Starting phenix.real_space_refine on Wed Feb 14 13:47:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hco_34660/02_2024/8hco_34660_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hco_34660/02_2024/8hco_34660.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hco_34660/02_2024/8hco_34660.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hco_34660/02_2024/8hco_34660.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hco_34660/02_2024/8hco_34660_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hco_34660/02_2024/8hco_34660_neut_updated.pdb" } resolution = 4.1 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 69 atoms to isotropic. 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 29 5.16 5 C 5966 2.51 5 N 1568 2.21 5 O 1767 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9330 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2507 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 314} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 387 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 1, 'TRANS': 48} Chain: "C" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 303 Classifications: {'peptide': 37} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 35} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 267 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 3, 'TRANS': 31} Chain: "E" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 295 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 4, 'TRANS': 31} Chain: "G" Number of atoms: 1791 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 224, 1790 Unusual residues: {'GYS': 1} Classifications: {'peptide': 223, 'undetermined': 1} Link IDs: {'PTRANS': 10, 'TRANS': 211, None: 2} Not linked: pdbres="PHE G 342 " pdbres="GYS G 344 " Not linked: pdbres="GYS G 344 " pdbres="VAL G 346 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'GYS:plan-3': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 224, 1790 Unusual residues: {'GYS': 1} Classifications: {'peptide': 223, 'undetermined': 1} Link IDs: {'PTRANS': 10, 'TRANS': 211, None: 2} Not linked: pdbres="PHE G 342 " pdbres="GYS G 344 " Not linked: pdbres="GYS G 344 " pdbres="VAL G 346 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'GYS:plan-3': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1829 Chain: "I" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2528 Classifications: {'peptide': 329} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 316} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 387 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 1, 'TRANS': 48} Chain: "K" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 303 Classifications: {'peptide': 37} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 35} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "L" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 267 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 3, 'TRANS': 31} Chain: "M" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 295 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 4, 'TRANS': 31} Time building chain proxies: 6.25, per 1000 atoms: 0.67 Number of scatterers: 9330 At special positions: 0 Unit cell: (98.44, 133.75, 120.91, 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 29 16.00 O 1767 8.00 N 1568 7.00 C 5966 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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 additional links: simple=2, symmetry=0 Simple link: pdb=" C GYS G 344 " - pdb=" N VAL G 346 " Simple link: pdb=" C PHE G 342 " - pdb=" N GYS G 344 " Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.55 Conformation dependent library (CDL) restraints added in 1.8 seconds 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2212 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 18 helices and 4 sheets defined 23.0% alpha, 34.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.68 Creating SS restraints... Processing helix chain 'A' and resid 50 through 54 removed outlier: 3.876A pdb=" N SER A 54 " --> pdb=" O SER A 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 50 through 54' Processing helix chain 'A' and resid 68 through 71 No H-bonds generated for 'chain 'A' and resid 68 through 71' Processing helix chain 'A' and resid 133 through 135 No H-bonds generated for 'chain 'A' and resid 133 through 135' Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'B' and resid 87 through 134 Proline residue: B 112 - end of helix Processing helix chain 'C' and resid 14 through 47 Proline residue: C 39 - end of helix Processing helix chain 'D' and resid 31 through 49 Processing helix chain 'D' and resid 52 through 57 Processing helix chain 'E' and resid 32 through 41 Processing helix chain 'E' and resid 50 through 54 Processing helix chain 'G' and resid 336 through 339 No H-bonds generated for 'chain 'G' and resid 336 through 339' Processing helix chain 'I' and resid 365 through 371 Processing helix chain 'J' and resid 87 through 134 Proline residue: J 112 - end of helix Processing helix chain 'K' and resid 14 through 47 Proline residue: K 39 - end of helix Processing helix chain 'L' and resid 31 through 49 Processing helix chain 'L' and resid 52 through 57 Processing helix chain 'M' and resid 32 through 42 Processing helix chain 'M' and resid 50 through 54 Processing sheet with id= A, first strand: chain 'A' and resid 85 through 91 removed outlier: 4.648A pdb=" N LYS A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ASP A 319 " --> pdb=" O LYS A 323 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER A 93 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N THR A 100 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ALA A 91 " --> pdb=" O THR A 100 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N HIS A 102 " --> pdb=" O ASN A 89 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ASN A 89 " --> pdb=" O HIS A 102 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N PHE A 104 " --> pdb=" O ASP A 87 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ASP A 87 " --> pdb=" O PHE A 104 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'G' and resid 304 through 313 removed outlier: 3.844A pdb=" N PHE G 305 " --> pdb=" O GLY G 298 