Starting phenix.real_space_refine on Sun Mar 10 23:21:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u1n_20612/03_2024/6u1n_20612_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u1n_20612/03_2024/6u1n_20612.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u1n_20612/03_2024/6u1n_20612.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u1n_20612/03_2024/6u1n_20612.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u1n_20612/03_2024/6u1n_20612_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u1n_20612/03_2024/6u1n_20612_updated.pdb" } resolution = 4.0 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 102 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 S 15 5.16 5 Cl 1 4.86 5 C 3739 2.51 5 N 1012 2.21 5 O 1090 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5863 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 1660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 1660 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 169} Link IDs: {'PTRANS': 10, 'TRANS': 267} Chain breaks: 2 Unresolved non-hydrogen bonds: 586 Unresolved non-hydrogen angles: 767 Unresolved non-hydrogen dihedrals: 475 Unresolved non-hydrogen chiralities: 86 Planarities with less than four sites: {'GLN:plan1': 3, 'TPO:plan-1': 2, 'ASP:plan': 5, 'TYR:plan': 7, 'ASN:plan1': 12, 'TRP:plan': 3, 'HIS:plan': 1, 'PHE:plan': 13, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 264 Chain: "C" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2547 Classifications: {'peptide': 359} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 331} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 308 Unresolved non-hydrogen angles: 379 Unresolved non-hydrogen dihedrals: 244 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 12, 'ASN:plan1': 5, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 20, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 204 Chain: "H" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 846 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 2, 'TRANS': 116} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 52 Chain: "L" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 781 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 101} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "R" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'2CU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.13, per 1000 atoms: 0.70 Number of scatterers: 5863 At special positions: 0 Unit cell: (118.72, 116.6, 90.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 15 16.00 P 6 15.00 O 1090 8.00 N 1012 7.00 C 3739 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 96 " - pdb=" SG CYS R 176 " distance=2.04 Simple disulfide: pdb=" SG CYS R 413 " - pdb=" SG CYS R 416 " distance=2.03 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.04 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.38 Conformation dependent library (CDL) restraints added in 1.3 seconds 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1632 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 20 helices and 11 sheets defined 29.1% alpha, 24.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.38 Creating SS restraints... Processing helix chain 'R' and resid 21 through 47 removed outlier: 4.113A pdb=" N LEU R 28 " --> pdb=" O VAL R 24 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY R 31 " --> pdb=" O VAL R 27 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU R 35 " --> pdb=" O GLY R 31 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL R 36 " --> pdb=" O SER R 32 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N THR R 37 " --> pdb=" O LEU R 33 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ILE R 38 " --> pdb=" O SER R 34 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY R 40 " --> pdb=" O VAL R 36 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE R 42 " --> pdb=" O ILE R 38 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU R 43 " --> pdb=" O ILE R 39 " (cutoff:3.500A) Processing helix chain 'R' and resid 57 through 74 removed outlier: 4.555A pdb=" N LEU R 62 " --> pdb=" O ASN R 58 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA R 66 " --> pdb=" O LEU R 62 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ILE R 71 " --> pdb=" O CYS R 67 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE R 72 " --> pdb=" O ALA R 68 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLY R 73 " --> pdb=" O ASP R 69 " (cutoff:3.500A) Processing helix chain 'R' and resid 76 through 86 removed outlier: 3.859A pdb=" N THR R 81 " --> pdb=" O MET R 77 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU R 82 " --> pdb=" O ASN R 78 " (cutoff:3.500A) Processing helix chain 'R' and resid 93 through 118 removed outlier: 4.083A pdb=" N LEU R 98 " --> pdb=" O VAL R 94 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU R 100 " --> pdb=" O CYS R 96 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA R 101 " --> pdb=" O ASP R 97 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE R 116 " --> pdb=" O MET R 112 " (cutoff:3.500A) Processing helix chain 'R' and resid 120 through 126 removed outlier: 3.766A pdb=" N VAL R 125 " --> pdb=" O ARG R 121 " (cutoff:3.500A) Processing helix chain 'R' and resid 128 through 134 Proline residue: R 132 - end of helix No H-bonds generated for 'chain 'R' and resid 128 through 134' Processing helix chain 'R' and resid 137 through 166 removed outlier: 4.142A pdb=" N MET R 142 " --> pdb=" O LYS R 138 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ALA R 147 " --> pdb=" O MET R 143 " (cutoff:3.500A) Proline residue: R 157 - end of helix removed outlier: 4.501A pdb=" N GLN R 163 " --> pdb=" O ILE R 159 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N PHE R 164 " --> pdb=" O LEU R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 184 through 212 removed outlier: 4.065A pdb=" N GLY R 189 " --> pdb=" O ALA R 185 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA R 191 " --> pdb=" O THR R 187 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ILE R 192 " --> pdb=" O PHE R 188 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEU R 197 " --> pdb=" O ALA R 193 " (cutoff:3.500A) Proline residue: R 198 - end of helix removed outlier: 3.756A pdb=" N ALA R 212 " --> pdb=" O HIS R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 383 through 416 removed outlier: 4.234A pdb=" N LEU R 390 " --> pdb=" O THR R 386 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ALA R 391 " --> pdb=" O ARG R 387 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TRP R 400 " --> pdb=" O PHE R 396 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA R 401 " --> pdb=" O ILE R 397 " (cutoff:3.500A) Proline residue: R 402 - end of helix removed outlier: 4.086A pdb=" N LEU R 408 " --> pdb=" O ASN R 404 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ILE R 409 " --> pdb=" O VAL R 405 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR R 411 " --> pdb=" O VAL R 407 " (cutoff:3.500A) Proline residue: R 415 - end of helix Processing helix chain 'R' and resid 419 through 440 removed outlier: 3.734A pdb=" N THR R 423 " --> pdb=" O ASN R 419 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ILE R 424 " --> pdb=" O THR R 420 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR R 426 " --> pdb=" O TRP R 422 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ASN R 432 " --> pdb=" O LEU R 428 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N SER R 433 " --> pdb=" O CYS R 429 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N THR R 434 " --> pdb=" O TYR R 430 " (cutoff:3.500A) Proline residue: R 437 - end of helix removed outlier: 3.747A pdb=" N TYR R 440 " --> pdb=" O ASN R 436 " (cutoff:3.500A) Processing helix chain 'R' and resid 445 through 451 Processing helix chain 'C' and resid 99 through 107 Processing helix chain 'C' and resid 160 through 162 No H-bonds generated for 'chain 'C' and resid 160 through 162' Processing helix chain 'C' and resid 279 through 281 No H-bonds generated for 'chain 'C' and resid 279 through 281' Processing helix chain 'H' and resid 32 through 34 No H-bonds generated for 'chain 'H' and resid 32 through 34' Processing helix chain 'H' and resid 56 through 58 No H-bonds generated for 'chain 'H' and resid 56 through 58' Processing helix chain 'H' and resid 65 through 67 No H-bonds generated for 'chain 'H' and resid 65 through 67' Processing helix chain 'H' and resid 77 through 79 No H-bonds generated for 'chain 'H' and resid 77 through 79' Processing helix chain 'H' and resid 91 through 93 No H-bonds generated for 'chain 'H' and resid 91 through 93' Processing helix chain 'L' and resid 81 through 83 No H-bonds generated for 'chain 'L' and resid 81 through 83' Processing sheet with id= A, first strand: chain 'C' and resid 9 through 12 Processing sheet with id= B, first strand: chain 'C' and resid 76 through 78 removed outlier: 3.872A pdb=" N TYR C 144 " --> pdb=" O ILE C 168 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 183 through 188 Processing sheet with id= D, first strand: chain 'C' and resid 207 through 209 removed outlier: 6.370A pdb=" N THR C 350 " --> pdb=" O TYR C 208 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'C' and