Starting phenix.real_space_refine on Fri Feb 16 19:53:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w5s_21546/02_2024/6w5s_21546_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w5s_21546/02_2024/6w5s_21546.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w5s_21546/02_2024/6w5s_21546.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w5s_21546/02_2024/6w5s_21546.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w5s_21546/02_2024/6w5s_21546_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w5s_21546/02_2024/6w5s_21546_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 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 6691 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 75 5.16 5 C 6276 2.51 5 N 1534 2.21 5 O 1814 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 143": "OE1" <-> "OE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A GLU 218": "OE1" <-> "OE2" Residue "A GLU 332": "OE1" <-> "OE2" Residue "A ARG 372": "NH1" <-> "NH2" Residue "A ARG 389": "NH1" <-> "NH2" Residue "A GLU 391": "OE1" <-> "OE2" Residue "A ARG 404": "NH1" <-> "NH2" Residue "A ARG 411": "NH1" <-> "NH2" Residue "A GLU 460": "OE1" <-> "OE2" Residue "A ARG 518": "NH1" <-> "NH2" Residue "A GLU 575": "OE1" <-> "OE2" Residue "A ARG 579": "NH1" <-> "NH2" Residue "A ARG 579": "NH1" <-> "NH2" Residue "A GLU 586": "OE1" <-> "OE2" Residue "A ARG 607": "NH1" <-> "NH2" Residue "A ARG 615": "NH1" <-> "NH2" Residue "A ARG 647": "NH1" <-> "NH2" Residue "A GLU 713": "OE1" <-> "OE2" Residue "A ARG 789": "NH1" <-> "NH2" Residue "A GLU 791": "OE1" <-> "OE2" Residue "A ARG 802": "NH1" <-> "NH2" Residue "A ARG 819": "NH1" <-> "NH2" Residue "A GLU 895": "OE1" <-> "OE2" Residue "A ARG 980": "NH1" <-> "NH2" Residue "A GLU 1120": "OE1" <-> "OE2" Residue "A GLU 1166": "OE1" <-> "OE2" Residue "A PHE 1167": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9700 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9360 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1194, 9338 Classifications: {'peptide': 1194} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 62, 'TRANS': 1130} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 1194, 9338 Classifications: {'peptide': 1194} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 62, 'TRANS': 1130} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 9558 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 206 Unusual residues: {'CLR': 1, 'NAG': 9, 'POV': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AARG A 579 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 579 " occ=0.50 residue: pdb=" N AARG A1032 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A1032 " occ=0.50 Time building chain proxies: 9.81, per 1000 atoms: 1.01 Number of scatterers: 9700 At special positions: 0 Unit cell: (101.374, 88.006, 157.074, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 75 16.00 P 1 15.00 O 1814 8.00 N 1534 7.00 C 6276 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 25 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 31 " - pdb=" SG CYS A 42 " distance=2.03 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 109 " distance=2.03 Simple disulfide: pdb=" SG CYS A 75 " - pdb=" SG CYS A 113 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 238 " distance=2.03 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 160 " distance=2.03 Simple disulfide: pdb=" SG CYS A 177 " - pdb=" SG CYS A 184 " distance=2.03 Simple disulfide: pdb=" SG CYS A 227 " - pdb=" SG CYS A 243 " distance=2.03 Simple disulfide: pdb=" SG CYS A 240 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 468 " - pdb=" SG CYS A 479 " distance=2.03 Simple disulfide: pdb=" SG CYS A 516 " - pdb=" SG CYS A 533 " distance=2.02 Simple disulfide: pdb=" SG CYS A 909 " - pdb=" SG CYS A 914 " distance=2.02 Simple disulfide: pdb=" SG CYS A 956 " - pdb=" SG CYS A1011 " distance=2.03 Simple disulfide: pdb=" SG CYS A 957 " - pdb=" SG CYS A 979 " distance=2.03 Simple disulfide: pdb=" SG CYS A 967 " - pdb=" SG CYS A 976 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " NAG C 2 " - " MAN C 3 " ALPHA1-4 " NAG D 2 " - " MAN D 3 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A1401 " - " ASN A 452 " " NAG A1402 " - " ASN A 459 " " NAG A1405 " - " ASN A 524 " " NAG A1409 " - " ASN A 598 " " NAG A1410 " - " ASN A 916 " " NAG A1414 " - " ASN A 961 " " NAG A1415 " - " ASN A 968 " " NAG A1416 " - " ASN A1064 " " NAG