Starting phenix.real_space_refine (version: 1.21rc1) on Sat Oct 7 22:58:18 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5u_33625/10_2023/7y5u_33625.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5u_33625/10_2023/7y5u_33625.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5u_33625/10_2023/7y5u_33625.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5u_33625/10_2023/7y5u_33625.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5u_33625/10_2023/7y5u_33625.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5u_33625/10_2023/7y5u_33625.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.015 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 6842 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 38 5.16 5 C 5599 2.51 5 N 1553 2.21 5 O 1675 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 564": "OE1" <-> "OE2" Residue "A GLU 602": "OE1" <-> "OE2" Residue "A PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 105": "OE1" <-> "OE2" Residue "D ASP 123": "OD1" <-> "OD2" Residue "C TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 116": "OE1" <-> "OE2" Residue "C GLU 126": "OE1" <-> "OE2" Residue "C TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 379": "OD1" <-> "OD2" Residue "C GLU 395": "OE1" <-> "OE2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B ASP 150": "OD1" <-> "OD2" Residue "B ASP 157": "OD1" <-> "OD2" Residue "B GLU 169": "OE1" <-> "OE2" Residue "B ASP 325": "OD1" <-> "OD2" Residue "B GLU 376": "OE1" <-> "OE2" Residue "B ASP 378": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 8865 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1256 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 7, 'TRANS': 168} Chain breaks: 1 Unresolved non-hydrogen bonds: 190 Unresolved non-hydrogen angles: 238 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 6, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 123 Chain: "D" Number of atoms: 898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 898 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 642 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 3165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3165 Classifications: {'peptide': 401} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 22, 'TRANS': 378} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 2904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2904 Classifications: {'peptide': 371} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 15, 'TRANS': 355} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 16 Time building chain proxies: 5.05, per 1000 atoms: 0.57 Number of scatterers: 8865 At special positions: 0 Unit cell: (81, 98, 133, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 38 16.00 O 1675 8.00 N 1553 7.00 C 5599 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.38 Conformation dependent library (CDL) restraints added in 1.5 seconds 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2146 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 16 sheets defined 20.5% alpha, 25.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 491 through 500 Processing helix chain 'A' and resid 550 through 554 Processing helix chain 'A' and resid 599 through 604 Processing helix chain 'A' and resid 635 through 647 Processing helix chain 'A' and resid 652 through 674 Processing helix chain 'A' and resid 675 through 677 No H-bonds generated for 'chain 'A' and resid 675 through 677' Processing helix chain 'A' and resid 697 through 706 Processing helix chain 'D' and resid 51 through 55 Processing helix chain 'D' and resid 63 through 79 removed outlier: 3.836A pdb=" N PHE D 67 " --> pdb=" O ARG D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 114 Processing helix chain 'D' and resid 120 through 132 Processing helix chain 'E' and resid 25 through 29 removed outlier: 4.361A pdb=" N ILE E 29 " --> pdb=" O ILE E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 41 Processing helix chain 'E' and resid 49 through 76 removed outlier: 4.450A pdb=" N GLU E 53 " --> pdb=" O LEU E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 94 Processing helix chain 'C' and resid 12 through 32 Proline residue: C 29 - end of helix Processing helix chain 'C' and resid 89 through 93 removed outlier: 3.534A pdb=" N PHE C 93 " --> pdb=" O ASP C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 157 No H-bonds generated for 'chain 'C' and resid 155 through 157' Processing helix chain 'C' and resid 355 through 359 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.199A pdb=" N TYR C 409 " --> pdb=" O ALA C 405 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN C 410 " --> pdb=" O GLU C 406 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 405 through 410' Processing sheet with id=AA1, first strand: chain 'A' and resid 570 through 572 removed outlier: 6.360A pdb=" N LEU A 559 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N THR C 37 " --> pdb=" O LEU A 559 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLN A 561 " --> pdb=" O THR C 37 " (cutoff:3.500A) removed outlier: 8.815A pdb=" N ALA C 39 " --> pdb=" O GLN A 561 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ILE C 398 " --> pdb=" O SER C 394 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 684 through 686 removed outlier: 3.807A pdb=" N TYR B 340 " --> pdb=" O ILE A 686 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ARG B 316 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N VAL B 296 " --> pdb=" O ARG B 316 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N VAL B 318 " --> pdb=" O CYS B 294 