resid 342 through 349 removed outlier: 4.065A pdb=" N TYR C 321 " --> pdb=" O PHE C 349 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N SER C 330 " --> pdb=" O VAL C 228 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL C 228 " --> pdb=" O SER C 330 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N GLN C 237 " --> pdb=" O PRO C 252 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ALA C 239 " --> pdb=" O LYS C 250 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N LYS C 250 " --> pdb=" O ALA C 239 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE C 241 " --> pdb=" O GLN C 248 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N GLN C 248 " --> pdb=" O ILE C 241 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 53 through 59 removed outlier: 6.788A pdb=" N VAL C 55 " --> pdb=" O GLN C 85 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N GLN C 85 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N LEU C 57 " --> pdb=" O ASN C 83 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ASN C 83 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N VAL C 59 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N VAL C 81 " --> pdb=" O VAL C 59 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'H' and resid 7 through 10 Processing sheet with id= H, first strand: chain 'H' and resid 117 through 119 removed outlier: 4.961A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'L' and resid 5 through 8 Processing sheet with id= J, first strand: chain 'L' and resid 12 through 14 Processing sheet with id= K, first strand: chain 'L' and resid 86 through 91 removed outlier: 5.473A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) 258 hydrogen bonds defined for protein. 720 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: 1.56 Time building geometry restraints manager: 2.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1004 1.32 - 1.46: 2108 1.46 - 1.59: 2846 1.59 - 1.73: 19 1.73 - 1.86: 21 Bond restraints: 5998 Sorted by residual: bond pdb=" C22 2CU R 601 " pdb=" S21 2CU R 601 " ideal model delta sigma weight residual 1.721 1.862 -0.141 2.00e-02 2.50e+03 4.95e+01 bond pdb=" C03 2CU R 601 " pdb=" N02 2CU R 601 " ideal model delta sigma weight residual 1.449 1.316 0.133 2.00e-02 2.50e+03 4.45e+01 bond pdb=" C07 2CU R 601 " pdb=" N02 2CU R 601 " ideal model delta sigma weight residual 1.448 1.318 0.130 2.00e-02 2.50e+03 4.25e+01 bond pdb=" C08 2CU R 601 " pdb=" N05 2CU R 601 " ideal model delta sigma weight residual 1.346 1.476 -0.130 2.00e-02 2.50e+03 4.20e+01 bond pdb=" C01 2CU R 601 " pdb=" N02 2CU R 601 " ideal model delta sigma weight residual 1.445 1.323 0.122 2.00e-02 2.50e+03 3.74e+01 ... (remaining 5993 not shown) Histogram of bond angle deviations from ideal: 59.81 - 75.14: 3 75.14 - 90.48: 1 90.48 - 105.82: 156 105.82 - 121.16: 6371 121.16 - 136.50: 1735 Bond angle restraints: 8266 Sorted by residual: angle pdb=" OG1 TPO R 490 " pdb=" P TPO R 490 " pdb=" O1P TPO R 490 " ideal model delta sigma weight residual 100.43 113.62 -13.19 3.00e+00 1.11e-01 1.93e+01 angle pdb=" CB TPO R 491 " pdb=" OG1 TPO R 491 " pdb=" P TPO R 491 " ideal model delta sigma weight residual 119.31 106.42 12.89 3.00e+00 1.11e-01 1.85e+01 angle pdb=" CB SEP R 493 " pdb=" OG SEP R 493 " pdb=" P SEP R 493 " ideal model delta sigma weight residual 110.00 120.57 -10.57 3.00e+00 1.11e-01 1.24e+01 angle pdb=" C17 2CU R 601 " pdb=" C18 2CU R 601 " pdb=" C20 2CU R 601 " ideal model delta sigma weight residual 111.70 122.11 -10.41 3.00e+00 1.11e-01 1.20e+01 angle pdb=" CA HIS C 362 " pdb=" C HIS C 362 " pdb=" O HIS C 362 " ideal model delta sigma weight residual 122.14 118.31 3.83 1.24e+00 6.50e-01 9.53e+00 ... (remaining 8261 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.11: 3441 29.11 - 58.21: 59 58.21 - 87.32: 5 87.32 - 116.42: 0 116.42 - 145.53: 1 Dihedral angle restraints: 3506 sinusoidal: 978 harmonic: 2528 Sorted by residual: dihedral pdb=" CB CYS R 96 " pdb=" SG CYS R 96 " pdb=" SG CYS R 176 " pdb=" CB CYS R 176 " ideal model delta sinusoidal sigma weight residual -86.00 -154.52 68.52 1 1.00e+01 1.00e-02 6.08e+01 dihedral pdb=" CB CYS R 413 " pdb=" SG CYS R 413 " pdb=" SG CYS R 416 " pdb=" CB CYS R 416 " ideal model delta sinusoidal sigma weight residual 93.00 150.39 -57.39 1 1.00e+01 1.00e-02 4.43e+01 dihedral pdb=" C29 2CU R 601 " pdb=" C27 2CU R 601 " pdb=" C28 2CU R 601 " pdb=" N26 2CU R 601 " ideal model delta sinusoidal sigma weight residual 250.71 105.18 145.53 1 3.00e+01 1.11e-03 1.95e+01 ... (remaining 3503 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 806 0.055 - 0.111: 167 0.111 - 0.166: 16 0.166 - 0.221: 0 0.221 - 0.276: 2 Chirality restraints: 991 Sorted by residual: chirality pdb=" C27 2CU R 601 " pdb=" C28 2CU R 601 " pdb=" C29 2CU R 601 " pdb=" N26 2CU R 601 " both_signs ideal model delta sigma weight residual True 2.31 2.59 -0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CA ILE L 22 " pdb=" N ILE L 22 " pdb=" C ILE L 22 " pdb=" CB ILE L 22 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CA TYR L 92 " pdb=" N TYR L 92 " pdb=" C TYR L 92 " pdb=" CB TYR L 92 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.08e-01 ... (remaining 988 not shown) Planarity restraints: 1056 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 106 " 0.018 2.00e-02 2.50e+03 1.55e-02 6.02e+00 pdb=" CG TRP H 106 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP H 106 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP H 106 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP H 106 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP H 106 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP H 106 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 106 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 106 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP H 106 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU R 197 " -0.028 5.00e-02 4.00e+02 4.20e-02 2.83e+00 pdb=" N PRO R 198 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO R 198 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO R 198 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER L 66 " 0.007 2.00e-02 2.50e+03 1.33e-02 1.76e+00 pdb=" C SER L 66 " -0.023 2.00e-02 2.50e+03 pdb=" O SER L 66 " 0.009 2.00e-02 2.50e+03 pdb=" N ARG L 67 " 0.008 2.00e-02 2.50e+03 ... (remaining 1053 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 712 2.74 - 3.28: 6451 3.28 - 3.82: 9400 3.82 - 4.36: 10753 4.36 - 4.90: 17857 Nonbonded interactions: 45173 Sorted by model distance: nonbonded pdb=" O LYS C 195 " pdb=" OG1 THR C 224 " model vdw 2.198 2.440 nonbonded pdb=" NH1 ARG L 19 " pdb=" OG1 THR L 75 " model vdw 2.204 2.520 nonbonded pdb=" O ASN C 222 " pdb=" N SER C 265 " model vdw 2.221 2.520 nonbonded pdb=" OH TYR H 63 " pdb=" N ILE H 73 " model vdw 2.248 2.520 nonbonded pdb=" OG1 THR C 183 " pdb=" O ALA C 201 " model vdw 2.255 2.440 ... (remaining 45168 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 3.220 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 21.410 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 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 0.141 5998 Z= 0.547 Angle : 0.808 13.192 8266 Z= 0.429 Chirality : 0.044 0.276 991 Planarity : 0.004 0.042 1056 Dihedral : 12.150 145.527 1862 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 17.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -4.67 (0.23), residues: 843 helix: -3.58 (0.23), residues: 186 sheet: -2.48 (0.29), residues: 263 loop : -3.24 (0.26), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP H 106 HIS 0.003 0.001 HIS C 353 PHE 0.020 0.002 PHE H 105 TYR 0.012 0.001 TYR L 50 ARG 0.006 0.001 ARG L 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 119 PHE cc_start: 0.9037 (m-80) cc_final: 0.8461 (m-80) REVERT: H 16 GLN cc_start: 0.8429 (mm110) cc_final: 0.8126 (mm-40) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1757 time to fit residues: 18.7807 Evaluate side-chains 61 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 70 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 58 ASN C 162 ASN C 172 GLN C 198 HIS H 16 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 91 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 5998 Z= 0.308 Angle : 0.604 6.963 8266 Z= 0.313 Chirality : 0.044 0.206 991 Planarity : 0.004 0.040 1056 Dihedral : 8.748 140.939 942 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 3.70 % Allowed : 16.96 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -3.54 (0.26), residues: 843 helix: -1.92 (0.31), residues: 210 sheet: -2.15 (0.29), residues: 263 loop : -2.63 (0.30), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 106 HIS 0.003 0.001 HIS C 353 PHE 0.017 0.002 PHE H 30 TYR 0.012 0.001 TYR L 50 ARG 0.005 0.001 ARG L 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 68 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 119 PHE cc_start: 0.8996 (m-80) cc_final: 0.8313 (m-80) REVERT: C 256 GLU cc_start: 0.8396 (tm-30) cc_final: 0.8113 (tm-30) REVERT: H 16 GLN cc_start: 0.8355 (mm-40) cc_final: 0.8155 (mm-40) REVERT: L 22 ILE cc_start: 0.9491 (mm) cc_final: 0.9274 (mt) outliers start: 17 outliers final: 13 residues processed: 82 average time/residue: 0.1460 time