Starting phenix.real_space_refine on Thu Feb 15 11:11:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dys_30924/02_2024/7dys_30924.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dys_30924/02_2024/7dys_30924.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dys_30924/02_2024/7dys_30924.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dys_30924/02_2024/7dys_30924.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dys_30924/02_2024/7dys_30924.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dys_30924/02_2024/7dys_30924.pdb" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.071 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 68 5.16 5 C 7897 2.51 5 N 1919 2.21 5 O 2181 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12065 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3012 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 4, 'TRANS': 382} Chain breaks: 7 Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 152 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 77 Chain: "B" Number of atoms: 3022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3022 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 4, 'TRANS': 382} Chain breaks: 7 Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 139 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 66 Chain: "C" Number of atoms: 3018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3018 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 4, 'TRANS': 382} Chain breaks: 7 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 70 Chain: "D" Number of atoms: 3013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3013 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 4, 'TRANS': 382} Chain breaks: 7 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 70 Time building chain proxies: 6.73, per 1000 atoms: 0.56 Number of scatterers: 12065 At special positions: 0 Unit cell: (111.24, 111.24, 106.92, 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 68 16.00 O 2181 8.00 N 1919 7.00 C 7897 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 164 " - pdb=" SG CYS A 190 " distance=2.03 Simple disulfide: pdb=" SG CYS A 243 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS B 164 " - pdb=" SG CYS B 190 " distance=2.03 Simple disulfide: pdb=" SG CYS B 243 " - pdb=" SG CYS B 274 " distance=2.03 Simple disulfide: pdb=" SG CYS C 164 " - pdb=" SG CYS C 190 " distance=2.03 Simple disulfide: pdb=" SG CYS C 243 " - pdb=" SG CYS C 274 " distance=2.03 Simple disulfide: pdb=" SG CYS D 164 " - pdb=" SG CYS D 190 " distance=2.03 Simple disulfide: pdb=" SG CYS D 243 " - pdb=" SG CYS D 274 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.96 Conformation dependent library (CDL) restraints added in 2.4 seconds 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2944 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 8 sheets defined 65.5% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 66 through 106 removed outlier: 4.014A pdb=" N LEU A 104 " --> pdb=" O ALA A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 140 Processing helix chain 'A' and resid 140 through 145 Processing helix chain 'A' and resid 194 through 199 Processing helix chain 'A' and resid 204 through 212 removed outlier: 6.761A pdb=" N SER A 209 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N PHE A 210 " --> pdb=" O GLN A 207 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE A 211 " --> pdb=" O THR A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 319 Processing helix chain 'A' and resid 346 through 366 Processing helix chain 'A' and resid 377 through 397 Processing helix chain 'A' and resid 400 through 440 Proline residue: A 415 - end of helix Processing helix chain 'A' and resid 448 through 461 Processing helix chain 'A' and resid 464 through 471 removed outlier: 3.847A pdb=" N THR A 468 " --> pdb=" O ASP A 464 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE A 469 " --> pdb=" O MET A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 517 removed outlier: 4.675A pdb=" N LEU A 501 " --> pdb=" O MET A 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 106 removed outlier: 3.516A pdb=" N LYS B 72 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU B 104 " --> pdb=" O ALA