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 710 through 711 removed outlier: 5.742A pdb=" N TYR B 267 " --> pdb=" O PRO B 252 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N PHE B 269 " --> pdb=" O LEU B 250 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N LEU B 250 " --> pdb=" O PHE B 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 118 through 119 removed outlier: 3.560A pdb=" N ILE D 119 " --> pdb=" O ARG E 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 47 through 54 removed outlier: 7.632A pdb=" N LEU C 50 " --> pdb=" O VAL C 67 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N VAL C 67 " --> pdb=" O LEU C 50 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASP C 52 " --> pdb=" O ARG C 65 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ARG C 65 " --> pdb=" O ASP C 52 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N ASN C 77 " --> pdb=" O ASN C 122 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ASN C 122 " --> pdb=" O ASN C 77 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LEU C 79 " --> pdb=" O LYS C 120 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LYS C 120 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE C 81 " --> pdb=" O GLU C 118 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 130 through 133 removed outlier: 10.266A pdb=" N ARG C 131 " --> pdb=" O CYS C 138 " (cutoff:3.500A) removed outlier: 8.973A pdb=" N CYS C 138 " --> pdb=" O ARG C 131 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N MET C 133 " --> pdb=" O ASN C 136 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ARG C 172 " --> pdb=" O VAL C 217 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 182 through 185 removed outlier: 4.105A pdb=" N GLY C 182 " --> pdb=" O ALA C 196 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 230 through 235 Processing sheet with id=AA9, first strand: chain 'C' and resid 276 through 281 removed outlier: 6.862A pdb=" N GLY C 292 " --> pdb=" O ASN C 277 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU C 279 " --> pdb=" O ALA C 290 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ALA C 290 " --> pdb=" O LEU C 279 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N PHE C 281 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N ILE C 288 " --> pdb=" O PHE C 281 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N HIS C 311 " --> pdb=" O LEU C 300 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 320 through 325 removed outlier: 5.722A pdb=" N ASP C 346 " --> pdb=" O LEU C 366 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N LEU C 366 " --> pdb=" O ASP C 346 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 2 through 5 removed outlier: 6.957A pdb=" N PHE B 360 " --> pdb=" O TRP B 354 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N TRP B 354 " --> pdb=" O PHE B 360 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALA B 362 " --> pdb=" O ILE B 352 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ILE B 352 " --> pdb=" O ALA B 362 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N SER B 364 " --> pdb=" O SER B 350 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 16 through 20 removed outlier: 6.721A pdb=" N ALA B 35 " --> pdb=" O TYR B 17 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LEU B 19 " --> pdb=" O ALA B 33 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ALA B 33 " --> pdb=" O LEU B 19 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL B 41 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ASN B 61 " --> pdb=" O VAL B 41 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE B 43 " --> pdb=" O LEU B 59 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU B 47 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ILE B 55 " --> pdb=" O GLU B 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 69 through 71 removed outlier: 6.997A pdb=" N GLY B 84 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LYS B 94 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N VAL B 121 " --> pdb=" O LYS B 94 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 132 through 137 removed outlier: 6.436A pdb=" N ASP B 157 " --> pdb=" O LYS B 163 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LYS B 163 " --> pdb=" O ASP B 157 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 174 through 179 removed outlier: 4.217A pdb=" N GLY B 176 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL B 194 " --> pdb=" O SER B 190 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N SER B 199 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL B 205 " --> pdb=" O SER B 199 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 211 through 213 315 hydrogen bonds defined for protein. 855 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.78 Time building geometry restraints manager: 3.