Starting phenix.real_space_refine on Thu Jun 27 14:53:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ut6_42531/06_2024/8ut6_42531_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ut6_42531/06_2024/8ut6_42531.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ut6_42531/06_2024/8ut6_42531.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ut6_42531/06_2024/8ut6_42531.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ut6_42531/06_2024/8ut6_42531_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ut6_42531/06_2024/8ut6_42531_updated.pdb" } resolution = 2.8 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= 0.026 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 54 5.16 5 C 8094 2.51 5 N 2314 2.21 5 O 2584 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 13046 Number of models: 1 Model: "" Number of chains: 11 Chain: "G" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 630 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 126} Link IDs: {'TRANS': 125} Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 378 Unresolved non-hydrogen dihedrals: 126 Planarities with less than four sites: {'UNK:plan-1': 126} Unresolved non-hydrogen planarities: 126 Chain: "H" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 535 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 107} Link IDs: {'TRANS': 106} Unresolved non-hydrogen bonds: 214 Unresolved non-hydrogen angles: 321 Unresolved non-hydrogen dihedrals: 107 Planarities with less than four sites: {'UNK:plan-1': 107} Unresolved non-hydrogen planarities: 107 Chain: "A" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3851 Classifications: {'peptide': 487} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 467} Chain breaks: 1 Chain: "C" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3851 Classifications: {'peptide': 487} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 467} Chain breaks: 1 Chain: "E" Number of atoms: 3843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3843 Classifications: {'peptide': 486} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 466} Chain breaks: 1 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 9.30, per 1000 atoms: 0.71 Number of scatterers: 13046 At special positions: 0 Unit cell: (84.1, 122.525, 145.725, 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 54 16.00 O 2584 8.00 N 2314 7.00 C 8094 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS A 466 " distance=2.03 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.04 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.03 Simple disulfide: pdb=" SG CYS A 473 " - pdb=" SG CYS A 477 " distance=2.02 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS C 466 " distance=2.03 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.04 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.03 Simple disulfide: pdb=" SG CYS C 473 " - pdb=" SG CYS C 477 " distance=2.03 Simple disulfide: pdb=" SG CYS E 14 " - pdb=" SG CYS E 466 " distance=2.03 Simple disulfide: pdb=" SG CYS E 52 " - pdb=" SG CYS E 277 " distance=2.04 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 76 " distance=2.03 Simple disulfide: pdb=" SG CYS E 97 " - pdb=" SG CYS E 139 " distance=2.04 Simple disulfide: pdb=" SG CYS E 281 " - pdb=" SG CYS E 305 " distance=2.03 Simple disulfide: pdb=" SG CYS E 473 " - pdb=" SG CYS E 477 " 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG D 1 " - " NAG D 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A 601 " - " ASN A 38 " " NAG A 602 " - " ASN A 63 " " NAG A 603 " - " ASN A 133 " " NAG A 604 " - " ASN A 246 " " NAG A 605 " - " ASN A 285 " " NAG A 606 " - " ASN A 483 " " NAG B 1 " - " ASN A 165 " " NAG C 601 " - " ASN C 38 " " NAG C 602 " - " ASN C 63 " " NAG C 603 " - " ASN C 133 " " NAG C 604 " - " ASN C 246 " " NAG C 605 " - " ASN C 285 " " NAG C 606 " - " ASN C 483 " " NAG D 1 " - " ASN C 165 " " NAG E 601 " - " ASN E 38 " " NAG E 602 " - " ASN E 63 " " NAG E 603 " - " ASN E 133 " " NAG E 604 " - " ASN E 246 " " NAG E 605 " - " ASN E 285 " " NAG E 606 " - " ASN E 483 " " NAG F 1 " - " ASN E 165 " Time building additional restraints: 5.10 Conformation dependent library (CDL) restraints added in 2.0 seconds 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3176 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 29 helices and 37 sheets defined 24.9% alpha, 23.