Starting phenix.real_space_refine (version: 1.21rc1) on Tue Jul 4 01:08:43 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u1n_20612/07_2023/6u1n_20612_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u1n_20612/07_2023/6u1n_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_20612/07_2023/6u1n_20612.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u1n_20612/07_2023/6u1n_20612.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u1n_20612/07_2023/6u1n_20612_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u1n_20612/07_2023/6u1n_20612_updated.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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: 3.63, per 1000 atoms: 0.62 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: 2.44 Conformation dependent library (CDL) restraints added in 1.1 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: 0.59 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: 1.53 Time building geometry restraints manager: 2.63 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: 58 58.21 - 87.32: 5 87.32 - 116.42: 0 116.42 - 145.53: 1 Dihedral angle restraints: 3505 sinusoidal: 977 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 3502 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: 0.570 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: 3.390 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 19.420 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.430 ------------------------------------------------------------------------------- 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 : 12.091 145.527 1861 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 % 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 *********************** 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 : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1744 time to fit residues: 18.8767 Evaluate side-chains 60 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.603 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8064 ------------------------------------------------------------------------------- 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 ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 91 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1318 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= 0.307 Angle : 0.606 7.480 8266 Z= 0.314 Chirality : 0.044 0.180 991 Planarity : 0.004 0.039 1056 Dihedral : 8.612 140.807 941 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer Outliers : 3.91 % 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: -3.49 (0.26), residues: 843 helix: -1.82 (0.31), residues: 207 sheet: -2.13 (0.29), residues: 263 loop : -2.64 (0.30), residues: 373 *********************** 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 86 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 68 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 14 residues processed: 83 average time/residue: 0.1460 time to fit residues: 17.0571 Evaluate side-chains 75 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 61 time to evaluate : 0.664 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0552 time to fit residues: 2.2290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 41 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 81 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 chunk 25 optimal weight: 0.0370 chunk 60 optimal weight: 20.0000 overall best weight: 2.6066 ------------------------------------------------------------------------------- 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: 0.8244 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 5998 Z= 0.284 Angle : 0.598 8.559 8266 Z= 0.306 Chirality : 0.043 0.176 991 Planarity : 0.004 0.031 1056 Dihedral : 8.459 140.624 941 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer Outliers : 2.83 % 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: -2.59 (0.27), residues: 843 helix: -0.81 (0.35), residues: 207 sheet: -1.77 (0.30), residues: 258 loop : -2.10 (0.31), residues: 378 *********************** 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 77 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 64 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 4 residues processed: 76 average time/residue: 0.1445 time to fit residues: 15.3653 Evaluate side-chains 62 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 58 time to evaluate : 0.633 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0619 time to fit residues: 1.2166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 50 optimal weight: 8.9990 chunk 75 optimal weight: 10.0000 chunk 80 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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: 0.8193 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 5998 Z= 0.170 Angle : 0.570 8.626 8266 Z= 0.281 Chirality : 0.043 0.189 991 Planarity : 0.003 0.029 1056 Dihedral : 8.163 140.612 941 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer Outliers : 3.48 % 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: -1.78 (0.28), residues: 843 helix: -0.04 (0.36), residues: 214 sheet: -1.42 (0.30), residues: 249 loop : -1.58 (0.32), residues: 380 *********************** 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 89 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 73 time to evaluate : 0.681 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 6 residues processed: 84 average time/residue: 0.1491 time to fit residues: 17.5101 Evaluate side-chains 69 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 63 time to evaluate : 0.601 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0582 time to fit residues: 1.4666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 45 optimal weight: 8.9990 chunk 1 optimal weight: 20.0000 chunk 59 optimal weight: 0.1980 chunk 33 optimal weight: 20.0000 chunk 68 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 0 optimal weight: 40.0000 chunk 40 optimal weight: 0.0570 chunk 72 optimal weight: 0.9990 chunk 20 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 overall best weight: 2.4504 ------------------------------------------------------------------------------- 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: 0.8230 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 5998 Z= 0.273 Angle : 0.601 8.940 8266 Z= 0.304 Chirality : 0.042 0.152 991 Planarity : 0.003 0.028 1056 Dihedral : 8.270 140.615 941 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer Outliers : 2.61 % 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: -1.57 (0.29), residues: 843 helix: 0.28 (0.37), residues: 214 sheet: -1.29 (0.30), residues: 245 loop : -1.56 (0.32), residues: 384 *********************** 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 75 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 63 time to evaluate : 0.871 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 72 average time/residue: 0.1308 time to fit residues: 13.9173 Evaluate side-chains 70 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 62 time to evaluate : 0.706 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0586 time to fit residues: 1.7910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 72 optimal weight: 1.9990 chunk 15 optimal weight: 40.0000 chunk 47 optimal weight: 3.9990 chunk 19 optimal weight: 0.0670 chunk 80 