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2880 1.34 - 1.46: 1276 1.46 - 1.57: 4851 1.57 - 1.69: 1 1.69 - 1.81: 56 Bond restraints: 9064 Sorted by residual: bond pdb=" CA ASP B 150 " pdb=" C ASP B 150 " ideal model delta sigma weight residual 1.522 1.576 -0.054 1.72e-02 3.38e+03 9.88e+00 bond pdb=" N ASN B 12 " pdb=" CA ASN B 12 " ideal model delta sigma weight residual 1.457 1.475 -0.018 1.29e-02 6.01e+03 1.89e+00 bond pdb=" CA PHE E 100 " pdb=" CB PHE E 100 " ideal model delta sigma weight residual 1.528 1.510 0.019 1.39e-02 5.18e+03 1.82e+00 bond pdb=" CA PHE E 100 " pdb=" C PHE E 100 " ideal model delta sigma weight residual 1.524 1.507 0.017 1.31e-02 5.83e+03 1.75e+00 bond pdb=" CB LYS B 286 " pdb=" CG LYS B 286 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.68e+00 ... (remaining 9059 not shown) Histogram of bond angle deviations from ideal: 99.47 - 106.38: 274 106.38 - 113.28: 4901 113.28 - 120.19: 3038 120.19 - 127.09: 3958 127.09 - 134.00: 131 Bond angle restraints: 12302 Sorted by residual: angle pdb=" N GLU D 97 " pdb=" CA GLU D 97 " pdb=" CB GLU D 97 " ideal model delta sigma weight residual 110.16 116.20 -6.04 1.48e+00 4.57e-01 1.66e+01 angle pdb=" CB LYS B 286 " pdb=" CG LYS B 286 " pdb=" CD LYS B 286 " ideal model delta sigma weight residual 111.30 120.13 -8.83 2.30e+00 1.89e-01 1.47e+01 angle pdb=" CA MET C 133 " pdb=" CB MET C 133 " pdb=" CG MET C 133 " ideal model delta sigma weight residual 114.10 121.36 -7.26 2.00e+00 2.50e-01 1.32e+01 angle pdb=" C HIS B 347 " pdb=" CA HIS B 347 " pdb=" CB HIS B 347 " ideal model delta sigma weight residual 110.45 116.39 -5.94 1.73e+00 3.34e-01 1.18e+01 angle pdb=" C SER A 614 " pdb=" N HIS A 615 " pdb=" CA HIS A 615 " ideal model delta sigma weight residual 122.32 128.01 -5.69 1.76e+00 3.23e-01 1.05e+01 ... (remaining 12297 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.57: 4968 16.57 - 33.13: 359 33.13 - 49.70: 72 49.70 - 66.26: 8 66.26 - 82.83: 7 Dihedral angle restraints: 5414 sinusoidal: 2107 harmonic: 3307 Sorted by residual: dihedral pdb=" CA MET C 133 " pdb=" C MET C 133 " pdb=" N PRO C 134 " pdb=" CA PRO C 134 " ideal model delta harmonic sigma weight residual 180.00 -151.78 -28.22 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA PHE B 236 " pdb=" C PHE B 236 " pdb=" N PHE B 237 " pdb=" CA PHE B 237 " ideal model delta harmonic sigma weight residual -180.00 -160.83 -19.17 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA ASP C 52 " pdb=" CB ASP C 52 " pdb=" CG ASP C 52 " pdb=" OD1 ASP C 52 " ideal model delta sinusoidal sigma weight residual -30.00 -89.73 59.73 1 2.00e+01 2.50e-03 1.19e+01 ... (remaining 5411 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 911 0.037 - 0.073: 299 0.073 - 0.110: 109 0.110 - 0.147: 43 0.147 - 0.183: 2 Chirality restraints: 1364 Sorted by residual: chirality pdb=" CA THR C 28 " pdb=" N THR C 28 " pdb=" C THR C 28 " pdb=" CB THR C 28 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.18 2.00e-01 2.50e+01 8.39e-01 chirality pdb=" CA GLU D 97 " pdb=" N GLU D 97 " pdb=" C GLU D 97 " pdb=" CB GLU D 97 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.35e-01 chirality pdb=" CA LEU D 65 " pdb=" N LEU D 65 " pdb=" C LEU D 65 " pdb=" CB LEU D 65 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.18e-01 ... (remaining 1361 not shown) Planarity restraints: 1594 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 615 " 0.020 2.00e-02 2.50e+03 2.55e-02 9.72e+00 pdb=" CG HIS A 615 " -0.054 2.00e-02 2.50e+03 pdb=" ND1 HIS A 615 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 HIS A 615 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 HIS A 615 " 0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS A 615 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 347 " 0.017 2.00e-02 2.50e+03 2.00e-02 5.97e+00 pdb=" CG HIS B 347 " -0.043 2.00e-02 2.50e+03 pdb=" ND1 HIS B 347 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 HIS B 347 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 HIS B 347 " 0.003 2.00e-02 2.50e+03 pdb=" NE2 HIS B 347 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS B 283 " 0.037 5.00e-02 4.00e+02 5.57e-02 4.96e+00 pdb=" N PRO B 284 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 284 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 284 " 0.031 5.00e-02 4.00e+02 ... (remaining 1591 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 850 2.75 - 3.29: 8672 3.29 - 3.82: 15009 3.82 - 4.36: 17059 4.36 - 4.90: 29554 Nonbonded interactions: 71144 Sorted by model distance: nonbonded pdb=" OG1 THR C 72 " pdb=" O GLU C 75 " model vdw 2.212 2.440 nonbonded pdb=" OD2 ASP B 180 " pdb=" NH2 ARG B 271 " model vdw 2.239 2.520 nonbonded pdb=" OG SER C 44 " pdb=" O THR C 46 " model vdw 2.260 2.440 nonbonded pdb=" O LEU D 48 " pdb=" OH TYR B 369 " model vdw 2.266 2.440 nonbonded pdb=" NH1 ARG B 73 " pdb=" O ILE B 135 " model vdw 2.284 2.520 ... (remaining 71139 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: 0.010 Normalize map: mean=0, sd=1: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 3.900 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 26.110 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 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 : 0.002 0.056 9064 Z= 0.161 Angle : 0.622 10.363 12302 Z= 0.323 Chirality : 0.044 0.183 1364 Planarity : 0.004 0.056 1594 Dihedral : 12.266 82.829 3268 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.11 % Allowed : 0.32 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.25), residues: 1121 helix: 2.60 (0.36), residues: 202 sheet: -0.03 (0.31), residues: 299 loop : -1.15 (0.23), residues: 620 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 209 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 210 average time/residue: 0.2294 time to fit residues: 65.2528 Evaluate side-chains 128 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 127 time to evaluate : 1.129 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0862 time to fit residues: 1.6662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 chunk 47 optimal weight: 9.9990 chunk 29 optimal weight: 0.9990 chunk 57 optimal weight: 9.9990 chunk 45 optimal weight: 8.9990 chunk 88 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 53 optimal weight: 8.9990 chunk 65 optimal weight: 6.9990 chunk 102 optimal weight: 0.0010 overall best weight: 2.