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.20 Creating SS restraints... Processing helix chain 'G' and resid 62 through 64 No H-bonds generated for 'chain 'G' and resid 62 through 64' Processing helix chain 'G' and resid 88 through 90 No H-bonds generated for 'chain 'G' and resid 88 through 90' Processing helix chain 'G' and resid 109 through 112 Processing helix chain 'H' and resid 31 through 33 No H-bonds generated for 'chain 'H' and resid 31 through 33' Processing helix chain 'H' and resid 81 through 83 No H-bonds generated for 'chain 'H' and resid 81 through 83' Processing helix chain 'A' and resid 66 through 71 Processing helix chain 'A' and resid 74 through 79 removed outlier: 4.086A pdb=" N ASP A 77 " --> pdb=" O PRO A 74 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N GLY A 78 " --> pdb=" O GLN A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 115 Processing helix chain 'A' and resid 188 through 195 Processing helix chain 'A' and resid 367 through 384 Processing helix chain 'A' and resid 405 through 455 Processing helix chain 'A' and resid 477 through 483 Processing helix chain 'A' and resid 492 through 500 Processing helix chain 'C' and resid 66 through 71 Processing helix chain 'C' and resid 74 through 79 removed outlier: 4.918A pdb=" N GLY C 78 " --> pdb=" O GLN C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 115 Processing helix chain 'C' and resid 188 through 195 Processing helix chain 'C' and resid 367 through 384 Processing helix chain 'C' and resid 405 through 455 Processing helix chain 'C' and resid 475 through 482 Processing helix chain 'C' and resid 492 through 499 Processing helix chain 'E' and resid 66 through 71 Processing helix chain 'E' and resid 74 through 79 removed outlier: 3.710A pdb=" N ASP E 77 " --> pdb=" O PRO E 74 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N GLY E 78 " --> pdb=" O GLN E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 115 Processing helix chain 'E' and resid 188 through 195 Processing helix chain 'E' and resid 367 through 384 Processing helix chain 'E' and resid 405 through 455 Processing helix chain 'E' and resid 475 through 482 Processing helix chain 'E' and resid 492 through 499 Processing sheet with id= A, first strand: chain 'G' and resid 3 through 6 Processing sheet with id= B, first strand: chain 'G' and resid 10 through 12 Processing sheet with id= C, first strand: chain 'G' and resid 92 through 98 removed outlier: 6.185A pdb=" N UNK G 38 " --> pdb=" O UNK G 47 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N UNK G 47 " --> pdb=" O UNK G 38 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N UNK G 40 " --> pdb=" O UNK G 45 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N UNK G 45 " --> pdb=" O UNK G 40 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.077A pdb=" N UNK H 105 " --> pdb=" O UNK H 11 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'H' and resid 19 through 24 Processing sheet with id= F, first strand: chain 'H' and resid 98 through 100 removed outlier: 5.896A pdb=" N UNK H 38 " --> pdb=" O UNK H 47 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N UNK H 47 " --> pdb=" O UNK H 38 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 361 through 365 Processing sheet with id= H, first strand: chain 'A' and resid 24 through 26 Processing sheet with id= I, first strand: chain 'A' and resid 39 through 41 Processing sheet with id= J, first strand: chain 'A' and resid 50 through 52 No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'A' and resid 58 through 60 removed outlier: 6.706A pdb=" N LEU A 86 " --> pdb=" O LEU A 59 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N SER A 266 " --> pdb=" O PHE A 87 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N GLU A 89 " --> pdb=" O SER A 266 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N MET A 268 " --> pdb=" O GLU A 89 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'A' and resid 151 through 153 Processing sheet with id= M, first strand: chain 'A' and resid 164 through 169 Processing sheet with id= N, first strand: chain 'A' and resid 176 through 184 Processing sheet with id= O, first strand: chain 'A' and resid 281 through 283 Processing sheet with id= P, first strand: chain 'A' and resid 136 through 141 removed outlier: 3.841A pdb=" N SER A 146 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N ALA A 138 " --> pdb=" O LYS A 144 " (cutoff:3.500A) removed outlier: 10.445A pdb=" N LYS A 144 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 360 through 366 removed outlier: 4.412A pdb=" N TYR C 351 " --> pdb=" O ASP C 366 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 24 through 26 Processing sheet with id= S, first strand: chain 'C' and resid 50 through 52 No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'C' and resid 58 through 60 removed outlier: 6.783A pdb=" N LEU C 86 " --> pdb=" O LEU C 59 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N SER C 266 " --> pdb=" O PHE C 87 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N GLU C 89 " --> pdb=" O SER C 266 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N MET C 268 " --> pdb=" O GLU C 89 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'C' and resid 120 through 122 Processing sheet with id= V, first strand: chain 'C' and resid 151 through 153 Processing sheet with id= W, first strand: chain 'C' and resid 164 through 169 Processing sheet with