to fit residues: 16.7910 Evaluate side-chains 73 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 60 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain C residue 317 ILE Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 95 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 41 optimal weight: 8.9990 chunk 23 optimal weight: 0.7980 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 chunk 20 optimal weight: 8.9990 chunk 75 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 60 optimal weight: 20.0000 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 5998 Z= 0.339 Angle : 0.620 7.870 8266 Z= 0.319 Chirality : 0.044 0.180 991 Planarity : 0.004 0.036 1056 Dihedral : 8.727 140.587 942 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 5.87 % Allowed : 18.48 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.27), residues: 843 helix: -1.04 (0.34), residues: 207 sheet: -1.77 (0.30), residues: 253 loop : -2.18 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 155 HIS 0.003 0.001 HIS C 111 PHE 0.018 0.002 PHE H 105 TYR 0.013 0.002 TYR R 403 ARG 0.005 0.001 ARG L 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 64 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 119 PHE cc_start: 0.8908 (m-10) cc_final: 0.8242 (m-80) REVERT: R 403 TYR cc_start: 0.7837 (t80) cc_final: 0.7449 (t80) outliers start: 27 outliers final: 18 residues processed: 87 average time/residue: 0.1474 time to fit residues: 18.0102 Evaluate side-chains 75 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 57 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 385 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain C residue 317 ILE Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 36 optimal weight: 0.2980 chunk 50 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5998 Z= 0.152 Angle : 0.572 8.597 8266 Z= 0.281 Chirality : 0.043 0.179 991 Planarity : 0.003 0.030 1056 Dihedral : 8.309 140.622 942 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.48 % Allowed : 21.74 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -1.88 (0.28), residues: 843 helix: -0.25 (0.36), residues: 214 sheet: -1.44 (0.30), residues: 249 loop : -1.58 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 155 HIS 0.002 0.001 HIS C 353 PHE 0.010 0.001 PHE C 27 TYR 0.010 0.001 TYR R 403 ARG 0.002 0.000 ARG C 7 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 72 time to evaluate : 0.616 Fit side-chains revert: symmetry clash REVERT: R 119 PHE cc_start: 0.8879 (m-10) cc_final: 0.8276 (m-80) REVERT: L 24 CYS cc_start: 0.3589 (t) cc_final: 0.3053 (t) REVERT: L 91 GLN cc_start: 0.8864 (OUTLIER) cc_final: 0.8464 (pp30) outliers start: 16 outliers final: 7 residues processed: 86 average time/residue: 0.1363 time to fit residues: 16.6043 Evaluate side-chains 70 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 62 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 385 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 91 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 45 optimal weight: 9.9990 chunk 1 optimal weight: 20.0000 chunk 59 optimal weight: 5.9990 chunk 33 optimal weight: 20.0000 chunk 68 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 0 optimal weight: 40.0000 chunk 40 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 20 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 5998 Z= 0.437 Angle : 0.656 7.113 8266 Z= 0.339 Chirality : 0.044 0.154 991 Planarity : 0.004 0.030 1056 Dihedral : 8.683 140.547 942 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 4.78 % Allowed : 22.61 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.28), residues: 843 helix: -0.05 (0.36), residues: 209 sheet: -1.48 (0.31), residues: 244 loop : -1.88 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 106 HIS 0.004 0.001 HIS C 353 PHE 0.022 0.002 PHE H 105 TYR 0.012 0.002 TYR C 113 ARG 0.006 0.001 ARG L 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 62 time to evaluate : 0.722 Fit side-chains revert: symmetry clash REVERT: R 119 PHE cc_start: 0.8934 (m-10) cc_final: 0.8311 (m-80) outliers start: 22 outliers final: 18 residues processed: 78 average time/residue: 0.1338 time to fit residues: 15.4293 Evaluate side-chains 78 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 60 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 385 VAL Chi-restraints excluded: chain R residue 403 TYR Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain C residue 317 ILE Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 95 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 72 optimal weight: 2.9990 chunk 15 optimal weight: 40.0000 chunk 47 optimal weight: 2.9990 chunk 19 optimal weight: 0.0970 chunk 80 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 42 optimal weight: 0.0970 chunk 77 optimal weight: 4.9990 overall best weight: 1.