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 75 HIS B 347 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9064 Z= 0.322 Angle : 0.682 9.324 12302 Z= 0.343 Chirality : 0.047 0.278 1364 Planarity : 0.005 0.048 1594 Dihedral : 4.377 26.256 1220 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 21.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.99 % Allowed : 10.68 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.25), residues: 1121 helix: 2.27 (0.37), residues: 208 sheet: -0.02 (0.30), residues: 306 loop : -1.14 (0.23), residues: 607 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 139 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 20 residues processed: 150 average time/residue: 0.2343 time to fit residues: 47.8945 Evaluate side-chains 137 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 117 time to evaluate : 1.130 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.0992 time to fit residues: 4.9318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 9.9990 chunk 31 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 102 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 chunk 91 optimal weight: 7.9990 chunk 101 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 706 GLN D 93 GLN ** B 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9064 Z= 0.216 Angle : 0.629 10.994 12302 Z= 0.309 Chirality : 0.045 0.194 1364 Planarity : 0.004 0.036 1594 Dihedral : 4.223 24.415 1220 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 18.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.18 % Allowed : 14.21 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.25), residues: 1121 helix: 2.40 (0.37), residues: 208 sheet: -0.09 (0.30), residues: 315 loop : -1.04 (0.24), residues: 598 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 133 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 2 residues processed: 136 average time/residue: 0.2081 time to fit residues: 39.5982 Evaluate side-chains 127 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 125 time to evaluate : 1.003 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0961 time to fit residues: 1.7007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 6.9990 chunk 77 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 11 optimal weight: 30.0000 chunk 49 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 90 optimal weight: 0.6980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 706 GLN C 403 GLN ** B 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9064 Z= 0.178 Angle : 0.615 11.742 12302 Z= 0.299 Chirality : 0.045 0.192 1364 Planarity : 0.004 0.044 1594 Dihedral : 4.091 24.374 1220 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.18 % Allowed : 15.71 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.25), residues: 1121 helix: 2.46 (0.37), residues: 208 sheet: -0.07 (0.30), residues: 300 loop : -1.01 (0.23), residues: 613 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 134 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 137 average time/residue: 0.2099 time to fit residues: 40.5980 Evaluate side-chains 127 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 119 time to evaluate : 1.136 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0895 time to fit residues: 2.9159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 9.9990 chunk 1 optimal weight: 4.9990 chunk 81 optimal weight: 9.9990 chunk 45 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 706 GLN ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 403 GLN ** B 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 9064 Z= 0.378 Angle : 0.692 10.398 12302 Z= 0.349 Chirality : 0.046 0.207 1364 Planarity : 0.005 0.037 1594 Dihedral : 4.458 23.682 1220 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 24.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.35 % Allowed : 16.13 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.25), residues: 1121 helix: 2.11 (0.37), residues: 208 sheet: -0.37 (0.29), residues: 316 loop : -1.02 (0.24), residues: 597 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 127 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 17 residues processed: 139 average time/residue: 0.2069 time to fit residues: 40.9404 Evaluate side-chains 134 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 117 time to evaluate : 1.015 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.0890 time to fit residues: 4.2802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 105 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 397 ASN ** B 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9064 Z= 0.255 Angle : 0.665 12.574 12302 Z= 0.327 Chirality : 0.045 0.201 1364 Planarity : 0.004 0.049 1594 Dihedral : 4.372 24.246 1220 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 21.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.85 % Allowed : 18.48 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.25), residues: 1121 helix: 2.18 (0.37), residues: 208 sheet: -0.28 (0.30), residues: 297 loop : -0.96 (0.24), residues: 616 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 124 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 127 average time/residue: 0.2217 time to fit residues: 39.6234 Evaluate side-chains 122 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 118 time to evaluate : 1.119 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0950 time to fit residues: 2.1124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 7.9990 chunk 62 optimal weight: 6.9990 chunk 79 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 chunk 92 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 chunk 66 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 403 GLN B 175 GLN ** B 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9064 Z= 0.280 Angle : 0.678 13.459 12302 Z= 0.334 Chirality : 0.045 0.202 1364 Planarity : 0.004 0.061 1594 Dihedral : 4.402 24.408 1220 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 23.