B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 140 Processing helix chain 'B' and resid 140 through 145 Processing helix chain 'B' and resid 194 through 199 Processing helix chain 'B' and resid 203 through 212 removed outlier: 6.839A pdb=" N SER B 209 " --> pdb=" O ALA B 206 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N PHE B 210 " --> pdb=" O GLN B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 319 Processing helix chain 'B' and resid 346 through 366 Processing helix chain 'B' and resid 377 through 397 Processing helix chain 'B' and resid 400 through 440 Proline residue: B 415 - end of helix Processing helix chain 'B' and resid 448 through 461 Processing helix chain 'B' and resid 464 through 471 removed outlier: 3.680A pdb=" N THR B 468 " --> pdb=" O ASP B 464 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE B 469 " --> pdb=" O MET B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 517 removed outlier: 4.668A pdb=" N LEU B 501 " --> pdb=" O MET B 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 106 removed outlier: 4.015A pdb=" N LEU C 104 " --> pdb=" O ALA C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 140 Processing helix chain 'C' and resid 140 through 145 Processing helix chain 'C' and resid 194 through 199 Processing helix chain 'C' and resid 203 through 212 removed outlier: 3.507A pdb=" N GLN C 207 " --> pdb=" O ASP C 204 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N SER C 209 " --> pdb=" O ALA C 206 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N PHE C 210 " --> pdb=" O GLN C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 319 Processing helix chain 'C' and resid 346 through 366 Processing helix chain 'C' and resid 377 through 397 Processing helix chain 'C' and resid 400 through 440 Proline residue: C 415 - end of helix Processing helix chain 'C' and resid 448 through 461 Processing helix chain 'C' and resid 464 through 471 removed outlier: 3.664A pdb=" N THR C 468 " --> pdb=" O ASP C 464 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE C 469 " --> pdb=" O MET C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 517 removed outlier: 4.670A pdb=" N LEU C 501 " --> pdb=" O MET C 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 106 removed outlier: 3.515A pdb=" N LYS D 72 " --> pdb=" O LEU D 68 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU D 104 " --> pdb=" O ALA D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 140 Processing helix chain 'D' and resid 140 through 145 Processing helix chain 'D' and resid 194 through 199 Processing helix chain 'D' and resid 204 through 212 removed outlier: 3.550A pdb=" N GLN D 207 " --> pdb=" O ASP D 204 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N SER D 209 " --> pdb=" O ALA D 206 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N PHE D 210 " --> pdb=" O GLN D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 319 Processing helix chain 'D' and resid 346 through 366 Processing helix chain 'D' and resid 377 through 397 Processing helix chain 'D' and resid 400 through 440 Proline residue: D 415 - end of helix Processing helix chain 'D' and resid 448 through 461 Processing helix chain 'D' and resid 464 through 471 removed outlier: 3.721A pdb=" N THR D 468 " --> pdb=" O ASP D 464 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE D 469 " --> pdb=" O MET D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 517 removed outlier: 4.669A pdb=" N LEU D 501 " --> pdb=" O MET D 497 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 119 through 121 removed outlier: 4.142A pdb=" N CYS A 119 " --> pdb=" O ILE A 263 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 121 removed outlier: 4.142A pdb=" N CYS A 119 " --> pdb=" O ILE A 263 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU A 218 " --> pdb=" O TYR A 168 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N TYR A 168 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 119 through 121 removed outlier: 4.140A pdb=" N CYS B 119 " --> pdb=" O ILE B 263 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 119 through 121 removed outlier: 4.140A pdb=" N CYS B 119 " --> pdb=" O ILE B 263 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU B 218 " --> pdb=" O TYR B 168 