id= X, first strand: chain 'C' and resid 176 through 184 Processing sheet with id= Y, first strand: chain 'C' and resid 281 through 283 removed outlier: 4.237A pdb=" N CYS C 281 " --> pdb=" O ILE C 288 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'C' and resid 303 through 305 Processing sheet with id= AA, first strand: chain 'E' and resid 361 through 365 Processing sheet with id= AB, first strand: chain 'E' and resid 24 through 26 Processing sheet with id= AC, first strand: chain 'E' and resid 39 through 41 Processing sheet with id= AD, first strand: chain 'E' and resid 50 through 52 No H-bonds generated for sheet with id= AD Processing sheet with id= AE, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.943A pdb=" N LEU E 86 " --> pdb=" O LEU E 59 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N SER E 266 " --> pdb=" O PHE E 87 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N GLU E 89 " --> pdb=" O SER E 266 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N MET E 268 " --> pdb=" O GLU E 89 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE Processing sheet with id= AF, first strand: chain 'E' and resid 100 through 102 removed outlier: 6.292A pdb=" N ILE E 230 " --> pdb=" O ASP E 101 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'E' and resid 120 through 122 Processing sheet with id= AH, first strand: chain 'E' and resid 151 through 153 Processing sheet with id= AI, first strand: chain 'E' and resid 164 through 169 Processing sheet with id= AJ, first strand: chain 'E' and resid 281 through 283 removed outlier: 4.265A pdb=" N CYS E 281 " --> pdb=" O ILE E 288 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'E' and resid 303 through 305 469 hydrogen bonds defined for protein. 1290 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.85 Time building geometry restraints manager: 5.60 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: 4407 1.34 - 1.47: 3094 1.47 - 1.59: 5707 1.59 - 1.72: 1 1.72 - 1.84: 72 Bond restraints: 13281 Sorted by residual: bond pdb=" CG PRO C 162 " pdb=" CD PRO C 162 " ideal model delta sigma weight residual 1.503 1.379 0.124 3.40e-02 8.65e+02 1.32e+01 bond pdb=" CA UNK G 118 " pdb=" CB UNK G 118 " ideal model delta sigma weight residual 1.530 1.475 0.055 2.00e-02 2.50e+03 7.56e+00 bond pdb=" CB PRO C 162 " pdb=" CG PRO C 162 " ideal model delta sigma weight residual 1.492 1.620 -0.128 5.00e-02 4.00e+02 6.53e+00 bond pdb=" N PRO C 162 " pdb=" CD PRO C 162 " ideal model delta sigma weight residual 1.473 1.507 -0.034 1.40e-02 5.10e+03 5.96e+00 bond pdb=" CA UNK H 65 " pdb=" CB UNK H 65 " ideal model delta sigma weight residual 1.530 1.486 0.044 2.00e-02 2.50e+03 4.75e+00 ... (remaining 13276 not shown) Histogram of bond angle deviations from ideal: 95.04 - 102.84: 31 102.84 - 110.64: 4019 110.64 - 118.43: 6345 118.43 - 126.23: 7433 126.23 - 134.02: 199 Bond angle restraints: 18027 Sorted by residual: angle pdb=" CA PRO C 162 " pdb=" N PRO C 162 " pdb=" CD PRO C 162 " ideal model delta sigma weight residual 112.00 99.07 12.93 1.40e+00 5.10e-01 8.52e+01 angle pdb=" N PRO C 162 " pdb=" CD PRO C 162 " pdb=" CG PRO C 162 " ideal model delta sigma weight residual 103.20 95.04 8.16 1.50e+00 4.44e-01 2.96e+01 angle pdb=" C UNK H 99 " pdb=" N UNK H 100 " pdb=" CA UNK H 100 " ideal model delta sigma weight residual 121.70 114.70 7.00 1.80e+00 3.09e-01 1.51e+01 angle pdb=" CB MET A 168 " pdb=" CG MET A 168 " pdb=" SD MET A 168 " ideal model delta sigma weight residual 112.70 102.44 10.26 3.00e+00 1.11e-01 1.17e+01 angle pdb=" N ARG C 354 " pdb=" CA ARG C 354 " pdb=" C ARG C 354 " ideal model delta sigma weight residual 109.24 103.65 5.59 1.67e+00 3.59e-01 1.12e+01 ... (remaining 18022 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 7655 17.99 - 35.98: 464 35.98 - 53.96: 158 53.96 - 71.95: 44 71.95 - 89.94: 15 Dihedral angle restraints: 8336 sinusoidal: 3427 harmonic: 4909 Sorted by residual: dihedral pdb=" CB CYS C 52 " pdb=" SG CYS C 52 " pdb=" SG CYS C 277 " pdb=" CB CYS C 277 " ideal model delta sinusoidal sigma weight residual 93.00 43.25 49.75 1 1.00e+01 1.00e-02 3.40e+01 dihedral pdb=" CA LYS C 276 " pdb=" C LYS C 276 " pdb=" N CYS C 277 " pdb=" CA CYS C 277 " ideal model delta harmonic sigma weight residual -180.00 -153.69 -26.31 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CB CYS A 64 " pdb=" SG CYS A 64 " pdb=" SG CYS A 76 " pdb=" CB CYS A 76 " ideal model delta sinusoidal sigma weight residual -86.00 -126.91 40.91 1 1.00e+01 1.00e-02 2.35e+01 ... (remaining 8333 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1554 0.053 - 0.105: 418 0.105 - 0.158: 98 0.158 - 0.210: 7 0.210 - 0.263: 5 Chirality restraints: 2082 Sorted by residual: chirality pdb=" C1 NAG A 606 " pdb=" ND2 ASN A 483 " pdb=" C2 NAG A 606 " pdb=" O5 NAG A 606 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA PRO C 162 " pdb=" N PRO C 162 " pdb=" C PRO C 