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.64 % Allowed : 19.98 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.25), residues: 1121 helix: 2.11 (0.37), residues: 208 sheet: -0.38 (0.30), residues: 303 loop : -0.96 (0.24), residues: 610 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 127 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 129 average time/residue: 0.2401 time to fit residues: 42.7514 Evaluate side-chains 126 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 121 time to evaluate : 1.167 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0815 time to fit residues: 2.1722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 99 optimal weight: 0.9980 chunk 104 optimal weight: 0.0980 chunk 95 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9064 Z= 0.190 Angle : 0.684 14.906 12302 Z= 0.330 Chirality : 0.045 0.211 1364 Planarity : 0.004 0.059 1594 Dihedral : 4.268 24.673 1220 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 20.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.64 % Allowed : 20.51 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.25), residues: 1121 helix: 2.14 (0.37), residues: 208 sheet: -0.32 (0.30), residues: 304 loop : -0.90 (0.24), residues: 609 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 128 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 130 average time/residue: 0.2258 time to fit residues: 40.8346 Evaluate side-chains 125 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 121 time to evaluate : 1.138 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1012 time to fit residues: 2.1494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 0.6980 chunk 104 optimal weight: 0.7980 chunk 61 optimal weight: 9.9990 chunk 44 optimal weight: 8.9990 chunk 79 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 95 optimal weight: 0.4980 chunk 66 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 chunk 65 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9064 Z= 0.189 Angle : 0.697 15.291 12302 Z= 0.331 Chirality : 0.046 0.200 1364 Planarity : 0.004 0.063 1594 Dihedral : 4.169 25.740 1220 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 18.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.43 % Allowed : 20.83 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.25), residues: 1121 helix: 2.14 (0.37), residues: 208 sheet: -0.27 (0.30), residues: 299 loop : -0.94 (0.24), residues: 614 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 125 time to evaluate : 1.083 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 126 average time/residue: 0.2268 time to fit residues: 40.5544 Evaluate side-chains 120 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 118 time to evaluate : 1.080 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0846 time to fit residues: 1.7909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 112 optimal weight: 4.9990 chunk 103 optimal weight: 0.5980 chunk 89 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 69 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 71 optimal weight: 0.0980 chunk 95 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 589 GLN ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.4027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9064 Z= 0.228 Angle : 0.713 15.237 12302 Z= 0.343 Chirality : 0.046 0.197 1364 Planarity : 0.004 0.063 1594 Dihedral : 4.198 24.871 1220 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 20.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.43 % Allowed : 21.05 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.25), residues: 1121 helix: 1.97 (0.37), residues: 208 sheet: -0.27 (0.30), residues: 297 loop : -0.96 (0.24), residues: 616 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 121 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 121 average time/residue: 0.2326 time to fit residues: 38.7751 Evaluate side-chains 116 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.070 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 7.9990 chunk 13 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 11 optimal weight: 30.0000 chunk 16 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.078391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.061002 restraints weight = 35477.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.063311 restraints weight = 20369.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.064886 restraints weight = 14240.482| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.4061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9064 Z= 0.209 Angle : 0.722 15.478 12302 Z= 0.345 Chirality : 0.046 0.201 1364 Planarity : 0.004 0.063 1594 Dihedral : 4.248 24.034 1220 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 19.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.43 % Allowed : 21.69 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.25), residues: 1121 helix: 1.92 (0.37), residues: 208 sheet: -0.30 (0.30), residues: 298 loop : -0.97 (0.24), residues: 615 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1884.85 seconds wall clock time: 35 minutes 38.86 seconds (2138.86 seconds total)