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N TYR B 168 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 119 through 121 removed outlier: 4.141A pdb=" N CYS C 119 " --> pdb=" O ILE C 263 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 119 through 121 removed outlier: 4.141A pdb=" N CYS C 119 " --> pdb=" O ILE C 263 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU C 218 " --> pdb=" O TYR C 168 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N TYR C 168 " --> pdb=" O LEU C 218 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 119 through 121 removed outlier: 4.140A pdb=" N CYS D 119 " --> pdb=" O ILE D 263 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 119 through 121 removed outlier: 4.140A pdb=" N CYS D 119 " --> pdb=" O ILE D 263 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU D 218 " --> pdb=" O TYR D 168 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N TYR D 168 " --> pdb=" O LEU D 218 " (cutoff:3.500A) 985 hydrogen bonds defined for protein. 2850 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: 4.09 Time building geometry restraints manager: 5.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3661 1.34 - 1.46: 3149 1.46 - 1.59: 5395 1.59 - 1.71: 0 1.71 - 1.83: 88 Bond restraints: 12293 Sorted by residual: bond pdb=" C GLU B 201 " pdb=" N PRO B 202 " ideal model delta sigma weight residual 1.329 1.361 -0.032 1.25e-02 6.40e+03 6.58e+00 bond pdb=" CB THR B 127 " pdb=" CG2 THR B 127 " ideal model delta sigma weight residual 1.521 1.470 0.051 3.30e-02 9.18e+02 2.38e+00 bond pdb=" CB THR A 127 " pdb=" CG2 THR A 127 " ideal model delta sigma weight residual 1.521 1.470 0.051 3.30e-02 9.18e+02 2.35e+00 bond pdb=" CB THR D 127 " pdb=" CG2 THR D 127 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.33e+00 bond pdb=" CB THR C 127 " pdb=" CG2 THR C 127 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.28e+00 ... (remaining 12288 not shown) Histogram of bond angle deviations from ideal: 100.84 - 107.47: 298 107.47 - 114.10: 7111 114.10 - 120.74: 5595 120.74 - 127.37: 3590 127.37 - 134.00: 84 Bond angle restraints: 16678 Sorted by residual: angle pdb=" C ILE C 437 " pdb=" N VAL C 438 " pdb=" CA VAL C 438 " ideal model delta sigma weight residual 122.97 118.96 4.01 9.80e-01 1.04e+00 1.67e+01 angle pdb=" C ILE D 437 " pdb=" N VAL D 438 " pdb=" CA VAL D 438 " ideal model delta sigma weight residual 122.97 118.99 3.98 9.80e-01 1.04e+00 1.65e+01 angle pdb=" C ILE B 437 " pdb=" N VAL B 438 " pdb=" CA VAL B 438 " ideal model delta sigma weight residual 122.97 119.00 3.97 9.80e-01 1.04e+00 1.64e+01 angle pdb=" C ILE A 437 " pdb=" N VAL A 438 " pdb=" CA VAL A 438 " ideal model delta sigma weight residual 122.97 119.06 3.91 9.80e-01 1.04e+00 1.59e+01 angle pdb=" N ASP A 204 " pdb=" CA ASP A 204 " pdb=" C ASP A 204 " ideal model delta sigma weight residual 113.55 109.06 4.49 1.26e+00 6.30e-01 1.27e+01 ... (remaining 16673 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.83: 6755 15.83 - 31.65: 317 31.65 - 47.48: 65 47.48 - 63.30: 11 63.30 - 79.13: 12 Dihedral angle restraints: 7160 sinusoidal: 2624 harmonic: 4536 Sorted by residual: dihedral pdb=" CA GLU A 201 " pdb=" C GLU A 201 " pdb=" N PRO A 202 " pdb=" CA PRO A 202 " ideal model delta harmonic sigma weight residual 180.00 131.48 48.52 0 5.00e+00 4.00e-02 9.42e+01 dihedral pdb=" CB CYS B 243 " pdb=" SG CYS B 243 " pdb=" SG CYS B 274 " pdb=" CB CYS B 274 " ideal model delta sinusoidal sigma weight residual -86.00 -158.42 72.42 1 1.00e+01 1.00e-02 6.70e+01 dihedral pdb=" CB CYS C 243 " pdb=" SG CYS C 243 " pdb=" SG CYS C 274 " pdb=" CB CYS C 274 " ideal model delta sinusoidal sigma weight residual -86.00 -158.40 72.40 1 1.00e+01 1.00e-02 6.70e+01 ... (remaining 7157 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1047 0.036 - 0.071: 625 0.071 - 0.107: 245 0.107 - 0.142: 64 0.142 - 0.178: 33 Chirality restraints: 2014 Sorted by residual: chirality pdb=" CA LEU C 414 " pdb=" N LEU C 414 " pdb=" C LEU C 414 " pdb=" CB LEU C 414 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.89e-01 chirality pdb=" CA LEU D 414 " pdb=" N LEU D 414 " pdb=" C LEU D 414 " pdb=" CB LEU D 414 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.64e-01 chirality pdb=" CA LEU A 414 " pdb=" N LEU A 414 " pdb=" C LEU A 414 " pdb=" CB LEU A 414 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.58e-01 ... (remaining 2011 not shown) Planarity restraints: 2027 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 201 " -0.064 5.00e-02 4.00e+02 9.65e-02 1.49e+01 pdb=" N PRO A 202 " 0.167 5.00e-02 4.00e+02 pdb=" CA PRO A 202 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 202 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 495 " -0.013 2.00e-02 2.50e+03 2.60e-02 6.75e+00 pdb=" C ILE A 495 " 0.045 2.00e-02 2.50e+03 pdb=" O ILE A 495 " -0.017 2.00e-02 2.50e+03 pdb=" N TYR A 496 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 495 " 0.013 2.00e-02 2.50e+03 2.54e-02 6.46e+00 pdb=" C ILE B 495 " -0.044 2.00e-02 2.50e+03 pdb=" O ILE B 495 " 0.016 2.00e-02 2.50e+03 pdb=" N TYR B 496 " 0.015 2.00e-02 2.50e+03 ... (remaining 2024 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 3906 2.84 - 3.35: 11731 3.35 - 3.87: 20018 3.87 - 4.38: 22160 4.38 - 4.90: 38672 Nonbonded interactions: 96487 Sorted by model distance: nonbonded pdb=" OE1 GLN C 473 " pdb=" OG SER C 476 " model vdw 2.320 2.440 nonbonded pdb=" OH TYR B 428 " pdb=" O ALA B 453 " model vdw 2.322 2.440 nonbonded pdb=" OE1 GLN D 473 " pdb=" OG SER D 476 " model vdw 2.322 2.440 nonbonded pdb=" OE1 GLN A 473 " pdb=" OG SER A 476 " model vdw 2.323 2.440 nonbonded pdb=" OE1 GLN B 473 " pdb=" OG SER B 476 " model vdw 2.324 2.440 ... (remaining 96482 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' and (resid 65 through 198 or (resid 199 through 201 and (name N or na \ me CA or name C or name O or name CB )) or resid 202 through 239 or (resid 240 a \ nd (name N or name CA or name C or name O or name CB )) or resid 241 through 492 \ or (resid 493 and (name N or name CA or name C or name O or name CB )) or resid \ 494 through 518)) selection = (chain 'B' and (resid 65 through 198 or (resid 199 through 201 and (name N or na \ me CA or name C or name O or name CB )) or resid 202 through 206 or (resid 207 a \ nd (name N or name CA or name C or name O or name CB )) or resid 208 through 239 \ or (resid 240 and (name N or name CA or name C or name O or name CB )) or resid \ 241 through 453 or (resid 454 and (name N or name CA or name C or name O or nam \ e CB )) or resid 455 through 462 or (resid 463 and (name N or name CA or name C \ or name O or name CB )) or resid 464 through 518)) selection = (chain 'C' and (resid 65 through 198 or (resid 199 through 201 and (name N or na \ me CA or name C or name O or name CB )) or resid 202 through 206 or (resid 207 a \ nd (name N or name CA or name C or name O or name CB )) or resid 208 through 239 \ or (resid 240 and (name N or name CA or name C or name O or name CB )) or resid \ 241 through 462 or (resid 463 and (name N or name CA or name C or name O or nam \ e CB )) or resid 464 through 518)) selection = (chain 'D' and (resid 65 through 199 or (resid 200 through 201 and (name N or na \ me CA or name C or name O or name CB )) or resid 202 through 206 or (resid 207 a \ nd (name N or name CA or name C or name O or name CB )) or resid 208 through 462 \ or (resid 463 and (name N or name CA or name C or name O or name CB )) or resid \ 464 through 518)) } 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: 1.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.360 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 35.450 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 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 : 0.008 0.059 12293 Z= 0.480 Angle : 0.919 8.430 16678 Z= 0.512 Chirality : 0.054 0.178 2014 Planarity : 0.006 0.097 2027 Dihedral : 10.265 79.130 4192 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.62 % Allowed : 3.10 % Favored : 96.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 12.50 % 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: -2.99 (0.18), residues: 1484 helix: -1.22 (0.14), residues: 932 sheet: -2.36 (0.34), residues: 220 loop : -3.35 (0.26), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP B 480 HIS 0.007 0.002 HIS D 257 PHE 0.023 0.003 PHE A 494 TYR 0.020 0.002 TYR A 488 ARG 0.010 0.001 ARG D 395 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 229 time to evaluate : 1.