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 chunk 6 optimal weight: 0.0970 chunk 26 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 overall best weight: 1.6322 ------------------------------------------------------------------------------- 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: 0.8208 moved from start: 0.2568 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 : 0.568 7.408 8266 Z= 0.283 Chirality : 0.042 0.169 991 Planarity : 0.003 0.031 1056 Dihedral : 8.114 140.575 941 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer Outliers : 1.09 % 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: -1.30 (0.29), residues: 843 helix: 0.48 (0.37), residues: 220 sheet: -1.18 (0.29), residues: 269 loop : -1.34 (0.34), residues: 354 *********************** 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 69 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 64 time to evaluate : 0.673 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 67 average time/residue: 0.1346 time to fit residues: 13.2739 Evaluate side-chains 62 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 61 time to evaluate : 0.676 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0595 time to fit residues: 0.9766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 3.9990 chunk 45 optimal weight: 7.9990 chunk 58 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 49 optimal weight: 8.9990 chunk 31 optimal weight: 0.6980 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 5998 Z= 0.150 Angle : 0.552 7.562 8266 Z= 0.270 Chirality : 0.042 0.159 991 Planarity : 0.003 0.031 1056 Dihedral : 7.894 140.598 941 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer Outliers : 1.09 % 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: -0.91 (0.30), residues: 843 helix: 0.92 (0.38), residues: 217 sheet: -1.01 (0.30), residues: 269 loop : -1.13 (0.34), residues: 357 *********************** 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 76 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 71 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 75 average time/residue: 0.1417 time to fit residues: 15.1457 Evaluate side-chains 69 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 67 time to evaluate : 0.673 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0584 time to fit residues: 1.1026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 47 optimal weight: 3.9990 chunk 24 optimal weight: 0.0030 chunk 15 optimal weight: 0.0170 chunk 50 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 overall best weight: 1.8034 ------------------------------------------------------------------------------- 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: 0.8205 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 5998 Z= 0.222 Angle : 0.592 9.678 8266 Z= 0.289 Chirality : 0.043 0.154 991 Planarity : 0.003 0.030 1056 Dihedral : 7.936 140.604 941 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer Outliers : 1.52 % 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: -0.83 (0.30), residues: 843 helix: 0.99 (0.37), residues: 217 sheet: -1.02 (0.30), residues: 264 loop : -1.03 (0.34), residues: 362 *********************** 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 70 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 63 time to evaluate : 0.697 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 67 average time/residue: 0.1446 time to fit residues: 13.9845 Evaluate side-chains 62 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 60 time to evaluate : 0.688 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0595 time to fit residues: 1.1002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 0.4980 chunk 76 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 67 optimal weight: 0.5980 chunk 70 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 chunk 78 optimal weight: 0.0370 chunk 37 optimal weight: 10.0000 overall best weight: 1.4262 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.3060 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= 0.192 Angle : 0.606 9.920 8266 Z= 0.293 Chirality : 0.044 0.333 991 Planarity : 0.003 0.030 1056 Dihedral : 7.870 140.574 941 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer Outliers : 0.00 % 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: -0.73 (0.30), residues: 843 helix: 1.03 (0.37), residues: 217 sheet: -0.85 (0.30), residues: 267 loop : -1.03 (0.34), residues: 359 *********************** 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 64 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.1534 time to fit residues: 14.1469 Evaluate side-chains 62 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.692 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 54 optimal weight: 0.1980 chunk 82 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 chunk 40 optimal weight: 0.0030 chunk 52 optimal weight: 9.9990 chunk 70 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 60 optimal weight: 0.7980 overall best weight: 0.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 42 GLN ** 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: 0.8166 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 5998 Z= 0.158 Angle : 0.623 10.184 8266 Z= 0.294 Chirality : 0.044 0.332 991 Planarity : 0.003 0.033 1056 Dihedral : 7.713 140.590 941 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer Outliers : 0.43 % 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: -0.59 (0.29), residues: 843 helix: 1.17 (0.37), residues: 213 sheet: -0.73 (0.30), residues: 267 loop : -0.97 (0.34), residues: 363 ********************** 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 71 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 69 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 71 average time/residue: 0.1508 time to fit residues: 15.1961 Evaluate side-chains 65 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.606 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 0.0020 chunk 18 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 3 optimal weight: 40.0000 chunk 47 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 overall best weight: 1.7794 ------------------------------------------------------------------------------- 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 ** 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 = 0.3488 r_free = 0.3488 target = 0.065306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.047010 restraints weight = 32222.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.048387 restraints weight = 17331.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.049211 restraints weight = 11882.875| |-----------------------------------------------------------------------------| r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 5998 Z= 0.225 Angle : 0.617 9.896 8266 Z= 0.299 Chirality : 0.043 0.316 991 Planarity : 0.003 0.032 1056 Dihedral : 7.772 140.614 941 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer Outliers : 0.00 % 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: -0.54 (0.30), residues: 843 helix: 1.34 (0.37), residues: 213 sheet: -0.77 (0.30), residues: 269 loop : -0.97 (0.34), residues: 361 =============================================================================== Job complete usr+sys time: 1392.32 seconds wall clock time: 25 minutes 57.99 seconds (1557.99 seconds total)