162 " pdb=" CB PRO C 162 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" C1 NAG A 604 " pdb=" ND2 ASN A 246 " pdb=" C2 NAG A 604 " pdb=" O5 NAG A 604 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 2079 not shown) Planarity restraints: 2378 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR C 161 " -0.095 5.00e-02 4.00e+02 1.32e-01 2.80e+01 pdb=" N PRO C 162 " 0.228 5.00e-02 4.00e+02 pdb=" CA PRO C 162 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO C 162 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA UNK H 99 " -0.020 2.00e-02 2.50e+03 3.89e-02 1.51e+01 pdb=" C UNK H 99 " 0.067 2.00e-02 2.50e+03 pdb=" O UNK H 99 " -0.025 2.00e-02 2.50e+03 pdb=" N UNK H 100 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA UNK G 116 " 0.020 2.00e-02 2.50e+03 3.85e-02 1.48e+01 pdb=" C UNK G 116 " -0.067 2.00e-02 2.50e+03 pdb=" O UNK G 116 " 0.025 2.00e-02 2.50e+03 pdb=" N UNK G 117 " 0.022 2.00e-02 2.50e+03 ... (remaining 2375 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 229 2.65 - 3.21: 11342 3.21 - 3.77: 20555 3.77 - 4.34: 29321 4.34 - 4.90: 47721 Nonbonded interactions: 109168 Sorted by model distance: nonbonded pdb=" O ASP E 438 " pdb=" OG SER E 442 " model vdw 2.085 2.440 nonbonded pdb=" NE2 GLN C 210 " pdb=" OD2 ASP E 101 " model vdw 2.144 2.520 nonbonded pdb=" OD2 ASP A 408 " pdb=" OG SER E 110 " model vdw 2.171 2.440 nonbonded pdb=" NZ LYS A 380 " pdb=" OE1 GLU A 432 " model vdw 2.179 2.520 nonbonded pdb=" OD1 ASN C 121 " pdb=" NZ LYS C 259 " model vdw 2.208 2.520 ... (remaining 109163 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 8 through 501 or resid 601 through 606)) selection = (chain 'C' and (resid 8 through 501 or resid 601 through 606)) selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } 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: 4.740 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: 17.780 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 39.120 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.080 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:10.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.128 13281 Z= 0.376 Angle : 0.947 12.926 18027 Z= 0.493 Chirality : 0.052 0.263 2082 Planarity : 0.006 0.132 2357 Dihedral : 13.948 89.941 5106 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.00 % Allowed : 13.70 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.19), residues: 1448 helix: 1.40 (0.23), residues: 351 sheet: 0.56 (0.28), residues: 294 loop : -0.29 (0.19), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 421 HIS 0.009 0.001 HIS A 156 PHE 0.030 0.002 PHE A 353 TYR 0.020 0.002 TYR E 195 ARG 0.010 0.001 ARG E 109 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 SER cc_start: 0.7393 (t) cc_final: 0.6975 (p) REVERT: A 415 ASP cc_start: 0.7405 (t0) cc_final: 0.6859 (m-30) REVERT: C 382 ASN cc_start: 0.7884 (t0) cc_final: 0.7603 (t0) outliers start: 0 outliers final: 1 residues processed: 133 average time/residue: 1.0897 time to fit residues: 160.1063 Evaluate side-chains 121 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 120 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 101 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 150 optimal weight: 0.8980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 HIS A 18 HIS A 57 GLN ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 211 GLN A 295 GLN A 355 HIS A 454 GLN C 56 HIS ** C 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 363 GLN C 435 HIS ** E 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 363 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 13281 Z= 0.392 Angle : 0.676 11.405 18027 Z= 0.348 Chirality : 0.047 0.264 2082 Planarity : 0.005 0.060 2357 Dihedral : 5.940 55.129 2314 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.27 % Allowed : 12.14 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.10 (0.20), residues: 1448 helix: 1.51 (0.25), residues: 354 sheet: -0.22 (0.27), residues: 275 loop : -0.43 (0.20), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 234 HIS 0.010 0.002 HIS A 184 PHE 0.019 0.002 PHE A 353 TYR 0.016 0.002 TYR C 486 ARG 0.007 0.001 ARG C 150 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 134 time to evaluate : 1.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLN cc_start: 0.7192 (OUTLIER) cc_final: 0.6586 (mt0) REVERT: A 340 GLU cc_start: 0.6407 (mt-10) cc_final: 0.6143 (tt0) REVERT: A 344 GLU cc_start: 0.6388 (OUTLIER) cc_final: 0.5566 (mp0) REVERT: A 396 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7411 (pm20) REVERT: E 139 CYS cc_start: 0.7391 (m) cc_final: 0.7143 (m) REVERT: E 242 ILE cc_start: 0.8134 (mt) cc_final: 0.7878 (mp) REVERT: E 261 ARG cc_start: 0.7027 (mmt90) cc_final: 0.6050 (ptt180) outliers start: 29 outliers final: 13 residues processed: 153 average time/residue: 1.1543 time to fit residues: 194.4518 Evaluate side-chains 132 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 116 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 CYS Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 235 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 83 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 125 optimal weight: 0.5980 chunk 102 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 151 optimal weight: 0.5980 chunk 163 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 149 optimal weight: 5.9990 chunk 51 optimal weight: 0.5980 chunk 121 optimal weight: 2.