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 TRP cc_start: 0.8366 (m100) cc_final: 0.8031 (m-90) REVERT: B 262 LYS cc_start: 0.9146 (mttt) cc_final: 0.8906 (mtpp) REVERT: B 346 TRP cc_start: 0.8393 (m100) cc_final: 0.8031 (m-90) REVERT: C 346 TRP cc_start: 0.8363 (m100) cc_final: 0.8023 (m-90) REVERT: D 346 TRP cc_start: 0.8401 (m100) cc_final: 0.8031 (m-90) outliers start: 8 outliers final: 0 residues processed: 237 average time/residue: 0.2569 time to fit residues: 85.5715 Evaluate side-chains 116 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 chunk 63 optimal weight: 8.9990 chunk 39 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 46 optimal weight: 6.9990 chunk 72 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 chunk 138 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN A 137 GLN A 220 GLN B 97 ASN B 137 GLN B 220 GLN C 97 ASN C 137 GLN D 97 ASN D 137 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12293 Z= 0.186 Angle : 0.584 10.663 16678 Z= 0.306 Chirality : 0.039 0.147 2014 Planarity : 0.005 0.085 2027 Dihedral : 4.971 38.819 1632 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.32 % Allowed : 8.92 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.25 % 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: -0.52 (0.22), residues: 1484 helix: 0.89 (0.16), residues: 952 sheet: -1.94 (0.31), residues: 248 loop : -2.84 (0.35), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 390 HIS 0.002 0.001 HIS D 192 PHE 0.010 0.001 PHE D 225 TYR 0.007 0.001 TYR D 138 ARG 0.003 0.001 ARG B 395 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 149 time to evaluate : 1.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 TYR cc_start: 0.7103 (p90) cc_final: 0.6689 (p90) REVERT: B 117 TYR cc_start: 0.7176 (p90) cc_final: 0.6610 (p90) REVERT: B 262 LYS cc_start: 0.9159 (mttt) cc_final: 0.8951 (mtpp) REVERT: C 117 TYR cc_start: 0.7191 (p90) cc_final: 0.6752 (p90) REVERT: D 117 TYR cc_start: 0.7131 (p90) cc_final: 0.6715 (p90) outliers start: 17 outliers final: 13 residues processed: 165 average time/residue: 0.2218 time to fit residues: 54.2171 Evaluate side-chains 121 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 108 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 492 SER Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 492 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 114 optimal weight: 7.9990 chunk 93 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 138 optimal weight: 0.9990 chunk 149 optimal weight: 7.9990 chunk 123 optimal weight: 0.9980 chunk 137 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 110 optimal weight: 5.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 GLN B 220 GLN B 471 GLN D 140 HIS D 471 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12293 Z= 0.231 Angle : 0.601 12.781 16678 Z= 0.303 Chirality : 0.039 0.156 2014 Planarity : 0.004 0.073 2027 Dihedral : 4.687 35.505 1632 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.33 % Allowed : 10.09 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.25 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.22), residues: 1484 helix: 1.62 (0.16), residues: 948 sheet: -1.89 (0.31), residues: 248 loop : -2.70 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 346 HIS 0.007 0.001 HIS A 443 PHE 0.018 0.001 PHE D 210 TYR 0.026 0.001 TYR B 117 ARG 0.009 0.001 ARG D 139 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 130 time to evaluate : 1.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 18 residues processed: 158 average time/residue: 0.2036 time to fit residues: 49.3392 Evaluate side-chains 130 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 112 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 492 SER Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 492 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 20.0000 chunk 103 optimal weight: 0.9990 chunk 71 optimal weight: 0.0570 chunk 15 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 138 optimal weight: 0.9990 chunk 146 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 chunk 131 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 overall best weight: 0.6500 ------------------------------------------------------------------------------- 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: 