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5998 Z= 0.202 Angle : 0.579 9.611 8266 Z= 0.286 Chirality : 0.043 0.178 991 Planarity : 0.003 0.032 1056 Dihedral : 8.376 140.556 942 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.13 % Allowed : 23.70 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -1.54 (0.29), residues: 843 helix: 0.34 (0.37), residues: 214 sheet: -1.34 (0.30), residues: 252 loop : -1.50 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 155 HIS 0.002 0.001 HIS C 353 PHE 0.014 0.001 PHE H 105 TYR 0.008 0.001 TYR H 107 ARG 0.003 0.000 ARG L 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 64 time to evaluate : 0.706 Fit side-chains revert: symmetry clash REVERT: R 119 PHE cc_start: 0.8887 (m-10) cc_final: 0.8274 (m-80) REVERT: C 256 GLU cc_start: 0.8125 (tm-30) cc_final: 0.7815 (tm-30) REVERT: H 16 GLN cc_start: 0.8465 (mm-40) cc_final: 0.8015 (mm-40) REVERT: L 91 GLN cc_start: 0.9107 (OUTLIER) cc_final: 0.8235 (pp30) outliers start: 19 outliers final: 13 residues processed: 80 average time/residue: 0.1281 time to fit residues: 14.9858 Evaluate side-chains 74 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 60 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 385 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 91 GLN Chi-restraints excluded: chain L residue 95 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 49 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5998 Z= 0.175 Angle : 0.563 7.785 8266 Z= 0.276 Chirality : 0.042 0.178 991 Planarity : 0.003 0.034 1056 Dihedral : 8.248 140.592 942 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.35 % Allowed : 24.35 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -1.16 (0.29), residues: 843 helix: 0.69 (0.37), residues: 214 sheet: -1.15 (0.31), residues: 257 loop : -1.27 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 155 HIS 0.003 0.001 HIS C 353 PHE 0.014 0.001 PHE H 105 TYR 0.008 0.001 TYR L 50 ARG 0.003 0.000 ARG L 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 63 time to evaluate : 0.673 Fit side-chains revert: symmetry clash REVERT: R 119 PHE cc_start: 0.8890 (m-10) cc_final: 0.8277 (m-80) REVERT: H 16 GLN cc_start: 0.8528 (mm-40) cc_final: 0.8231 (mm-40) REVERT: L 24 CYS cc_start: 0.4348 (t) cc_final: 0.4100 (t) REVERT: L 91 GLN cc_start: 0.8995 (OUTLIER) cc_final: 0.8487 (pp30) outliers start: 20 outliers final: 14 residues processed: 78 average time/residue: 0.1350 time to fit residues: 15.4007 Evaluate side-chains 77 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 62 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 385 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 91 GLN Chi-restraints excluded: chain L residue 95 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 47 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 15 optimal weight: 0.0370 chunk 50 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 7 optimal weight: 20.0000 chunk 62 optimal weight: 0.0980 chunk 72 optimal weight: 0.5980 chunk 76 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 overall best weight: 0.5460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 130 GLN L 91 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 5998 Z= 0.139 Angle : 0.574 9.238 8266 Z= 0.276 Chirality : 0.043 0.169 991 Planarity : 0.003 0.036 1056 Dihedral : 8.032 140.602 942 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.39 % Allowed : 25.65 % Favored : 71.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.84 (0.30), residues: 843 helix: 0.92 (0.37), residues: 217 sheet: -0.96 (0.31), residues: 255 loop : -1.06 (0.34), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 36 HIS 0.004 0.001 HIS C 353 PHE 0.026 0.001 PHE H 30 TYR 0.014 0.001 TYR L 92 ARG 0.002 0.000 ARG C 7 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 67 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 119 PHE cc_start: 0.8869 (m-10) cc_final: 0.8274 (m-80) REVERT: H 16 GLN cc_start: 0.8664 (mm-40) cc_final: 0.8366 (mm-40) REVERT: L 24 CYS cc_start: 0.4249 (t) cc_final: 0.3457 (t) REVERT: L 99 PHE cc_start: 0.8942 (m-80) cc_final: 0.8632 (m-80) outliers start: 11 outliers final: 8 residues processed: 76 average time/residue: 0.1373 time to fit residues: 14.9704 Evaluate side-chains 73 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 65 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 385 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain L residue 95 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 20.0000 chunk 76 optimal weight: 3.9990 chunk 44 optimal weight: 0.0770 chunk 32 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 22 optimal weight: 8.9990 chunk 67 optimal weight: 3.9990 chunk 70 optimal weight: 9.9990 chunk 48 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 37 optimal weight: 8.9990 overall best weight: 1.