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLY G 298 " --> pdb=" O PHE G 305 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL G 307 " --> pdb=" O LEU G 296 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU G 296 " --> pdb=" O VAL G 307 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLY G 309 " --> pdb=" O VAL G 294 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL G 294 " --> pdb=" O GLY G 309 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY G 313 " --> pdb=" O VAL G 290 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL G 290 " --> pdb=" O GLY G 313 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N LEU G 397 " --> pdb=" O LEU G 293 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N GLU G 295 " --> pdb=" O LEU G 397 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ASN G 399 " --> pdb=" O GLU G 295 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ASP G 297 " --> pdb=" O ASN G 399 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ILE G 401 " --> pdb=" O ASP G 297 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N ASP G 299 " --> pdb=" O ILE G 401 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N LEU G 403 " --> pdb=" O ASP G 299 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS G 391 " --> pdb=" O VAL G 398 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE G 406 " --> pdb=" O THR G 383 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP G 458 " --> pdb=" O SER G 377 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N HIS G 447 " --> pdb=" O GLN G 455 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA G 457 " --> pdb=" O ILE G 445 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE G 443 " --> pdb=" O HIS G 459 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE G 439 " --> pdb=" O ASN G 463 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N TYR G 429 " --> pdb=" O ASN G 442 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N LYS G 444 " --> pdb=" O ASN G 427 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ASN G 427 " --> pdb=" O LYS G 444 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR G 478 " --> pdb=" O ALA G 505 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER G 486 " --> pdb=" O VAL G 497 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL G 497 " --> pdb=" O SER G 486 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS G 323 " --> pdb=" O GLU G 310 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG G 308 " --> pdb=" O ILE G 325 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'I' and resid 99 through 105 removed outlier: 3.773A pdb=" N ALA I 257 " --> pdb=" O THR I 273 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'I' and resid 279 through 281 522 hydrogen bonds defined for protein. 1494 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: 2.72 Time building geometry restraints manager: 3.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1874 1.33 - 1.45: 2305 1.45 - 1.57: 5309 1.57 - 1.69: 1 1.69 - 1.81: 48 Bond restraints: 9537 Sorted by residual: bond pdb=" CB1 GYS G 344 " pdb=" OG1BGYS G 344 " ideal model delta sigma weight residual 1.408 1.611 -0.203 2.00e-02 2.50e+03 1.04e+02 bond pdb=" N VAL G 339 " pdb=" CA VAL G 339 " ideal model delta sigma weight residual 1.461 1.503 -0.042 1.17e-02 7.31e+03 1.26e+01 bond pdb=" N THR G 340 " pdb=" CA THR G 340 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.05e+01 bond pdb=" N MET G 366 " pdb=" CA MET G 366 " ideal model delta sigma weight residual 1.459 1.493 -0.033 1.04e-02 9.25e+03 1.03e+01 bond pdb=" N ASN I 95 " pdb=" CA ASN I 95 " ideal model delta sigma weight residual 1.461 1.490 -0.029 9.20e-03 1.18e+04 9.94e+00 ... (remaining 9532 not shown) Histogram of bond angle deviations from ideal: 100.41 - 107.37: 369 107.37 - 114.33: 5328 114.33 - 121.29: 4579 121.29 - 128.26: 2570 128.26 - 135.22: 92 Bond angle restraints: 12938 Sorted by residual: angle pdb=" N VAL G 339 " pdb=" CA VAL G 339 " pdb=" C VAL G 339 " ideal model delta sigma weight residual 110.42 116.05 -5.63 9.60e-01 1.09e+00 3.44e+01 angle pdb=" C LYS G 436 " pdb=" N ASN G 437 " pdb=" CA ASN G 437 " ideal model delta sigma weight residual 121.54 131.47 -9.93 1.91e+00 2.74e-01 2.70e+01 angle pdb=" N PRO I 96 " pdb=" CA PRO I 96 " pdb=" C PRO I 96 " ideal model delta sigma weight residual 112.47 102.27 10.20 2.06e+00 2.36e-01 2.45e+01 angle pdb=" C ASN A 133 " pdb=" N ASP A 134 " pdb=" CA ASP A 134 " ideal model delta sigma weight residual 121.54 130.26 -8.72 1.91e+00 2.74e-01 2.08e+01 angle pdb=" CA VAL G 339 " pdb=" C VAL G 339 " pdb=" O VAL G 339 " ideal model delta sigma weight residual 121.17 116.63 4.54 1.06e+00 8.90e-01 1.84e+01 ... (remaining 12933 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 5007 17.86 - 35.73: 448 35.73 - 53.59: 124 53.59 - 71.45: 35 71.45 - 89.31: 5 Dihedral angle restraints: 5619 sinusoidal: 2192 harmonic: 3427 Sorted by residual: dihedral pdb=" CA THR G 316 " pdb=" C THR G 316 " pdb=" N ASN G 317 " pdb=" CA ASN G 317 " ideal model delta harmonic sigma weight residual 180.00 155.87 24.13 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA ASN A 95 " pdb=" C ASN A 95 " pdb=" N PRO A 96 " pdb=" CA PRO A 96 " ideal model delta harmonic sigma weight residual 180.00 156.97 23.03 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA ASN A 133 " pdb=" C ASN A 133 " pdb=" N ASP A 134 " pdb=" CA ASP A 134 " ideal model delta harmonic sigma weight residual -180.00 -159.42 -20.58 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 5616 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1081 0.058 - 0.117: 274 0.117 - 0.175: 76 0.175 - 0.233: 14 0.233 - 0.292: 5 Chirality restraints: 1450 Sorted by residual: chirality pdb=" CB ILE I 106 " pdb=" CA ILE I 106 " pdb=" CG1 ILE I 106 " pdb=" CG2 ILE I 106 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CB ILE I 150 " pdb=" CA ILE I 150 " pdb=" CG1 ILE I 150 " pdb=" CG2 ILE I 150 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" CA PHE I 98 " pdb=" N PHE I 98 " pdb=" C PHE I 98 " pdb=" CB PHE I 98 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 1447 not shown) Planarity restraints: 1668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB2 GYS G 344 " -0.013 2.00e-02 2.50e+03 8.89e-02 1.97e+02 pdb=" CG2 GYS G 344 " -0.141 2.00e-02 2.50e+03 pdb=" C1 GYS G 344 " 0.043 2.00e-02 2.50e+03 pdb=" C2 GYS G 344 " 0.065 2.00e-02 2.50e+03 pdb=" CA1 GYS G 344 " -0.024 2.00e-02 2.50e+03 pdb=" CA2 GYS G 344 " 0.088 2.00e-02 2.50e+03 pdb=" CA3 GYS G 344 " -0.186 2.00e-02 2.50e+03 pdb=" N2 GYS G 344 " 0.072 2.00e-02 2.50e+03 pdb=" N3 GYS G 344 " 0.055 2.00e-02 2.50e+03 pdb=" O2 GYS G 344 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR G 337 " 0.024 2.00e-02 2.50e+03 4.88e-02 2.38e+01 pdb=" C THR G 337 " -0.084 2.00e-02 2.50e+03 pdb=" O THR G 337 " 0.031 2.00e-02 2.50e+03 pdb=" N LEU G 338 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB2 GYS G 344 " 0.028 2.00e-02 2.50e+03 2.40e-02 1.15e+01 pdb=" CG2 GYS G 344 " 0.007 2.00e-02 2.50e+03 pdb=" CD1 GYS G 344 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 GYS G 344 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 GYS G 344 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 GYS G 344 " -0.025 2.00e-02 2.50e+03 pdb=" CZ GYS G 344 " -0.023 2.00e-02 2.50e+03 pdb=" OH GYS G 344 " 0.046 2.00e-02 2.50e+03 ... (remaining 1665 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2545 2.81 - 3.33: 7171 3.33 - 3.86: 15929 3.86 - 4.38: 16852 4.38 - 4.90: 30158 Nonbonded interactions: 72655 Sorted by model distance: nonbonded pdb=" OG1 THR G 383 " pdb=" NZ LYS G 385 " model vdw 2.290 2.520 nonbonded pdb=" O ALA B 99 " pdb=" OG1 THR B 103 " model vdw 2.363 2.440 nonbonded pdb=" O ALA J 99 " pdb=" OG1 THR J 103 " model vdw 2.365 2.440 nonbonded pdb=" OG SER A 238 " pdb=" O TRP A 243 " model vdw 2.367 2.440 nonbonded pdb=" O GLN C 20 " pdb=" OG1 THR C 24 " model vdw 2.380 2.440 ... (remaining 72650 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'I' and (resid 49 through 282 or resid 291 through 382)) } ncs_group { reference = chain 'B' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'M' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 4.920 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 29.020 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.070 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:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6545 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 : 0.007 0.203 9537 Z= 0.437 Angle : 0.965 12.753 12938 Z= 0.561 Chirality : 0.060 0.292 1450 Planarity : 0.008 0.089 1667 Dihedral : 15.439 89.313 3405 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 10.99 % Allowed : 13.76 % Favored : 75.25 % 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: -2.36 (0.21), residues: 1166 helix: -2.53 (0.18), residues: 308 sheet: -0.48 (0.22), residues: 497 loop : -1.91 (0.28), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 42 HIS 0.004 0.001 HIS M 29 PHE 0.028 0.003 PHE G 342 TYR 0.014 0.002 TYR M 30 ARG 0.003 0.000 ARG A 315 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 383 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8022 (ttm-80) cc_final: 0.7142 (ttm-80) REVERT: A 69 GLU cc_start: 0.8313 (mp0) cc_final: 0.7725 (mp0) REVERT: A 120 PHE cc_start: 0.8599 (t80) cc_final: 0.8358 (t80) REVERT: A 132 ASP cc_start: 0.8517 (m-30) cc_final: 0.8210 (m-30) REVERT: A 169 GLN cc_start: 0.7818 (mt0) cc_final: 0.7413 (mt0) REVERT: A 183 LEU cc_start: 0.8856 (tp) cc_final: 0.8499 (tp) REVERT: A 184 ASN cc_start: 0.8548 (m-40) cc_final: 0.8153 (m110) REVERT: A 203 GLN cc_start: 0.7945 (tt0) cc_final: 0.7105 (tt0) REVERT: A 235 ARG cc_start: 0.8632 (ttt180) cc_final: 0.8132 (ttt180) REVERT: A 240 LYS cc_start: 0.8096 (ptpt) cc_final: 0.7798 (ttpt) REVERT: A 249 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8694 (mp) REVERT: A 250 GLN cc_start: 0.7998 (mm110) cc_final: 0.7696 (tp40) REVERT: A 314 TYR cc_start: 0.8950 (t80) cc_final: 0.8205 (t80) REVERT: A 336 LEU cc_start: 0.8848 (tp) cc_final: 0.8575 (tt) REVERT: A 349 ASN cc_start: 0.8280 (m110) cc_final: 0.7971 (t0) REVERT: A 369 MET cc_start: 0.7713 (mmm) cc_final: 0.7375 (mmm) REVERT: B 122 GLN cc_start: 0.8078 (tt0) cc_final: 0.7865 (tp40) REVERT: D 54 MET cc_start: 0.8329 (tpt) cc_final: 0.7844 (tpp) REVERT: D 56 MET cc_start: 0.6597 (mtt) cc_final: 0.6152 (mtt) REVERT: E 49 ASN cc_start: 0.8443 (p0) cc_final: 0.7802 (p0) REVERT: E 52 ASN cc_start: 0.8864 (t0) cc_final: 0.8425 (t0) REVERT: G 300 VAL cc_start: 0.5146 (OUTLIER) cc_final: 0.4757 (m) REVERT: G 338 LEU cc_start: -0.1170 (OUTLIER) cc_final: -0.1798 (mp) REVERT: G 397 LEU cc_start: -0.0330 (OUTLIER) cc_final: -0.0620 (tm) REVERT: G 398 VAL cc_start: 0.2215 (t) cc_final: 0.1997 (t) REVERT: G 447 HIS cc_start: 0.3455 (OUTLIER) cc_final: 0.1646 (m-70) REVERT: I 74 VAL cc_start: 0.9295 (t) cc_final: 0.8932 (m) REVERT: I 75 PHE cc_start: 0.8939 (m-80) cc_final: 0.8566 (m-80) REVERT: I 79 TYR cc_start: 0.8508 (m-80) cc_final: 0.8013 (m-10) REVERT: I 94 MET cc_start: 0.6299 (tpt) cc_final: 0.5888 (tmm) REVERT: I 120 PHE cc_start: 0.8463 (t80) cc_final: 0.8010 (t80) REVERT: I 140 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.8099 (ttp-110) REVERT: I 143 TYR cc_start: 0.8661 (t80) cc_final: 0.7905 (t80) REVERT: I 179 ASN cc_start: 0.7816 (t0) cc_final: 0.7509 (t0) REVERT: I 181 LYS cc_start: 0.9231 (ptpp) cc_final: 0.8871 (ptmt) REVERT: I 183 LEU cc_start: 0.8940 (tp) cc_final: 0.8588 (tp) REVERT: I 184 ASN cc_start: 0.9088 (m-40) cc_final: 0.8708 (m-40) REVERT: I 187 PHE cc_start: 0.7021 (m-80) cc_final: 0.5501 (p90) REVERT: I 198 VAL cc_start: 0.9238 (OUTLIER) cc_final: 0.8806 (t) REVERT: I 211 LEU cc_start: 0.9050 (tp) cc_final: 0.8835 (mm) REVERT: I 227 ASP cc_start: 0.8182 (m-30) cc_final: 0.7500 (t0) REVERT: I 297 VAL cc_start: 0.9067 (OUTLIER) cc_final: 0.8857 (p) REVERT: I 310 ARG cc_start: 0.8120 (ptp90) cc_final: 0.7360 (ptm-80) REVERT: I 324 VAL cc_start: 0.9259 (t) cc_final: 0.9018 (p) REVERT: I 359 PHE cc_start: 0.8440 (t80) cc_final: 0.8126 (t80) REVERT: I 375 ASP cc_start: 0.7520 (t0) cc_final: 0.6698 (t0) REVERT: J 89 ARG cc_start: 0.5330 (tpt90) cc_final: 0.3900 (mtt90) REVERT: K 18 GLN cc_start: 0.8250 (tt0) cc_final: 0.7930 (pt0) REVERT: K 22 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7383 (mt-10) REVERT: K 30 TYR cc_start: 0.6043 (m-10) cc_final: 0.5832 (t80) REVERT: L 55 ASP