0.7504 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12293 Z= 0.157 Angle : 0.525 9.472 16678 Z= 0.269 Chirality : 0.038 0.146 2014 Planarity : 0.003 0.066 2027 Dihedral : 4.265 29.524 1632 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.48 % Allowed : 10.94 % Favored : 86.58 % 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 (0.22), residues: 1484 helix: 2.06 (0.16), residues: 952 sheet: -1.44 (0.33), residues: 236 loop : -2.53 (0.32), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 346 HIS 0.004 0.001 HIS C 443 PHE 0.011 0.001 PHE D 210 TYR 0.017 0.001 TYR B 117 ARG 0.006 0.001 ARG D 139 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 139 time to evaluate : 1.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 16 residues processed: 166 average time/residue: 0.2240 time to fit residues: 55.7124 Evaluate side-chains 138 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 122 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 449 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 5.9990 chunk 83 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 109 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 125 optimal weight: 0.9990 chunk 101 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 HIS B 103 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12293 Z= 0.223 Angle : 0.566 10.642 16678 Z= 0.289 Chirality : 0.039 0.153 2014 Planarity : 0.003 0.060 2027 Dihedral : 4.248 27.734 1632 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.94 % Allowed : 13.34 % Favored : 84.72 % 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: 1.07 (0.23), residues: 1484 helix: 2.24 (0.17), residues: 952 sheet: -1.47 (0.34), residues: 228 loop : -2.59 (0.32), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 346 HIS 0.004 0.001 HIS C 443 PHE 0.010 0.001 PHE A 388 TYR 0.012 0.001 TYR B 117 ARG 0.005 0.000 ARG D 139 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 132 time to evaluate : 1.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.6057 (ttm) cc_final: 0.5704 (ttt) REVERT: B 317 ARG cc_start: 0.8327 (mmm160) cc_final: 0.8124 (mmm160) REVERT: B 356 MET cc_start: 0.8078 (mmm) cc_final: 0.7485 (mtm) REVERT: C 75 MET cc_start: 0.5921 (ttm) cc_final: 0.5566 (ttt) REVERT: C 390 TRP cc_start: 0.8458 (m100) cc_final: 0.8081 (m100) REVERT: D 356 MET cc_start: 0.8069 (mmm) cc_final: 0.7485 (mtm) REVERT: D 501 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8445 (mm) outliers start: 25 outliers final: 10 residues processed: 155 average time/residue: 0.2472 time to fit residues: 57.4799 Evaluate side-chains 131 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 120 time to evaluate : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 501 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 147 optimal weight: 0.2980 chunk 122 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 12 optimal weight: 8.9990 chunk 48 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 103 HIS D 103 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12293 Z= 0.211 Angle : 0.579 13.712 16678 Z= 0.288 Chirality : 0.039 0.160 2014 Planarity : 0.003 0.056 2027 Dihedral : 4.194 25.122 1632 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.86 % Allowed : 13.50 % Favored : 84.64 % 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: 1.20 (0.23), residues: 1484 helix: 2.31 (0.16), residues: 952 sheet: -1.40 (0.33), residues: 236 loop : -2.47 (0.33), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 390 HIS 0.003 0.001 HIS C 443 PHE 0.009 0.001 PHE B 494 TYR 0.011 0.001 TYR A 117 ARG 0.004 0.000 ARG D 139 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 136 time to evaluate : 1.