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 435 HIS ** E 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 211 GLN E 296 ASN E 312 ASN E 363 GLN E 454 GLN E 497 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13281 Z= 0.190 Angle : 0.512 10.427 18027 Z= 0.267 Chirality : 0.041 0.228 2082 Planarity : 0.004 0.040 2357 Dihedral : 5.291 51.504 2312 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.35 % Allowed : 12.76 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.20), residues: 1448 helix: 1.99 (0.26), residues: 348 sheet: -0.32 (0.28), residues: 269 loop : -0.44 (0.20), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 421 HIS 0.004 0.001 HIS A 184 PHE 0.015 0.001 PHE A 353 TYR 0.013 0.001 TYR E 195 ARG 0.005 0.000 ARG C 321 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 136 time to evaluate : 1.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 SER cc_start: 0.7449 (t) cc_final: 0.7032 (p) REVERT: A 82 LYS cc_start: 0.7173 (OUTLIER) cc_final: 0.6807 (ttmm) REVERT: A 340 GLU cc_start: 0.6425 (mt-10) cc_final: 0.6123 (tt0) REVERT: A 344 GLU cc_start: 0.6389 (OUTLIER) cc_final: 0.5562 (mp0) REVERT: A 396 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7385 (pm20) REVERT: C 33 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7526 (mt0) REVERT: E 242 ILE cc_start: 0.8094 (mt) cc_final: 0.7824 (mp) REVERT: E 261 ARG cc_start: 0.6942 (mmt90) cc_final: 0.6028 (ptt180) outliers start: 30 outliers final: 10 residues processed: 152 average time/residue: 1.1662 time to fit residues: 194.8149 Evaluate side-chains 132 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 118 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 CYS Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain C residue 33 GLN Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain E residue 235 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 149 optimal weight: 7.9990 chunk 113 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 16 optimal weight: 9.9990 chunk 72 optimal weight: 1.9990 chunk 101 optimal weight: 0.4980 chunk 151 optimal weight: 4.9990 chunk 160 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 HIS C 363 GLN C 435 HIS ** E 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 ASN E 312 ASN E 363 GLN E 497 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13281 Z= 0.298 Angle : 0.571 11.490 18027 Z= 0.293 Chirality : 0.043 0.244 2082 Planarity : 0.004 0.043 2357 Dihedral : 5.420 56.590 2312 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.74 % Allowed : 12.61 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.01 (0.20), residues: 1448 helix: 1.77 (0.26), residues: 352 sheet: -0.54 (0.28), residues: 273 loop : -0.59 (0.20), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 234 HIS 0.006 0.002 HIS A 184 PHE 0.013 0.002 PHE A 353 TYR 0.012 0.002 TYR E 195 ARG 0.005 0.000 ARG C 150 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 131 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 SER cc_start: 0.7488 (t) cc_final: 0.7048 (p) REVERT: A 75 GLN cc_start: 0.7102 (OUTLIER) cc_final: 0.6493 (mt0) REVERT: A 82 LYS cc_start: 0.7271 (OUTLIER) cc_final: 0.6940 (ttmm) REVERT: A 189 LYS cc_start: 0.7343 (mttt) cc_final: 0.6760 (mtpm) REVERT: A 340 GLU cc_start: 0.6422 (mt-10) cc_final: 0.6109 (tt0) REVERT: A 344 GLU cc_start: 0.6372 (OUTLIER) cc_final: 0.5546 (mp0) REVERT: A 396 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7573 (pm20) REVERT: E 242 ILE cc_start: 0.8160 (mt) cc_final: 0.7878 (mp) REVERT: E 261 ARG cc_start: 0.6964 (mmt90) cc_final: 0.6028 (ptt180) outliers start: 35 outliers final: 17 residues processed: 157 average time/residue: 1.1888 time to fit residues: 204.4311 Evaluate side-chains 141 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 120 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 CYS Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 312 ASN Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 335 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 133 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 chunk 119 optimal weight: 6.9990 chunk 66 optimal weight: 0.6980 chunk 136 optimal weight: 2.9990 chunk 110 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 144 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN A 371 GLN ** C 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 