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5998 Z= 0.203 Angle : 0.575 8.870 8266 Z= 0.281 Chirality : 0.042 0.160 991 Planarity : 0.003 0.034 1056 Dihedral : 8.073 140.617 942 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.83 % Allowed : 25.43 % Favored : 71.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.74 (0.30), residues: 843 helix: 1.03 (0.37), residues: 217 sheet: -0.92 (0.31), residues: 259 loop : -0.98 (0.34), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 106 HIS 0.004 0.001 HIS C 353 PHE 0.015 0.001 PHE H 105 TYR 0.020 0.001 TYR R 403 ARG 0.004 0.000 ARG L 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 64 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 119 PHE cc_start: 0.8860 (m-10) cc_final: 0.8244 (m-80) REVERT: H 15 VAL cc_start: 0.9056 (t) cc_final: 0.8684 (m) REVERT: H 16 GLN cc_start: 0.8662 (mm-40) cc_final: 0.8299 (mm-40) REVERT: L 5 MET cc_start: 0.8182 (tpt) cc_final: 0.7936 (tpt) REVERT: L 99 PHE cc_start: 0.8911 (m-80) cc_final: 0.8600 (m-80) outliers start: 13 outliers final: 10 residues processed: 73 average time/residue: 0.1353 time to fit residues: 14.2695 Evaluate side-chains 71 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 61 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 385 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 95 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 54 optimal weight: 0.0980 chunk 82 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 70 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 60 optimal weight: 7.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5998 Z= 0.220 Angle : 0.583 9.135 8266 Z= 0.287 Chirality : 0.043 0.150 991 Planarity : 0.003 0.033 1056 Dihedral : 8.096 140.568 942 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.04 % Allowed : 25.43 % Favored : 71.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.66 (0.30), residues: 843 helix: 1.07 (0.37), residues: 220 sheet: -0.84 (0.31), residues: 257 loop : -0.97 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 106 HIS 0.004 0.001 HIS C 353 PHE 0.028 0.001 PHE H 30 TYR 0.023 0.001 TYR R 403 ARG 0.004 0.000 ARG L 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 61 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 119 PHE cc_start: 0.8864 (m-10) cc_final: 0.8262 (m-80) REVERT: H 15 VAL cc_start: 0.9062 (t) cc_final: 0.8682 (m) REVERT: H 16 GLN cc_start: 0.8666 (mm-40) cc_final: 0.8294 (mm-40) REVERT: L 5 MET cc_start: 0.8316 (tpt) cc_final: 0.8076 (tpp) outliers start: 14 outliers final: 11 residues processed: 72 average time/residue: 0.1258 time to fit residues: 13.7650 Evaluate side-chains 72 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 61 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 385 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 95 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 12 optimal weight: 20.0000 chunk 57 optimal weight: 0.0970 chunk 3 optimal weight: 40.0000 chunk 47 optimal weight: 0.5980 chunk 75 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.066353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.047815 restraints weight = 31770.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.049196 restraints weight = 17078.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.050097 restraints weight = 11792.956| |-----------------------------------------------------------------------------| r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 5998 Z= 0.153 Angle : 0.593 12.692 8266 Z= 0.283 Chirality : 0.043 0.147 991 Planarity : 0.003 0.034 1056 Dihedral : 7.924 140.573 942 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.52 % Allowed : 26.74 % Favored : 71.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.30), residues: 843 helix: 1.34 (0.37), residues: 213 sheet: -0.66 (0.32), residues: 257 loop : -0.89 (0.33), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 155 HIS 0.002 0.000 HIS C 210 PHE 0.018 0.001 PHE H 30 TYR 0.021 0.001 TYR R 403 ARG 0.003 0.000 ARG L 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1383.03 seconds wall clock time: 25 minutes 46.76 seconds (1546.76 seconds total)