A1419 " - " ASN A 158 " " NAG B 1 " - " ASN A 478 " " NAG C 1 " - " ASN A 557 " " NAG D 1 " - " ASN A 931 " " NAG E 1 " - " ASN A 222 " Time building additional restraints: 4.30 Conformation dependent library (CDL) restraints added in 3.3 seconds 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2242 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 49 helices and 4 sheets defined 51.7% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.53 Creating SS restraints... Processing helix chain 'A' and resid 56 through 62 Processing helix chain 'A' and resid 64 through 66 No H-bonds generated for 'chain 'A' and resid 64 through 66' Processing helix chain 'A' and resid 77 through 96 removed outlier: 3.900A pdb=" N THR A 82 " --> pdb=" O ARG A 78 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP A 85 " --> pdb=" O GLN A 81 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN A 86 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN A 88 " --> pdb=" O LYS A 84 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N LEU A 89 " --> pdb=" O ASP A 85 " (cutoff:3.500A) Proline residue: A 90 - end of helix removed outlier: 4.708A pdb=" N ARG A 96 " --> pdb=" O GLN A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 113 removed outlier: 3.897A pdb=" N ASN A 103 " --> pdb=" O SER A 99 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLU A 110 " --> pdb=" O ASN A 106 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU A 111 " --> pdb=" O LEU A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 120 Processing helix chain 'A' and resid 150 through 160 removed outlier: 3.675A pdb=" N ALA A 155 " --> pdb=" O SER A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 186 through 194 removed outlier: 4.159A pdb=" N ILE A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 198 No H-bonds generated for 'chain 'A' and resid 196 through 198' Processing helix chain 'A' and resid 269 through 291 removed outlier: 3.539A pdb=" N TRP A 273 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA A 278 " --> pdb=" O ILE A 274 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA A 286 " --> pdb=" O VAL A 282 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE A 287 " --> pdb=" O PHE A 283 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE A 288 " --> pdb=" O PHE A 284 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA A 289 " --> pdb=" O GLY A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 348 removed outlier: 3.785A pdb=" N CYS A 334 " --> pdb=" O ALA A 330 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU A 335 " --> pdb=" O PHE A 331 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ARG A 336 " --> pdb=" O GLU A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 370 removed outlier: 4.852A pdb=" N GLY A 367 " --> pdb=" O ALA A 363 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N LEU A 368 " --> pdb=" O CYS A 364 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N VAL A 369 " --> pdb=" O SER A 365 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N PHE A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 381 Processing helix chain 'A' and resid 387 through 398 Processing helix chain 'A' and resid 437 through 452 Processing helix chain 'A' and resid 464 through 467 No H-bonds generated for 'chain 'A' and resid 464 through 467' Processing helix chain 'A' and resid 484 through 487 removed outlier: 3.574A pdb=" N TYR A 487 " --> pdb=" O VAL A 484 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 484 through 487' Processing helix chain 'A' and resid 492 through 496 Processing helix chain 'A' and resid 509 through 518 removed outlier: 3.661A pdb=" N ARG A 518 " --> pdb=" O LEU A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 546 No H-bonds generated for 'chain 'A' and resid 543 through 546' Processing helix chain 'A' and resid 555 through 557 No H-bonds generated for 'chain 'A' and resid 555 through 557' Processing helix chain 'A' and resid 575 through 592 removed outlier: 3.671A pdb=" N GLU A 586 " --> pdb=" O ALA A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 616 Processing helix chain 'A' and resid 621 through 638 removed outlier: 3.642A pdb=" N ILE A 626 " --> pdb=" O PHE A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 678 Processing helix chain 'A' and resid 686 through 710 Proline residue: A 691 - end of helix Processing helix chain 'A' and resid 720 through 749 Proline