363 GLN C 435 HIS ** E 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 ASN E 312 ASN E 363 GLN E 497 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13281 Z= 0.202 Angle : 0.507 10.827 18027 Z= 0.262 Chirality : 0.041 0.236 2082 Planarity : 0.004 0.040 2357 Dihedral : 5.107 53.974 2312 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.58 % Allowed : 13.70 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.02 (0.20), residues: 1448 helix: 1.92 (0.26), residues: 350 sheet: -0.63 (0.28), residues: 273 loop : -0.58 (0.20), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 421 HIS 0.017 0.001 HIS C 18 PHE 0.013 0.001 PHE A 353 TYR 0.011 0.002 TYR E 195 ARG 0.003 0.000 ARG C 150 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 137 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 SER cc_start: 0.7440 (t) cc_final: 0.7045 (p) REVERT: A 75 GLN cc_start: 0.7120 (OUTLIER) cc_final: 0.6519 (mt0) REVERT: A 82 LYS cc_start: 0.7188 (OUTLIER) cc_final: 0.6871 (ttmm) REVERT: A 189 LYS cc_start: 0.7326 (mttt) cc_final: 0.6743 (mtpm) REVERT: A 340 GLU cc_start: 0.6363 (mt-10) cc_final: 0.6077 (tt0) REVERT: A 344 GLU cc_start: 0.6382 (OUTLIER) cc_final: 0.5550 (mp0) REVERT: A 396 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7408 (pm20) REVERT: E 242 ILE cc_start: 0.8126 (mt) cc_final: 0.7818 (mp) REVERT: E 261 ARG cc_start: 0.6945 (mmt90) cc_final: 0.6003 (ptt180) outliers start: 33 outliers final: 19 residues processed: 158 average time/residue: 1.2049 time to fit residues: 208.8016 Evaluate side-chains 145 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 122 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 CYS Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 83 LYS Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 312 ASN Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 335 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 53 optimal weight: 4.9990 chunk 144 optimal weight: 0.9980 chunk 31 optimal weight: 0.0060 chunk 94 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 160 optimal weight: 5.9990 chunk 133 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 13 optimal weight: 20.0000 chunk 84 optimal weight: 0.9980 chunk 154 optimal weight: 0.9980 overall best weight: 0.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN ** C 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 363 GLN C 435 HIS ** E 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 312 ASN E 363 GLN E 497 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13281 Z= 0.225 Angle : 0.514 10.770 18027 Z= 0.263 Chirality : 0.042 0.236 2082 Planarity : 0.004 0.040 2357 Dihedral : 5.056 53.695 2312 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.43 % Allowed : 14.17 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.02 (0.21), residues: 1448 helix: 1.97 (0.26), residues: 349 sheet: -0.65 (0.28), residues: 273 loop : -0.59 (0.20), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 127 HIS 0.006 0.001 HIS C 18 PHE 0.017 0.001 PHE E 125 TYR 0.011 0.002 TYR E 195 ARG 0.003 0.000 ARG C 150 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 127 time to evaluate : 1.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 SER cc_start: 0.7475 (t) cc_final: 0.7085 (p) REVERT: A 75 GLN cc_start: 0.7132 (OUTLIER) cc_final: 0.6545 (mt0) REVERT: A 82 LYS cc_start: 0.7192 (OUTLIER) cc_final: 0.6880 (ttmm) REVERT: A 189 LYS cc_start: 0.7329 (mttt) cc_final: 0.6755 (mtpm) REVERT: A 340 GLU cc_start: 0.6379 (mt-10) cc_final: 0.6069 (tt0) REVERT: A 344 GLU cc_start: 0.6397 (OUTLIER) cc_final: 0.5553 (mp0) REVERT: A 396 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7444 (pm20) REVERT: E 96 ASN cc_start: 0.7907 (m-40) cc_final: 0.7575 (m110) REVERT: E 242 ILE cc_start: 0.8097 (mt) cc_final: 0.7815 (mp) REVERT: E 261 ARG cc_start: 0.7009 (mmt90) cc_final: 0.6044 (ptt180) outliers start: 31 outliers final: 19 residues processed: 148 average time/residue: 1.2444 time to fit residues: 203.7382 Evaluate side-chains 138 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 115 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 CYS Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 83 LYS Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 312 ASN Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 335 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 18 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 chunk 117 optimal weight: 6.9990 chunk 90 optimal weight: 0.9990 chunk 135 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 57 GLN A 488 HIS C 18 HIS C 435 HIS ** E 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 312 ASN E 363 GLN E 497 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 13281 Z= 0.394 Angle : 0.624 12.289 18027 Z= 0.316 Chirality : 0.045 0.243 2082 Planarity : 0.004 0.046 2357 Dihedral : 5.706 58.294 2312 