc_final: 0.6740 (tt) REVERT: B 302 GLN cc_start: 0.8523 (tm-30) cc_final: 0.7892 (tm-30) REVERT: B 477 TRP cc_start: 0.7292 (m100) cc_final: 0.6532 (m100) REVERT: C 56 GLU cc_start: 0.8294 (mp0) cc_final: 0.8075 (mp0) REVERT: C 302 GLN cc_start: 0.6414 (OUTLIER) cc_final: 0.5958 (tm-30) REVERT: C 304 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.8471 (pm20) outliers start: 20 outliers final: 16 residues processed: 105 average time/residue: 0.1862 time to fit residues: 27.2361 Evaluate side-chains 104 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 352 CYS Chi-restraints excluded: chain B residue 353 HIS Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 302 GLN Chi-restraints excluded: chain C residue 304 GLN Chi-restraints excluded: chain C residue 352 CYS Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 370 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 22 optimal weight: 0.7980 chunk 68 optimal weight: 0.3980 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 75 optimal weight: 0.2980 chunk 9 optimal weight: 0.5980 chunk 13 optimal weight: 0.3980 chunk 64 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.137329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.095722 restraints weight = 14390.152| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 3.73 r_work: 0.3104 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7524 Z= 0.191 Angle : 0.646 12.270 10293 Z= 0.303 Chirality : 0.040 0.400 1167 Planarity : 0.004 0.053 1314 Dihedral : 5.288 53.778 1253 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.42 % Allowed : 16.11 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.29), residues: 916 helix: 2.47 (0.54), residues: 107 sheet: 0.74 (0.26), residues: 382 loop : -0.51 (0.31), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 398 HIS 0.004 0.001 HIS B 317 PHE 0.014 0.001 PHE C 354 TYR 0.010 0.001 TYR B 328 ARG 0.004 0.000 ARG C 464 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1870.77 seconds wall clock time: 34 minutes 34.17 seconds (2074.17 seconds total)