residue: A 733 - end of helix Processing helix chain 'A' and resid 755 through 791 removed outlier: 3.636A pdb=" N THR A 759 " --> pdb=" O PRO A 755 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL A 780 " --> pdb=" O ILE A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 821 No H-bonds generated for 'chain 'A' and resid 818 through 821' Processing helix chain 'A' and resid 826 through 829 No H-bonds generated for 'chain 'A' and resid 826 through 829' Processing helix chain 'A' and resid 835 through 851 Processing helix chain 'A' and resid 853 through 855 No H-bonds generated for 'chain 'A' and resid 853 through 855' Processing helix chain 'A' and resid 871 through 882 Processing helix chain 'A' and resid 902 through 906 Processing helix chain 'A' and resid 919 through 929 Processing helix chain 'A' and resid 942 through 950 Processing helix chain 'A' and resid 984 through 987 No H-bonds generated for 'chain 'A' and resid 984 through 987' Processing helix chain 'A' and resid 993 through 1004 Proline residue: A1000 - end of helix Processing helix chain 'A' and resid 1029 through 1031 No H-bonds generated for 'chain 'A' and resid 1029 through 1031' Processing helix chain 'A' and resid 1048 through 1069 Processing helix chain 'A' and resid 1083 through 1088 removed outlier: 4.139A pdb=" N VAL A1086 " --> pdb=" O VAL A1083 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1092 No H-bonds generated for 'chain 'A' and resid 1090 through 1092' Processing helix chain 'A' and resid 1094 through 1116 Processing helix chain 'A' and resid 1121 through 1145 Processing helix chain 'A' and resid 1153 through 1176 removed outlier: 4.147A pdb=" N GLY A1162 " --> pdb=" O VAL A1158 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE A1163 " --> pdb=" O MET A1159 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL A1165 " --> pdb=" O CYS A1161 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU A1166 " --> pdb=" O GLY A1162 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N HIS A1170 " --> pdb=" O GLU A1166 " (cutoff:3.500A) Processing helix chain 'A' and resid 1183 through 1201 removed outlier: 4.018A pdb=" N SER A1197 " --> pdb=" O HIS A1193 " (cutoff:3.500A) Processing helix chain 'A' and resid 1203 through 1213 Processing helix chain 'A' and resid 1219 through 1224 Processing helix chain 'A' and resid 1226 through 1251 Proline residue: A1245 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 206 through 209 removed outlier: 5.967A pdb=" N GLN A 145 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N VAL A 123 " --> pdb=" O GLN A 145 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N TYR A 147 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LEU A 121 " --> pdb=" O TYR A 147 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 409 through 411 Processing sheet with id= C, first strand: chain 'A' and resid 418 through 420 Processing sheet with id= D, first strand: chain 'A' and resid 1036 through 1041 402 hydrogen bonds defined for protein. 1180 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: 2.67 Time building geometry restraints manager: 4.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3004 1.34 - 1.46: 2507 1.46 - 1.59: 4330 1.59 - 1.71: 2 1.71 - 1.84: 105 Bond restraints: 9948 Sorted by residual: bond pdb=" C31 POV A1421 " pdb=" O31 POV A1421 " ideal model delta sigma weight residual 1.327 1.452 -0.125 2.00e-02 2.50e+03 3.88e+01 bond pdb=" C21 POV A1421 " pdb=" O21 POV A1421 " ideal model delta sigma weight residual 1.330 1.453 -0.123 2.00e-02 2.50e+03 3.78e+01 bond pdb=" C1 NAG A1410 " pdb=" O5 NAG A1410 " ideal model delta sigma weight residual 1.406 1.471 -0.065 2.00e-02 2.50e+03 1.04e+01 bond pdb=" C1 NAG A1405 " pdb=" O5 NAG A1405 " ideal model delta sigma weight residual 1.406 1.465 -0.059 2.00e-02 2.50e+03 8.70e+00 bond pdb=" O12 POV A1421 " pdb=" P POV A1421 " ideal model delta sigma weight residual 1.657 1.608 0.049 2.00e-02 2.50e+03 6.03e+00 ... (remaining 9943 not shown) Histogram of bond angle deviations from ideal: 86.06 - 95.65: 1 95.65 - 105.24: 220 105.24 - 114.82: 6041 114.82 - 124.41: 7115 124.41 - 134.00: 166 Bond angle restraints: 13543 Sorted by residual: angle pdb=" N ASN A 70 " pdb=" CA ASN A 70 " pdb=" C ASN A 70 " ideal model delta sigma weight residual 110.80 86.06 24.74 2.13e+00 2.20e-01 1.35e+02 angle pdb=" N LYS A 142 " pdb=" CA LYS A 142 " pdb=" C LYS A 