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.66 % Allowed : 14.25 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 (0.20), residues: 1448 helix: 1.52 (0.26), residues: 351 sheet: -0.94 (0.27), residues: 273 loop : -0.79 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 234 HIS 0.008 0.002 HIS A 18 PHE 0.018 0.002 PHE E 125 TYR 0.013 0.002 TYR E 195 ARG 0.005 0.000 ARG C 150 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 121 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 SER cc_start: 0.7566 (t) cc_final: 0.7119 (p) REVERT: A 75 GLN cc_start: 0.7112 (OUTLIER) cc_final: 0.6615 (mt0) REVERT: A 82 LYS cc_start: 0.7271 (OUTLIER) cc_final: 0.6914 (ttmm) REVERT: A 189 LYS cc_start: 0.7286 (mttt) cc_final: 0.6722 (mtpm) REVERT: A 340 GLU cc_start: 0.6393 (mt-10) cc_final: 0.6164 (tt0) REVERT: A 344 GLU cc_start: 0.6394 (OUTLIER) cc_final: 0.5564 (mp0) REVERT: A 396 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7553 (pm20) REVERT: E 96 ASN cc_start: 0.7964 (m-40) cc_final: 0.7650 (m110) REVERT: E 242 ILE cc_start: 0.8188 (mt) cc_final: 0.7906 (mp) REVERT: E 261 ARG cc_start: 0.7060 (mmt90) cc_final: 0.6095 (ptt180) REVERT: E 401 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.6460 (pm20) outliers start: 34 outliers final: 18 residues processed: 144 average time/residue: 1.1797 time to fit residues: 186.5463 Evaluate side-chains 137 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 114 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 CYS Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 312 ASN Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 401 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 63 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 chunk 125 optimal weight: 0.5980 chunk 145 optimal weight: 0.8980 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 18 HIS A 57 GLN C 18 HIS C 435 HIS ** E 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 363 GLN E 497 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13281 Z= 0.204 Angle : 0.518 10.847 18027 Z= 0.265 Chirality : 0.042 0.235 2082 Planarity : 0.004 0.041 2357 Dihedral : 5.272 55.749 2312 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.11 % Allowed : 15.51 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.16 (0.21), residues: 1448 helix: 1.84 (0.26), residues: 350 sheet: -0.83 (0.27), residues: 279 loop : -0.69 (0.20), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 127 HIS 0.009 0.001 HIS A 18 PHE 0.011 0.001 PHE A 353 TYR 0.010 0.001 TYR E 195 ARG 0.003 0.000 ARG C 150 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 123 time to evaluate : 1.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 SER cc_start: 0.7474 (t) cc_final: 0.7099 (p) REVERT: A 75 GLN cc_start: 0.7071 (OUTLIER) cc_final: 0.6559 (mt0) REVERT: A 82 LYS cc_start: 0.7182 (OUTLIER) cc_final: 0.6867 (ttmm) REVERT: A 189 LYS cc_start: 0.7301 (mttt) cc_final: 0.6740 (mtpm) REVERT: A 261 ARG cc_start: 0.6889 (mtm110) cc_final: 0.6372 (mtt90) REVERT: A 340 GLU cc_start: 0.6354 (mt-10) cc_final: 0.6147 (tt0) REVERT: A 344 GLU cc_start: 0.6393 (OUTLIER) cc_final: 0.5573 (mp0) REVERT: A 396 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7475 (pm20) REVERT: E 96 ASN cc_start: 0.7934 (m-40) cc_final: 0.7635 (m110) REVERT: E 242 ILE cc_start: 0.8196 (mt) cc_final: 0.7882 (mp) REVERT: E 261 ARG cc_start: 0.6986 (mmt90) cc_final: 0.6021 (ptt180) REVERT: E 401 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.6490 (pm20) outliers start: 27 outliers final: 16 residues processed: 143 average time/residue: 1.2453 time to fit residues: 194.7752 Evaluate side-chains 137 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 116 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 CYS Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 312 ASN Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 401 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 153 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 149 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 117 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 chunk 134 optimal weight: 4.9990 chunk 141 optimal weight: 0.9980 chunk 148 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 57 GLN C 18 HIS C 363 GLN C 435 HIS ** E 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 363 GLN E 497 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13281 Z= 0.308 Angle : 0.575 11.506 18027 Z= 0.291 Chirality : 0.044 0.271 2082 Planarity : 0.004 0.044 2357 Dihedral : 5.499 57.058 2312 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.04 % Allowed : 16.05 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.21), residues: 1448 helix: 1.65 (0.26), residues: 355 sheet: -0.90 (0.27), residues: 275 loop : -0.79 (0.20), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 234 HIS 0.009 0.002 HIS C 17 PHE 0.014 0.002 PHE E 125 TYR 0.012 0.002 TYR C 105 ARG 0.004 0.000 ARG C 150 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 116 time to evaluate : 1.