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.6074 (ttm) cc_final: 0.5721 (ttt) REVERT: A 356 MET cc_start: 0.7993 (mmm) cc_final: 0.7750 (mmt) REVERT: C 75 MET cc_start: 0.6038 (ttm) cc_final: 0.5695 (ttt) REVERT: C 356 MET cc_start: 0.7945 (mmm) cc_final: 0.7713 (mmt) outliers start: 24 outliers final: 19 residues processed: 155 average time/residue: 0.2122 time to fit residues: 49.6560 Evaluate side-chains 146 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 127 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 449 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 8.9990 chunk 16 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 123 optimal weight: 0.6980 chunk 82 optimal weight: 0.5980 chunk 146 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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: 0.7512 moved from start: 0.3951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12293 Z= 0.179 Angle : 0.604 14.531 16678 Z= 0.288 Chirality : 0.039 0.165 2014 Planarity : 0.003 0.052 2027 Dihedral : 4.100 22.554 1632 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.86 % Allowed : 14.12 % Favored : 84.02 % 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: 1.27 (0.22), residues: 1484 helix: 2.36 (0.16), residues: 952 sheet: -1.38 (0.32), residues: 236 loop : -2.43 (0.34), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 390 HIS 0.003 0.001 HIS A 443 PHE 0.012 0.001 PHE B 388 TYR 0.011 0.001 TYR B 117 ARG 0.003 0.000 ARG D 139 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 137 time to evaluate : 1.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.6024 (ttm) cc_final: 0.5653 (ttt) REVERT: B 356 MET cc_start: 0.8043 (mmm) cc_final: 0.7591 (mtm) REVERT: C 75 MET cc_start: 0.5953 (ttm) cc_final: 0.5612 (ttt) REVERT: C 494 PHE cc_start: 0.8577 (m-80) cc_final: 0.8321 (m-80) REVERT: D 356 MET cc_start: 0.8028 (mmm) cc_final: 0.7584 (mtm) outliers start: 24 outliers final: 19 residues processed: 157 average time/residue: 0.2050 time to fit residues: 48.2859 Evaluate side-chains 138 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 119 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 449 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 9.9990 chunk 87 optimal weight: 1.9990 chunk 44 optimal weight: 0.4980 chunk 28 optimal weight: 0.8980 chunk 93 optimal weight: 0.0370 chunk 99 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 chunk 133 optimal weight: 3.9990 chunk 140 optimal weight: 5.9990 overall best weight: 0.8860 ------------------------------------------------------------------------------- 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: 0.7512 moved from start: 0.4094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12293 Z= 0.187 Angle : 0.618 14.935 16678 Z= 0.297 Chirality : 0.039 0.169 2014 Planarity : 0.003 0.049 2027 Dihedral : 4.034 19.986 1632 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.78 % Allowed : 15.67 % Favored : 82.54 % 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: 1.39 (0.22), residues: 1484 helix: 2.53 (0.16), residues: 940 sheet: -1.47 (0.32), residues: 236 loop : -2.31 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 390 HIS 0.002 0.001 HIS C 443 PHE 0.012 0.001 PHE B 494 TYR 0.010 0.001 TYR B 486 ARG 0.003 0.000 ARG D 139 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 130 time to evaluate : 1.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 MET cc_start: 0.8075 (mmm) cc_final: 0.7737 (mmt) REVERT: B 356 MET cc_start: 0.8020 (mmm) cc_final: 0.7589 (mtm) REVERT: C 75 MET cc_start: 0.5947 (ttm) cc_final: 0.5600 (ttt) REVERT: C 356 MET cc_start: 0.8066 (mmm) cc_final: 0.7732 (mmt) REVERT: D 356 MET cc_start: 0.7996 (mmm) cc_final: 0.7649 (mtm) REVERT: D 390 TRP cc_start: 0.8469 (m100) cc_final: 0.8110 (m100) outliers start: 23 outliers final: 20 residues processed: 148 average time/residue: 0.2132 time to fit residues: 47.6932 Evaluate side-chains 141 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 121 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 449 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 2.9990 chunk 136 optimal weight: 9.9990 chunk 140 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 123 optimal weight: 10.0000 chunk 129 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 144 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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: 0.7511 moved from start: 0.4192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12293 Z= 0.189 Angle : 0.627 14.516 16678 Z= 0.298 Chirality : 0.039 0.170 2014 Planarity : 0.003 0.045 2027 Dihedral : 3.969 19.373 1632 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.94 % Allowed : 15.44 % Favored : 82.62 % 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: 1.39 (0.22), residues: 