142 " ideal model delta sigma weight residual 111.14 118.85 -7.71 1.08e+00 8.57e-01 5.10e+01 angle pdb=" N LYS A 822 " pdb=" CA LYS A 822 " pdb=" C LYS A 822 " ideal model delta sigma weight residual 111.36 118.57 -7.21 1.09e+00 8.42e-01 4.38e+01 angle pdb=" C ASN A 70 " pdb=" N VAL A 71 " pdb=" CA VAL A 71 " ideal model delta sigma weight residual 120.56 113.02 7.54 1.26e+00 6.30e-01 3.58e+01 angle pdb=" N SER A 863 " pdb=" CA SER A 863 " pdb=" C SER A 863 " ideal model delta sigma weight residual 113.97 107.18 6.79 1.28e+00 6.10e-01 2.81e+01 ... (remaining 13538 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.93: 5981 35.93 - 71.86: 166 71.86 - 107.80: 24 107.80 - 143.73: 21 143.73 - 179.66: 2 Dihedral angle restraints: 6194 sinusoidal: 2706 harmonic: 3488 Sorted by residual: dihedral pdb=" CD BARG A 579 " pdb=" NE BARG A 579 " pdb=" CZ BARG A 579 " pdb=" NH1BARG A 579 " ideal model delta sinusoidal sigma weight residual 0.00 -179.66 179.66 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CB CYS A 240 " pdb=" SG CYS A 240 " pdb=" SG CYS A 247 " pdb=" CB CYS A 247 " ideal model delta sinusoidal sigma weight residual -86.00 1.75 -87.75 1 1.00e+01 1.00e-02 9.22e+01 dihedral pdb=" CB CYS A 909 " pdb=" SG CYS A 909 " pdb=" SG CYS A 914 " pdb=" CB CYS A 914 " ideal model delta sinusoidal sigma weight residual -86.00 -14.78 -71.22 1 1.00e+01 1.00e-02 6.51e+01 ... (remaining 6191 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.939: 1575 0.939 - 1.877: 0 1.877 - 2.816: 0 2.816 - 3.755: 0 3.755 - 4.694: 1 Chirality restraints: 1576 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 2.29 -4.69 2.00e-02 2.50e+03 5.51e+04 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-02 2.50e+03 4.10e+02 chirality pdb=" C1 MAN C 3 " pdb=" O3 NAG C 2 " pdb=" C2 MAN C 3 " pdb=" O5 MAN C 3 " both_signs ideal model delta sigma weight residual False 2.40 2.18 0.22 2.00e-02 2.50e+03 1.22e+02 ... (remaining 1573 not shown) Planarity restraints: 1711 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " -0.351 2.00e-02 2.50e+03 3.03e-01 1.15e+03 pdb=" C7 NAG E 2 " 0.081 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " -0.084 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " 0.537 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " -0.184 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " -0.339 2.00e-02 2.50e+03 2.92e-01 1.07e+03 pdb=" C7 NAG D 2 " 0.078 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " -0.044 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " 0.511 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " -0.207 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 2 " 0.264 2.00e-02 2.50e+03 2.19e-01 6.01e+02 pdb=" C7 NAG B 2 " -0.072 2.00e-02 2.50e+03 pdb=" C8 NAG B 2 " 0.181 2.00e-02 2.50e+03 pdb=" N2 NAG B 2 " -0.365 2.00e-02 2.50e+03 pdb=" O7 NAG B 2 " -0.008 2.00e-02 2.50e+03 ... (remaining 1708 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 77 2.54 - 3.13: 8286 3.13 - 3.72: 14502 3.72 - 4.31: 21508 4.31 - 4.90: 35533 Nonbonded interactions: 79906 Sorted by model distance: nonbonded pdb=" OE2 GLU A 164 " pdb=" NE2 GLN A 241 " model vdw 1.946 2.520 nonbonded pdb=" O PHE A 821 " pdb=" OG SER A 826 " model vdw 2.026 2.440 nonbonded pdb=" O GLN A 119 " pdb=" SD MET A 217 " model vdw 2.032 3.400 nonbonded pdb=" NH2 ARG A 78 " pdb=" OE1 GLN A 81 " model vdw 2.055 2.520 nonbonded pdb=" O CYS A 909 " pdb=" OG SER A 918 " model vdw 2.066 2.440 ... (remaining 79901 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'D' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 3.490 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 35.590 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 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 : 0.005 0.125 9948 Z= 0.325 Angle : 0.829 24.740 13543 Z= 0.469 Chirality : 0.129 4.694 1576 Planarity : 0.013 0.303 1698 Dihedral : 18.493 179.661 3907 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 31.03 Ramachandran Plot: Outliers : 0.42 % Allowed : 7.58 % Favored : 92.00 % Rotamer: Outliers : 2.70 % Allowed : 3.67 % Favored : 93.63 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -3.24 (0.22), residues: 1194 helix: -1.31 (0.19), residues: 626 sheet: -1.98 (0.56), residues: 88 loop : -3.30 (0.24), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 949 HIS 0.006 0.001 HIS A1042 PHE 0.012 0.001 PHE A1079 TYR 0.013 0.001 TYR A 570 ARG 0.002 