cc_start: 0.7731 (OUTLIER) cc_final: 0.7474 (m-30) REVERT: L 56 MET cc_start: 0.6355 (mtt) cc_final: 0.5766 (mtp) REVERT: M 32 TRP cc_start: 0.8257 (t-100) cc_final: 0.7847 (t-100) REVERT: M 35 PHE cc_start: 0.8328 (t80) cc_final: 0.7812 (t80) REVERT: M 49 ASN cc_start: 0.8231 (p0) cc_final: 0.7538 (p0) outliers start: 111 outliers final: 29 residues processed: 443 average time/residue: 0.1919 time to fit residues: 118.8370 Evaluate side-chains 314 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 276 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.8980 chunk 86 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 89 optimal weight: 0.3980 chunk 34 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 chunk 66 optimal weight: 7.9990 chunk 103 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN ** D 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 317 ASN I 67 ASN I 89 ASN ** I 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 ASN ** M 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6584 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9537 Z= 0.206 Angle : 0.634 7.286 12938 Z= 0.326 Chirality : 0.044 0.177 1450 Planarity : 0.005 0.051 1667 Dihedral : 4.839 41.354 1252 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.20 % Allowed : 3.07 % Favored : 96.73 % 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: -0.91 (0.23), residues: 1166 helix: 0.36 (0.27), residues: 285 sheet: -0.55 (0.22), residues: 520 loop : -1.20 (0.30), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 243 HIS 0.005 0.001 HIS G 355 PHE 0.012 0.001 PHE I 359 TYR 0.015 0.001 TYR G 478 ARG 0.003 0.000 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 334 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 GLU cc_start: 0.8408 (mp0) cc_final: 0.8041 (mp0) REVERT: A 169 GLN cc_start: 0.7871 (mt0) cc_final: 0.7373 (mt0) REVERT: A 183 LEU cc_start: 0.8791 (tp) cc_final: 0.8359 (tp) REVERT: A 184 ASN cc_start: 0.8609 (m-40) cc_final: 0.8181 (m110) REVERT: A 240 LYS cc_start: 0.7949 (ptpt) cc_final: 0.7681 (ttpt) REVERT: A 259 LEU cc_start: 0.9342 (tp) cc_final: 0.9001 (tp) REVERT: A 313 VAL cc_start: 0.9340 (t) cc_final: 0.9128 (t) REVERT: A 314 TYR cc_start: 0.8885 (t80) cc_final: 0.8040 (t80) REVERT: A 336 LEU cc_start: 0.8795 (tp) cc_final: 0.8504 (tt) REVERT: A 349 ASN cc_start: 0.8543 (m110) cc_final: 0.8132 (t0) REVERT: A 357 LEU cc_start: 0.9311 (pt) cc_final: 0.9094 (pt) REVERT: A 369 MET cc_start: 0.8009 (mmm) cc_final: 0.7681 (mmm) REVERT: B 122 GLN cc_start: 0.8239 (tt0) cc_final: 0.8038 (tp40) REVERT: C 20 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7237 (tp-100) REVERT: C 23 LYS cc_start: 0.8982 (mttt) cc_final: 0.8559 (mppt) REVERT: C 24 THR cc_start: 0.9361 (m) cc_final: 0.8573 (m) REVERT: E 49 ASN cc_start: 0.8524 (p0) cc_final: 0.7889 (p0) REVERT: I 79 TYR cc_start: 0.8324 (m-80) cc_final: 0.7865 (m-80) REVERT: I 94 MET cc_start: 0.6668 (tpt) cc_final: 0.6116 (tmm) REVERT: I 150 ILE cc_start: 0.9300 (tp) cc_final: 0.9017 (mt) REVERT: I 159 ASP cc_start: 0.7102 (t70) cc_final: 0.6851 (t70) REVERT: I 179 ASN cc_start: 0.8282 (t0) cc_final: 0.8000 (t0) REVERT: I 181 LYS cc_start: 0.9201 (ptpp) cc_final: 0.8847 (ptmt) REVERT: I 227 ASP cc_start: 0.8518 (m-30) cc_final: 0.7985 (t0) REVERT: I 310 ARG cc_start: 0.8095 (ptp90) cc_final: 0.7463 (ptm-80) REVERT: I 357 LEU cc_start: 0.9105 (pp) cc_final: 0.8897 (pt) REVERT: I 359 PHE cc_start: 0.8563 (t80) cc_final: 0.8286 (t80) REVERT: J 89 ARG cc_start: 0.5589 (tpt90) cc_final: 0.3894 (mtt90) REVERT: J 121 GLN cc_start: 0.7545 (mm110) cc_final: 0.7029 (mt0) REVERT: K 22 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7508 (mt-10) outliers start: 2 outliers final: 1 residues processed: 335 average time/residue: 0.1872 time to fit residues: 89.2491 Evaluate side-chains 281 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 279 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 8.9990 chunk 32 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 112 optimal weight: 0.6980 chunk 92 optimal weight: 6.9990 chunk 102 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6597 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9537 Z= 0.207 Angle : 0.596 7.561 12938 Z= 0.308 Chirality : 0.043 0.170 1450 Planarity : 0.004 0.037 1667 Dihedral : 4.571 33.249 1252 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % 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: -0.25 (0.24), residues: 1166 helix: 1.35 (0.29), residues: 285 sheet: -0.47 (0.22), residues: 516 loop : -0.68 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 243 HIS 0.003 0.001 HIS G 355 PHE 0.020 0.002 PHE D 41 TYR 0.013 0.001 TYR A 307 ARG 0.004 0.000 ARG A 315 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 315 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 GLU cc_start: 0.8462 (mp0) cc_final: 0.8047 (mp0) REVERT: A 111 LEU cc_start: 0.9614 (mm) cc_final: 0.9257 (mm) REVERT: A 169 GLN cc_start: 0.7925 (mt0) cc_final: 0.7425 (mt0) REVERT: A 183 LEU cc_start: 0.8829 (tp) cc_final: 0.8431 (tp) REVERT: A 184 ASN cc_start: 0.8589 (m-40) cc_final: 0.8154 (m110) REVERT: A 219 ARG cc_start: 0.8149 (tpp80) cc_final: 0.6946 (tpp80) REVERT: A 240 LYS cc_start: 0.8075 (ptpt) cc_final: 0.7797 (ttpt) REVERT: A 259 LEU cc_start: 0.9370 (tp) cc_final: 0.9073 (tp) REVERT: A 349 ASN cc_start: 0.8566 (m110) cc_final: 0.8211 (t0) REVERT: A 357 LEU cc_start: 0.9300 (pt) cc_final: 0.9087 (pt) REVERT: A 369 MET cc_start: 0.8071 (mmm) cc_final: 0.7740 (mmm) REVERT: B 109 LEU cc_start: 0.9079 (mm) cc_final: 0.8791 (mm) REVERT: C 23 LYS cc_start: 0.8959 (mttt) cc_final: 0.8729 (mttm) REVERT: E 49 ASN cc_start: 0.8595 (p0) cc_final: 0.7976 (p0) REVERT: G 496 MET cc_start: 0.0243 (mpp) cc_final: -0.0661 (mtp) REVERT: I 120 PHE cc_start: 0.8592 (t80) cc_final: 0.8191 (t80) REVERT: I 179 ASN cc_start: 0.8364 (t0) cc_final: 0.7778 (t0) REVERT: I 181 LYS cc_start: 0.9169 (ptpp) cc_final: 0.8873 (ptmt) REVERT: I 227 ASP cc_start: 0.8695 (m-30) cc_final: 0.8003 (t0) REVERT: I 310 ARG cc_start: 0.8063 (ptp90) cc_final: 0.7425 (ptm-80) REVERT: I 357 LEU cc_start: 0.9153 (pp) cc_final: 0.8885 (pt) REVERT: I 359 PHE cc_start: 0.8503 (t80) cc_final: 0.8141 (t80) REVERT: J 87 PHE cc_start: 0.4032 (t80) cc_final: 0.3807 (t80) REVERT: J 89 ARG cc_start: 0.5630 (tpt90) cc_final: 0.4055 (mtt90) REVERT: J 121 GLN cc_start: 0.7568 (mm110) cc_final: 0.7112 (mt0) REVERT: K 22 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7481 (mt-10) REVERT: M 52 ASN cc_start: 0.8271 (m-40) cc_final: 0.7947 (p0) outliers start: 0 outliers final: 0 residues processed: 315 average time/residue: 0.1782 time to fit residues: 80.7495 Evaluate side-chains 275 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 275 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 0.5980 chunk 77 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 chunk 69 optimal weight: 0.0070 chunk 104 optimal weight: 6.9990 chunk 110 optimal weight: 0.5980 chunk 54 optimal weight: 8.9990 chunk 98 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.2402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 203 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6643 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9537 Z= 0.245 Angle : 0.614 6.830 12938 Z= 0.316 Chirality : 0.044 0.184 1450 Planarity : 0.004 0.050 1667 Dihedral : 4.631 33.073 1252 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.10 % Allowed : 2.77 % Favored : 97.13 % 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: 0.08 (0.25), residues: 1166 helix: 1.71 (0.30), residues: 286 sheet: -0.28 (0.22), residues: 514 loop : -0.58 (0.35), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 243 HIS 0.004 0.001 HIS M 25 PHE 0.021 0.001 PHE A 120 TYR 0.022 0.001 TYR A 307 ARG 0.010 0.001 ARG A 315 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 314 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ASN cc_start: 0.8189 (t0) cc_final: 0.7828 (t0) REVERT: A 169 GLN cc_start: 0.7996 (mt0) cc_final: 0.7530 (mt0) REVERT: A 183 LEU cc_start: 0.8820 (tp) cc_final: 0.8421 (tp) REVERT: A 184 ASN cc_start: 0.8640 (m-40) cc_final: 0.8209 (m110) REVERT: A 240 LYS cc_start: 0.8125 (ptpt) cc_final: 0.7825 (ttpt) REVERT: A 259 LEU cc_start: 0.9413 (tp) cc_final: 0.9127 (tp) REVERT: A 343 GLU cc_start: 0.7987 (tt0) cc_final: 0.7720 (tt0) REVERT: A 349 ASN cc_start: 0.8567 (m110) cc_final: 0.8191 (t0) REVERT: A 369 MET cc_start: 0.8158 (mmm) cc_final: 0.7793 (mmm) REVERT: C 23 LYS cc_start: 0.8972 (mttt) cc_final: 0.8449 (mttp) REVERT: C 40 MET cc_start: 0.8851 (mpp) cc_final: 0.8430 (mpp) REVERT: E 49 ASN cc_start: 0.8601 (p0) cc_final: 0.8022 (p0) REVERT: G 366 MET cc_start: 0.0920 (tpt) cc_final: -0.1293 (mtp) REVERT: G 496 MET cc_start: 0.0214 (mpp) cc_final: -0.0738 (mtp) REVERT: I 120 PHE cc_start: 0.8661 (t80) cc_final: 0.8231 (t80) REVERT: I 132 ASP cc_start: 0.8033 (m-30) cc_final: 0.7807 (m-30) REVERT: I 143 TYR cc_start: 0.8673 (t80) cc_final: 0.8451 (t80) REVERT: I 179 ASN cc_start: 0.8200 (t0) cc_final: 0.7807 (t0) REVERT: I 187 PHE cc_start: 0.6660 (m-80) cc_final: 0.5381 (p90) REVERT: I 225 PRO cc_start: 0.6139 (Cg_exo) cc_final: 0.5779 (Cg_endo) REVERT: I 227 ASP cc_start: 0.8734 (m-30) cc_final: 0.8020 (t0) REVERT: I 310 ARG cc_start: 0.8253 (ptp90) cc_final: 0.7490 (ptm-80) REVERT: I 341 CYS cc_start: 0.8264 (p) cc_final: 0.7995 (p) REVERT: I 343 GLU cc_start: 0.7696 (tt0) cc_final: 0.7108 (tt0) REVERT: I 359 PHE cc_start: 0.8539 (t80) cc_final: 0.8251 (t80) REVERT: J 87 PHE cc_start: 0.4161 (t80) cc_final: 0.3945 (t80) REVERT: J 89 ARG cc_start: 0.5787 (tpt90) cc_final: 0.4114 (mtt90) REVERT: J 121 GLN cc_start: 0.7693 (mm110) cc_final: 0.7235 (mt0) REVERT: K 22 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7796 (tp30) REVERT: M 52 ASN cc_start: 0.8649 (m-40) cc_final: 0.8306 (p0) outliers start: 1 outliers final: 0 residues processed: 314 average time/residue: 0.1850 time to fit residues: 83.4456 Evaluate side-chains 271 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 271 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 10.0000 chunk 62 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 76 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 27 optimal weight: 0.3980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 294 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6619 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9537 Z= 0.186 Angle : 0.594 6.208 12938 Z= 0.303 Chirality : 0.043 0.175 1450 Planarity : 0.004 0.036 1667 Dihedral : 4.480 28.174 1252 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % 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: 0.25 (0.26), residues: 1166 helix: 1.80 (0.29), residues: 300 sheet: -0.30 (0.22), residues: 528 loop : -0.30 (0.37), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 243 HIS 0.003 0.001 HIS K 17 PHE 0.023 0.001 PHE A 359 TYR 0.019 0.001 TYR A 307 ARG 0.005 0.000 ARG A 315 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 313 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 GLN cc_start: 0.8017 (tp40) cc_final: 0.7713 (tp40) REVERT: A 169 GLN cc_start: 0.8013 (mt0) cc_final: 0.7542 (mt0) REVERT: A 183 LEU cc_start: 0.8772 (tp) cc_final: 0.8376 (tp) REVERT: A 184 ASN cc_start: 0.8664 (m-40) cc_final: 0.8261 (m110) REVERT: A 219 ARG cc_start: 0.8164 (tpp80) cc_final: 0.6960 (tpp80) REVERT: A 240 LYS cc_start: 0.8120 (ptpt) cc_final: 0.7815 (ttpt) REVERT: A 259 LEU cc_start: 0.9428 (tp) cc_final: 0.9121 (tp) REVERT: A 323 LYS cc_start: 0.8643 (ttpt) cc_final: 0.8438 (ttpt) REVERT: A 349 ASN cc_start: 0.8558 (m110) cc_final: 0.8216 (t0) REVERT: A 369 MET cc_start: 0.8170 (mmm) cc_final: 0.7804 (mmm) REVERT: B 121 GLN cc_start: 0.8624 (mm-40) cc_final: 0.8400 (mm-40) REVERT: C 23 LYS cc_start: 0.8959 (mttt) cc_final: 0.8476 (mttp) REVERT: C 40 MET cc_start: 0.8822 (mpp) cc_final: 0.8427 (mpp) REVERT: E 49 ASN cc_start: 0.8608 (p0) cc_final: 0.8036 (p0) REVERT: G 384 TYR cc_start: 0.3486 (m-80) cc_final: 0.3249 (m-80) REVERT: G 496 MET cc_start: 0.0155 (mpp) cc_final: -0.0805 (mtp) REVERT: I 120 PHE cc_start: 0.8705 (t80) cc_final: 0.8255 (t80) REVERT: I 132 ASP cc_start: 0.7949 (m-30) cc_final: 0.7717 (m-30) REVERT: I 155 LEU cc_start: 0.9045 (mt) cc_final: 0.8839 (mt) REVERT: I 159 ASP cc_start: 0.6958 (t70) cc_final: 0.6656 (t70) REVERT: I 183 LEU cc_start: 0.9007 (mp) cc_final: 0.8770 (mt) REVERT: I 227 ASP cc_start: 0.8534 (m-30) cc_final: 0.8004 (t0) REVERT: I 310 ARG cc_start: 0.8274 (ptp90) cc_final: 0.7511 (ptm-80) REVERT: I 341 CYS cc_start: 0.8209 (p) cc_final: 0.7967 (p) REVERT: I 359 PHE cc_start: 0.8469 (t80) cc_final: 0.8139 (t80) REVERT: J 89 ARG cc_start: 0.5973 (tpt90) cc_final: 0.4327 (mtt90) REVERT: J 121 GLN cc_start: 0.7742 (mm110) cc_final: 0.7260 (mt0) REVERT: K 22 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7734 (tp30) REVERT: M 52 ASN cc_start: 0.8704 (m-40) cc_final: 0.8268 (p0) outliers start: 0 outliers final: 0 residues processed: 313 average time/residue: 0.1927 time to fit residues: 87.1929 Evaluate side-chains 270 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 270 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 64 optimal weight: 0.0980 chunk 27 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 91 optimal weight: 0.0670 chunk 51 optimal weight: 0.9990 chunk 9 optimal weight: 0.0770 chunk 36 optimal weight: 7.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 166 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6574 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 9537 Z= 0.156 Angle : 0.582 7.154 12938 Z= 0.294 Chirality : 0.042 0.177 1450 Planarity : 0.003 0.035 1667 Dihedral : 4.251 22.735 1252 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.10 % Allowed : 2.18 % Favored : 97.72 % 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: 0.39 (0.26), residues: 1166 helix: 2.03 (0.29), residues: 300 sheet: -0.21 (0.23), residues: 515 loop : -0.36 (0.37), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 243 HIS 0.002 0.001 HIS C 43 PHE 0.025 0.001 PHE A 201 TYR 0.010 0.001 TYR A 217 ARG 0.004 0.000 ARG A 85 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 318 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 LEU cc_start: 0.9667 (mm) cc_final: 0.9437 (mt) REVERT: A 169 GLN cc_start: 0.8019 (mt0) cc_final: 0.7493 (mt0) REVERT: A 219 ARG cc_start: 0.8140 (tpp80) cc_final: 0.7406 (tpp80) REVERT: A 240 LYS cc_start: 0.8049 (ptpt) cc_final: 0.7720 (ttpt) REVERT: A 259 LEU cc_start: 0.9395 (tp) cc_final: 0.9121 (tp) REVERT: A 314 TYR cc_start: 0.8959 (t80) cc_final: 0.8088 (t80) REVERT: A 343 GLU cc_start: 0.7789 (tt0) cc_final: 0.7582 (tt0) REVERT: A 349 ASN cc_start: 0.8565 (m110) cc_final: 0.8254 (t0) REVERT: A 369 MET cc_start: 0.8091 (mmm) cc_final: 0.7713 (mmm) REVERT: C 40 MET cc_start: 0.8854 (mpp) cc_final: 0.8460 (mpp) REVERT: E 49 ASN cc_start: 0.8236 (p0) cc_final: 0.7932 (p0) REVERT: G 384 TYR cc_start: 0.3200 (m-80) cc_final: 0.2983 (m-80) REVERT: G 496 MET cc_start: 0.0202 (mpp) cc_final: -0.1115 (mtp) REVERT: I 69 GLU cc_start: 0.8806 (mp0) cc_final: 0.8087 (mp0) REVERT: I 120 PHE cc_start: 0.8743 (t80) cc_final: 0.8293 (t80) REVERT: I 132 ASP cc_start: 0.7696 (m-30) cc_final: 0.7493 (m-30) REVERT: I 134 ASP cc_start: 0.7724 (t70) cc_final: 0.7456 (t70) REVERT: I 155 LEU cc_start: 0.8989 (mt) cc_final: 0.8754 (mt) REVERT: I 175 ASP cc_start: 0.7265 (p0) cc_final: 0.6827 (p0) REVERT: I 183 LEU cc_start: 0.9225 (mp) cc_final: 0.8926 (mt) REVERT: I 203 GLN cc_start: 0.7373 (tt0) cc_final: 0.6315 (tt0) REVERT: I 227 ASP cc_start: 0.8655 (m-30) cc_final: 0.8066 (t0) REVERT: I 310 ARG cc_start: 0.8293 (ptp90) cc_final: 0.7535 (ptm-80) REVERT: I 359 PHE cc_start: 0.8360 (t80) cc_final: 0.7943 (t80) REVERT: I 368 LEU cc_start: 0.9286 (tt) cc_final: 0.8587 (tt) REVERT: J 89 ARG cc_start: 0.5970 (tpt90) cc_final: 0.4296 (mtt90) REVERT: J 121 GLN cc_start: 0.7641 (mm110) cc_final: 0.7210 (mt0) REVERT: K 22 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7730 (tp30) REVERT: M 52 ASN cc_start: 0.8605 (m-40) cc_final: 0.8204 (p0) outliers start: 1 outliers final: 0 residues processed: 318 average time/residue: 0.1845 time to fit residues: 84.3085 Evaluate side-chains 272 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 272 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 0.7980 chunk 12 optimal weight: 6.9990 chunk 62 optimal weight: 20.0000 chunk 80 optimal weight: 5.9990 chunk 92 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 chunk 68 optimal weight: 9.9990 chunk 66 optimal weight: 9.9990 chunk 50 optimal weight: 10.0000 chunk 67 optimal weight: 7.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 417 HIS G 482 GLN ** L 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 43 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6847 moved from start: 0.4768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.103 9537 Z= 0.747 Angle : 0.986 13.657 12938 Z= 0.512 Chirality : 0.057 0.365 1450 Planarity : 0.006 0.074 1667 Dihedral : 6.216 44.760 1252 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 22.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % 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: -0.86 (0.25), residues: 1166 helix: 0.38 (0.29), residues: 300 sheet: -0.73 (0.23), residues: 519 loop : -0.82 (0.36), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP I 243 HIS 0.011 0.002 HIS C 43 PHE 0.034 0.003 PHE A 359 TYR 0.041 0.004 TYR A 307 ARG 0.013 0.001 ARG A 315 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 295 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 GLU cc_start: 0.8710 (mp0) cc_final: 0.8387 (mp0) REVERT: A 169 GLN cc_start: 0.7924 (mt0) cc_final: 0.7668 (mt0) REVERT: A 183 LEU cc_start: 0.8946 (tp) cc_final: 0.8603 (tp) REVERT: A 184 ASN cc_start: 0.8663 (m-40) cc_final: 0.8263 (m110) REVERT: A 240 LYS cc_start: 0.8248 (ptpt) cc_final: 0.7955 (ttpt) REVERT: A 259 LEU cc_start: 0.9432 (tp) cc_final: 0.9187 (tp) REVERT: A 323 LYS cc_start: 0.8874 (ttpt) cc_final: 0.8604 (ttpt) REVERT: A 349 ASN cc_start: 0.8472 (m110) cc_final: 0.8177 (t0) REVERT: A 369 MET cc_start: 0.8621 (mmm) cc_final: 0.8285 (mmm) REVERT: C 23 LYS cc_start: 0.9092 (mttt) cc_final: 0.8813 (mttm) REVERT: C 24 THR cc_start: 0.9603 (p) cc_final: 0.9273 (p) REVERT: C 27 GLN cc_start: 0.8944 (pp30) cc_final: 0.8386 (mm-40) REVERT: E 37 LEU cc_start: 0.9295 (mt) cc_final: 0.9024 (mt) REVERT: E 46 ASN cc_start: 0.8736 (p0) cc_final: 0.8317 (p0) REVERT: E 48 PRO cc_start: 0.8986 (Cg_endo) cc_final: 0.8380 (Cg_exo) REVERT: E 49 ASN cc_start: 0.8317 (p0) cc_final: 0.7931 (p0) REVERT: G 433 ASP cc_start: 