1484 helix: 2.50 (0.16), residues: 952 sheet: -1.51 (0.31), residues: 236 loop : -2.33 (0.34), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 390 HIS 0.002 0.001 HIS C 443 PHE 0.012 0.001 PHE B 494 TYR 0.009 0.001 TYR B 486 ARG 0.003 0.000 ARG D 139 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 124 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 MET cc_start: 0.8057 (mmm) cc_final: 0.7726 (mmt) REVERT: A 494 PHE cc_start: 0.8781 (m-80) cc_final: 0.8576 (m-80) REVERT: B 356 MET cc_start: 0.7964 (mmm) cc_final: 0.7566 (mtm) REVERT: B 494 PHE cc_start: 0.8609 (OUTLIER) cc_final: 0.8243 (m-80) REVERT: C 356 MET cc_start: 0.8045 (mmm) cc_final: 0.7717 (mmt) REVERT: C 494 PHE cc_start: 0.8602 (m-80) cc_final: 0.8317 (m-80) REVERT: D 356 MET cc_start: 0.7936 (mmm) cc_final: 0.7636 (mtm) outliers start: 25 outliers final: 20 residues processed: 143 average time/residue: 0.2260 time to fit residues: 48.8063 Evaluate side-chains 141 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 120 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 449 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 151 optimal weight: 0.9980 chunk 139 optimal weight: 4.9990 chunk 120 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 93 optimal weight: 0.0980 chunk 73 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.7499 moved from start: 0.4289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 12293 Z= 0.174 Angle : 0.621 17.545 16678 Z= 0.293 Chirality : 0.039 0.174 2014 Planarity : 0.003 0.044 2027 Dihedral : 3.954 19.107 1632 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.63 % Allowed : 15.83 % Favored : 82.54 % 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: 1.41 (0.22), residues: 1484 helix: 2.50 (0.16), residues: 948 sheet: -1.50 (0.31), residues: 236 loop : -2.25 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 346 HIS 0.002 0.001 HIS C 443 PHE 0.012 0.001 PHE B 494 TYR 0.009 0.001 TYR B 486 ARG 0.003 0.000 ARG D 139 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 123 time to evaluate : 1.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 MET cc_start: 0.8053 (mmm) cc_final: 0.7695 (mmt) REVERT: B 356 MET cc_start: 0.7936 (mmm) cc_final: 0.7662 (mtm) REVERT: B 494 PHE cc_start: 0.8608 (OUTLIER) cc_final: 0.8206 (m-80) REVERT: C 356 MET cc_start: 0.8004 (mmm) cc_final: 0.7673 (mmt) REVERT: C 494 PHE cc_start: 0.8660 (m-80) cc_final: 0.8397 (m-80) REVERT: D 356 MET cc_start: 0.7937 (mmm) cc_final: 0.7643 (mtm) REVERT: D 390 TRP cc_start: 0.8481 (m100) cc_final: 0.8127 (m100) outliers start: 21 outliers final: 18 residues processed: 140 average time/residue: 0.2144 time to fit residues: 45.5261 Evaluate side-chains 133 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 114 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 449 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 120 optimal weight: 0.7980 chunk 50 optimal weight: 0.0030 chunk 124 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 22 optimal weight: 10.0000 chunk 106 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.7194 ------------------------------------------------------------------------------- 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 = 0.3935 r_free = 0.3935 target = 0.098790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.076185 restraints weight = 42051.070| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 3.54 r_work: 0.3461 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.4449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 12293 Z= 0.177 Angle : 0.635 16.337 16678 Z= 0.298 Chirality : 0.039 0.173 2014 Planarity : 0.003 0.042 2027 Dihedral : 3.874 18.140 1632 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.86 % Allowed : 15.36 % Favored : 82.78 % 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: 1.45 (0.22), residues: 1484 helix: 2.52 (0.16), residues: 952 sheet: -1.47 (0.32), residues: 236 loop : -2.27 (0.34), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 346 HIS 0.002 0.001 HIS C 443 PHE 0.017 0.001 PHE A 494 TYR 0.009 0.001 TYR B 486 ARG 0.003 0.000 ARG D 139 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2540.73 seconds wall clock time: 47 minutes 16.74 seconds (2836.74 seconds total)