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 SER cc_start: 0.7538 (t) cc_final: 0.7143 (p) REVERT: A 75 GLN cc_start: 0.7112 (OUTLIER) cc_final: 0.6573 (mt0) REVERT: A 82 LYS cc_start: 0.7227 (OUTLIER) cc_final: 0.6885 (ttmm) REVERT: A 261 ARG cc_start: 0.6922 (mtm110) cc_final: 0.6409 (mtt180) REVERT: A 344 GLU cc_start: 0.6387 (OUTLIER) cc_final: 0.5571 (mp0) REVERT: A 396 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7528 (pm20) REVERT: E 96 ASN cc_start: 0.7955 (m-40) cc_final: 0.7655 (m110) REVERT: E 168 MET cc_start: 0.6380 (mmm) cc_final: 0.6158 (ttm) REVERT: E 242 ILE cc_start: 0.8213 (mt) cc_final: 0.7888 (mp) REVERT: E 261 ARG cc_start: 0.7036 (mmt90) cc_final: 0.6065 (ptt180) REVERT: E 401 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.6497 (pm20) outliers start: 26 outliers final: 16 residues processed: 134 average time/residue: 1.2092 time to fit residues: 177.7067 Evaluate side-chains 132 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 111 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 CYS Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 312 ASN Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 401 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 157 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 165 optimal weight: 7.9990 chunk 152 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 13 optimal weight: 20.0000 chunk 101 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 104 optimal weight: 7.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 57 GLN C 18 HIS C 363 GLN C 435 HIS ** E 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 363 GLN E 497 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13281 Z= 0.318 Angle : 0.585 11.645 18027 Z= 0.297 Chirality : 0.044 0.260 2082 Planarity : 0.004 0.050 2357 Dihedral : 5.650 58.236 2312 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.11 % Allowed : 16.05 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.20), residues: 1448 helix: 1.58 (0.26), residues: 355 sheet: -0.99 (0.27), residues: 275 loop : -0.84 (0.20), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 234 HIS 0.007 0.001 HIS A 18 PHE 0.013 0.002 PHE E 125 TYR 0.012 0.002 TYR E 195 ARG 0.004 0.000 ARG C 150 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 115 time to evaluate : 1.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 SER cc_start: 0.7554 (t) cc_final: 0.7153 (p) REVERT: A 75 GLN cc_start: 0.7096 (OUTLIER) cc_final: 0.6560 (mt0) REVERT: A 82 LYS cc_start: 0.7228 (OUTLIER) cc_final: 0.6870 (ttmm) REVERT: A 261 ARG cc_start: 0.6941 (mtm110) cc_final: 0.6426 (mtt180) REVERT: A 344 GLU cc_start: 0.6515 (OUTLIER) cc_final: 0.5675 (mp0) REVERT: A 396 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7507 (pm20) REVERT: E 96 ASN cc_start: 0.7959 (m-40) cc_final: 0.7654 (m110) REVERT: E 242 ILE cc_start: 0.8188 (mt) cc_final: 0.7878 (mp) REVERT: E 261 ARG cc_start: 0.7047 (mmt90) cc_final: 0.6091 (ptt180) REVERT: E 401 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.6511 (pm20) outliers start: 27 outliers final: 17 residues processed: 135 average time/residue: 1.2035 time to fit residues: 178.3798 Evaluate side-chains 133 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 111 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 CYS Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 339 ILE Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 401 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 121 optimal weight: 7.9990 chunk 19 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 135 optimal weight: 0.9980 chunk 16 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 115 optimal weight: 0.6980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN C 18 HIS C 363 GLN C 435 HIS ** E 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 363 GLN E 497 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.161918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.142923 restraints weight = 15353.135| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 1.62 r_work: 0.3514 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13281 Z= 0.270 Angle : 0.558 11.258 18027 Z= 0.283 Chirality : 0.043 0.256 2082 Planarity : 0.004 0.043 2357 Dihedral : 5.568 56.749 2312 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.04 % Allowed : 16.21 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.34 (0.20), residues: 1448 helix: 1.71 (0.26), residues: 351 sheet: -0.98 (0.27), residues: 273 loop : -0.80 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 127 HIS 0.010 0.001 HIS A 18 PHE 0.013 0.002 PHE E 125 TYR 0.011 0.002 TYR E 195 ARG 0.003 0.000 ARG C 150 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4188.61 seconds wall clock time: 74 minutes 36.49 seconds (4476.49 seconds total)