0.3803 (p0) cc_final: 0.2236 (m-30) REVERT: I 72 ARG cc_start: 0.8249 (ttp-170) cc_final: 0.7817 (mtt90) REVERT: I 175 ASP cc_start: 0.7806 (p0) cc_final: 0.7205 (p0) REVERT: I 176 PHE cc_start: 0.8920 (p90) cc_final: 0.8706 (p90) REVERT: I 179 ASN cc_start: 0.8232 (t0) cc_final: 0.7868 (t0) REVERT: I 187 PHE cc_start: 0.7422 (m-80) cc_final: 0.5761 (p90) REVERT: I 203 GLN cc_start: 0.7566 (tt0) cc_final: 0.6432 (tt0) REVERT: I 215 THR cc_start: 0.8942 (m) cc_final: 0.8718 (p) REVERT: I 272 GLU cc_start: 0.9072 (pt0) cc_final: 0.8709 (pt0) REVERT: I 310 ARG cc_start: 0.8491 (ptp90) cc_final: 0.7868 (ptm-80) REVERT: I 347 PHE cc_start: 0.7690 (t80) cc_final: 0.7026 (t80) REVERT: I 359 PHE cc_start: 0.8627 (t80) cc_final: 0.8277 (t80) REVERT: J 89 ARG cc_start: 0.6009 (tpt90) cc_final: 0.4256 (mtt90) REVERT: J 121 GLN cc_start: 0.7850 (mm110) cc_final: 0.7517 (mt0) REVERT: K 22 GLU cc_start: 0.8306 (mm-30) cc_final: 0.7993 (tp30) REVERT: K 24 THR cc_start: 0.8575 (p) cc_final: 0.8326 (p) REVERT: M 52 ASN cc_start: 0.8972 (m-40) cc_final: 0.8370 (p0) outliers start: 0 outliers final: 0 residues processed: 295 average time/residue: 0.1793 time to fit residues: 76.3965 Evaluate side-chains 245 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 245 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 0.4980 chunk 65 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 105 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 ASN G 424 ASN K 17 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6685 moved from start: 0.4683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9537 Z= 0.218 Angle : 0.695 9.536 12938 Z= 0.354 Chirality : 0.045 0.248 1450 Planarity : 0.004 0.039 1667 Dihedral : 5.126 36.017 1252 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 (0.26), residues: 1166 helix: 1.14 (0.29), residues: 300 sheet: -0.58 (0.23), residues: 519 loop : -0.49 (0.37), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP I 243 HIS 0.005 0.001 HIS C 43 PHE 0.025 0.002 PHE A 201 TYR 0.031 0.001 TYR A 307 ARG 0.007 0.001 ARG A 315 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 313 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 GLU cc_start: 0.8613 (mp0) cc_final: 0.8140 (mp0) REVERT: A 120 PHE cc_start: 0.8698 (t80) cc_final: 0.8336 (t80) REVERT: A 130 ASN cc_start: 0.8610 (t0) cc_final: 0.8274 (t0) REVERT: A 169 GLN cc_start: 0.7741 (mt0) cc_final: 0.7269 (mt0) REVERT: A 183 LEU cc_start: 0.8834 (tp) cc_final: 0.8424 (tp) REVERT: A 184 ASN cc_start: 0.8602 (m-40) cc_final: 0.8183 (m110) REVERT: A 219 ARG cc_start: 0.7994 (tpp80) cc_final: 0.7342 (tpp80) REVERT: A 240 LYS cc_start: 0.8148 (ptpt) cc_final: 0.7803 (ttpt) REVERT: A 259 LEU cc_start: 0.9359 (tp) cc_final: 0.9098 (tp) REVERT: A 314 TYR cc_start: 0.8937 (t80) cc_final: 0.8165 (t80) REVERT: A 323 LYS cc_start: 0.8627 (ttpt) cc_final: 0.8323 (ttpt) REVERT: A 349 ASN cc_start: 0.8504 (m110) cc_final: 0.8148 (t0) REVERT: A 369 MET cc_start: 0.8309 (mmm) cc_final: 0.7953 (mmm) REVERT: C 24 THR cc_start: 0.9567 (p) cc_final: 0.9314 (p) REVERT: C 27 GLN cc_start: 0.8793 (pp30) cc_final: 0.8511 (mm-40) REVERT: C 40 MET cc_start: 0.8715 (mpp) cc_final: 0.8420 (mpp) REVERT: E 37 LEU cc_start: 0.9273 (mt) cc_final: 0.9058 (mt) REVERT: E 41 TRP cc_start: 0.8220 (t60) cc_final: 0.7937 (t60) REVERT: E 46 ASN cc_start: 0.8596 (p0) cc_final: 0.8127 (p0) REVERT: E 48 PRO cc_start: 0.8925 (Cg_endo) cc_final: 0.8247 (Cg_exo) REVERT: E 49 ASN cc_start: 0.8328 (p0) cc_final: 0.8009 (p0) REVERT: G 433 ASP cc_start: 0.3798 (p0) cc_final: 0.2284 (m-30) REVERT: I 72 ARG cc_start: 0.7899 (ttp-170) cc_final: 0.7655 (mtm-85) REVERT: I 78 GLN cc_start: 0.7798 (mt0) cc_final: 0.7141 (mt0) REVERT: I 120 PHE cc_start: 0.8742 (t80) cc_final: 0.8453 (t80) REVERT: I 176 PHE cc_start: 0.8660 (p90) cc_final: 0.8443 (p90) REVERT: I 179 ASN cc_start: 0.7928 (t0) cc_final: 0.7717 (t0) REVERT: I 187 PHE cc_start: 0.6678 (m-80) cc_final: 0.5270 (p90) REVERT: I 310 ARG cc_start: 0.8376 (ptp90) cc_final: 0.7668 (ptm-80) REVERT: I 343 GLU cc_start: 0.7891 (tt0) cc_final: 0.7242 (tt0) REVERT: I 347 PHE cc_start: 0.7426 (t80) cc_final: 0.6977 (t80) REVERT: I 359 PHE cc_start: 0.8626 (t80) cc_final: 0.8228 (t80) REVERT: J 89 ARG cc_start: 0.6037 (tpt90) cc_final: 0.4356 (mtt90) REVERT: J 120 GLU cc_start: 0.7537 (tp30) cc_final: 0.7335 (tp30) REVERT: J 121 GLN cc_start: 0.7700 (mm110) cc_final: 0.7261 (mt0) REVERT: K 22 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7663 (tp30) REVERT: K 27 GLN cc_start: 0.9109 (pm20) cc_final: 0.8871 (pm20) REVERT: M 52 ASN cc_start: 0.8782 (m-40) cc_final: 0.8198 (p0) outliers start: 0 outliers final: 0 residues processed: 313 average time/residue: 0.2003 time to fit residues: 90.1937 Evaluate side-chains 270 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 270 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.5980 chunk 102 optimal weight: 0.7980 chunk 105 optimal weight: 8.9990 chunk 61 optimal weight: 0.0970 chunk 44 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 92 optimal weight: 0.3980 chunk 67 optimal weight: 0.6980 chunk 108 optimal weight: 0.0470 chunk 66 optimal weight: 0.0170 overall best weight: 0.2314 ------------------------------------------------------------------------------- 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: 0.6607 moved from start: 0.4904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9537 Z= 0.169 Angle : 0.665 8.956 12938 Z= 0.335 Chirality : 0.044 0.174 1450 Planarity : 0.004 0.036 1667 Dihedral : 4.570 31.601 1252 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.05 (0.26), residues: 1166 helix: 1.59 (0.30), residues: 299 sheet: -0.40 (0.23), residues: 520 loop : -0.38 (0.38), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 243 HIS 0.003 0.001 HIS G 355 PHE 0.020 0.001 PHE I 201 TYR 0.006 0.001 TYR G 370 ARG 0.004 0.000 ARG A 85 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 299 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.7481 (ttm-80) cc_final: 0.7207 (ttm-80) REVERT: A 69 GLU cc_start: 0.8450 (mp0) cc_final: 0.8190 (mp0) REVERT: A 130 ASN cc_start: 0.8331 (t0) cc_final: 0.8039 (t0) REVERT: A 169 GLN cc_start: 0.7891 (mt0) cc_final: 0.7485 (mt0) REVERT: A 219 ARG cc_start: 0.8032 (tpp80) cc_final: 0.6899 (tpp80) REVERT: A 240 LYS cc_start: 0.8124 (ptpt) cc_final: 0.7768 (ttpt) REVERT: A 314 TYR cc_start: 0.8584 (t80) cc_final: 0.8155 (t80) REVERT: A 323 LYS cc_start: 0.8676 (ttpt) cc_final: 0.8423 (ttpt) REVERT: A 349 ASN cc_start: 0.8533 (m110) cc_final: 0.8294 (t0) REVERT: A 369 MET cc_start: 0.8230 (mmm) cc_final: 0.7878 (mmm) REVERT: C 23 LYS cc_start: 0.9003 (mttt) cc_final: 0.8782 (mttp) REVERT: C 24 THR cc_start: 0.9556 (p) cc_final: 0.9330 (p) REVERT: C 40 MET cc_start: 0.8772 (mpp) cc_final: 0.8368 (mpp) REVERT: D 56 MET cc_start: 0.7453 (ttm) cc_final: 0.7121 (ttm) REVERT: E 49 ASN cc_start: 0.8203 (p0) cc_final: 0.7862 (p0) REVERT: G 384 TYR cc_start: 0.3575 (m-80) cc_final: 0.3194 (m-80) REVERT: G 433 ASP cc_start: 0.3820 (p0) cc_final: 0.2442 (m-30) REVERT: G 496 MET cc_start: -0.0042 (mpp) cc_final: -0.1771 (mtp) REVERT: I 227 ASP cc_start: 0.8492 (m-30) cc_final: 0.8047 (t0) REVERT: I 310 ARG cc_start: 0.8488 (ptp90) cc_final: 0.7615 (ptm160) REVERT: I 359 PHE cc_start: 0.8484 (t80) cc_final: 0.8110 (t80) REVERT: J 89 ARG cc_start: 0.5738 (tpt90) cc_final: 0.4332 (mtt90) REVERT: J 121 GLN cc_start: 0.7665 (mm110) cc_final: 0.7157 (mt0) REVERT: K 22 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7621 (tp30) REVERT: K 40 MET cc_start: 0.9064 (mpp) cc_final: 0.8740 (mpp) REVERT: M 52 ASN cc_start: 0.8607 (m-40) cc_final: 0.8153 (p0) outliers start: 0 outliers final: 0 residues processed: 299 average time/residue: 0.1894 time to fit residues: 80.4463 Evaluate side-chains 252 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 252 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 0.1980 chunk 75 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 311 GLN G 424 ASN ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6638 moved from start: 0.4954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9537 Z= 0.205 Angle : 0.669 8.878 12938 Z= 0.340 Chirality : 0.044 0.178 1450 Planarity : 0.004 0.036 1667 Dihedral : 4.530 32.660 1252 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.05 (0.26), residues: 1166 helix: 1.65 (0.29), residues: 297 sheet: -0.40 (0.23), residues: 523 loop : -0.45 (0.38), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 243 HIS 0.003 0.001 HIS A 51 PHE 0.026 0.002 PHE A 201 TYR 0.020 0.001 TYR A 307 ARG 0.005 0.000 ARG A 315 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 278 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.7548 (ttm-80) cc_final: 0.7295 (ttm-80) REVERT: A 85 ARG cc_start: 0.8364 (ttt90) cc_final: 0.8081 (ttt90) REVERT: A 130 ASN cc_start: 0.8428 (t0) cc_final: 0.8102 (t0) REVERT: A 142 ASN cc_start: 0.9224 (m-40) cc_final: 0.9002 (m110) REVERT: A 169 GLN cc_start: 0.7933 (mt0) cc_final: 0.7460 (mt0) REVERT: A 201 PHE cc_start: 0.8920 (t80) cc_final: 0.8685 (t80) REVERT: A 219 ARG cc_start: 0.8019 (tpp80) cc_final: 0.7344 (tpp80) REVERT: A 240 LYS cc_start: 0.8126 (ptpt) cc_final: 0.7788 (ttpt) REVERT: A 259 LEU cc_start: 0.9317 (tp) cc_final: 0.9111 (tp) REVERT: A 323 LYS cc_start: 0.8669 (ttpt) cc_final: 0.8357 (ttpt) REVERT: A 349 ASN cc_start: 0.8521 (m110) cc_final: 0.8303 (t0) REVERT: A 369 MET cc_start: 0.8275 (mmm) cc_final: 0.7919 (mmm) REVERT: C 40 MET cc_start: 0.8815 (mpp) cc_final: 0.8384 (mpp) REVERT: D 56 MET cc_start: 0.7350 (ttm) cc_final: 0.7042 (ttm) REVERT: E 49 ASN cc_start: 0.8152 (p0) cc_final: 0.7804 (p0) REVERT: G 384 TYR cc_start: 0.3691 (m-80) cc_final: 0.3318 (m-80) REVERT: G 433 ASP cc_start: 0.3651 (p0) cc_final: 0.2284 (m-30) REVERT: G 496 MET cc_start: -0.0185 (mpp) cc_final: -0.1857 (mtp) REVERT: I 72 ARG cc_start: 0.7391 (mtt90) cc_final: 0.7015 (mtm-85) REVERT: I 94 MET cc_start: 0.6827 (tpt) cc_final: 0.6210 (tmm) REVERT: I 150 ILE cc_start: 0.9325 (mp) cc_final: 0.8988 (tp) REVERT: I 168 GLU cc_start: 0.7656 (pt0) cc_final: 0.7313 (tt0) REVERT: I 179 ASN cc_start: 0.8001 (t0) cc_final: 0.7243 (t0) REVERT: I 227 ASP cc_start: 0.8459 (m-30) cc_final: 0.8038 (t0) REVERT: I 310 ARG cc_start: 0.8356 (ptp90) cc_final: 0.7671 (ptm160) REVERT: I 359 PHE cc_start: 0.8487 (t80) cc_final: 0.8102 (t80) REVERT: J 89 ARG cc_start: 0.5610 (tpt90) cc_final: 0.4235 (mtt90) REVERT: J 120 GLU cc_start: 0.7710 (tp30) cc_final: 0.7398 (tp30) REVERT: J 121 GLN cc_start: 0.7622 (mm110) cc_final: 0.7121 (mt0) REVERT: K 22 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7658 (tp30) REVERT: K 30 TYR cc_start: 0.5949 (m-80) cc_final: 0.5384 (t80) REVERT: K 40 MET cc_start: 0.9071 (mpp) cc_final: 0.8757 (mpp) REVERT: M 52 ASN cc_start: 0.8686 (m-40) cc_final: 0.8225 (p0) outliers start: 0 outliers final: 0 residues processed: 278 average time/residue: 0.1901 time to fit residues: 74.9720 Evaluate side-chains 246 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 246 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 25 optimal weight: 0.0670 chunk 90 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.166071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.125427 restraints weight = 16564.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.124752 restraints weight = 11010.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.125966 restraints weight = 8062.926| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3552 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3552 r_free = 0.3552 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3552 r_free = 0.3552 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| r_final: 0.3552 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.5021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9537 Z= 0.197 Angle : 0.660 8.929 12938 Z= 0.332 Chirality : 0.044 0.186 1450 Planarity : 0.004 0.035 1667 Dihedral : 4.472 32.312 1252 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.12 (0.26), residues: 1166 helix: 1.76 (0.30), residues: 294 sheet: -0.39 (0.23), residues: 518 loop : -0.38 (0.37), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 243 HIS 0.003 0.001 HIS C 43 PHE 0.025 0.002 PHE A 201 TYR 0.021 0.001 TYR A 307 ARG 0.004 0.000 ARG A 315 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2412.29 seconds wall clock time: 44 minutes 21.39 seconds (2661.39 seconds total)