0.000 ARG A 372 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 151 time to evaluate : 1.043 Fit side-chains REVERT: A 156 MET cc_start: 0.8738 (ttt) cc_final: 0.8538 (ttm) REVERT: A 233 GLU cc_start: 0.7428 (mp0) cc_final: 0.6874 (pm20) REVERT: A 260 TRP cc_start: 0.6129 (m-10) cc_final: 0.5482 (m-90) REVERT: A 586 GLU cc_start: 0.6921 (tp30) cc_final: 0.6641 (tp30) REVERT: A 822 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8387 (tttp) REVERT: A 1158 VAL cc_start: 0.9175 (t) cc_final: 0.8971 (t) outliers start: 27 outliers final: 10 residues processed: 173 average time/residue: 1.1415 time to fit residues: 212.5847 Evaluate side-chains 118 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 107 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 575 GLU Chi-restraints excluded: chain A residue 711 ARG Chi-restraints excluded: chain A residue 822 LYS Chi-restraints excluded: chain A residue 862 GLN Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain A residue 1161 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 88 GLN A 92 GLN A 103 ASN A 122 ASN A 136 GLN ** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 387 GLN A 553 GLN A 554 ASN ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 707 GLN ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 793 ASN A 884 HIS A 906 ASN ** A1008 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1016 HIS A1046 GLN A1137 ASN A1193 HIS A1239 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9948 Z= 0.329 Angle : 0.829 11.163 13543 Z= 0.391 Chirality : 0.050 0.300 1576 Planarity : 0.005 0.046 1698 Dihedral : 17.712 175.455 1821 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.73 % Favored : 92.93 % Rotamer: Outliers : 2.61 % Allowed : 11.97 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -1.98 (0.23), residues: 1194 helix: -0.29 (0.20), residues: 635 sheet: -1.28 (0.59), residues: 82 loop : -2.74 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 949 HIS 0.009 0.002 HIS A1042 PHE 0.018 0.002 PHE A1224 TYR 0.023 0.002 TYR A1037 ARG 0.004 0.001 ARG A1173 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 102 time to evaluate : 1.033 Fit side-chains revert: symmetry clash REVERT: A 260 TRP cc_start: 0.5797 (m-10) cc_final: 0.5185 (m-90) REVERT: A 265 LEU cc_start: 0.7660 (mp) cc_final: 0.7447 (OUTLIER) REVERT: A 288 PHE cc_start: 0.6879 (m-10) cc_final: 0.6028 (OUTLIER) REVERT: A 586 GLU cc_start: 0.6908 (tp30) cc_final: 0.6584 (tp30) REVERT: A 862 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7967 (pt0) outliers start: 26 outliers final: 16 residues processed: 120 average time/residue: 1.0736 time to fit residues: 140.2170 Evaluate side-chains 105 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 90 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 497 HIS Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 688 GLU Chi-restraints excluded: chain A residue 862 GLN Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1161 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 60 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 73 optimal weight: 0.4980 chunk 29 optimal weight: 0.7980 chunk 108 optimal weight: 0.8980 chunk 116 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 GLN ** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 553 GLN ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 793 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9948 Z= 0.208 Angle : 0.746 14.573 13543 Z= 0.348 Chirality : 0.046 0.281 1576 Planarity : 0.004 0.046 1698 Dihedral : 16.517 179.228 1803 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.06 % Favored : 93.69 % Rotamer: Outliers : 2.70 % Allowed : 13.51 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -1.29 (0.24), residues: 1194 helix: 0.28 (0.20), residues: 638 sheet: -1.32 (0.56), residues: 88 loop : -2.38 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 273 HIS 0.009 0.001 HIS A1042 PHE 0.012 0.001 PHE A 370 TYR 0.018 0.001 TYR A 570 ARG 0.004 0.000 ARG A 615 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 95 time to evaluate : 0.971 Fit side-chains revert: symmetry clash REVERT: A 241 GLN cc_start: 0.7482 (tm-30) cc_final: 0.7193 (tm-30) REVERT: A 260 TRP cc_start: 0.5727 (m-10) cc_final: 0.5194 (m-90) REVERT: A 586 GLU cc_start: 0.6909 (tp30) cc_final: 0.6597 (tp30) REVERT: A 666 SER cc_start: 0.8927 (OUTLIER) cc_final: 0.8500 (p) REVERT: A 1111 LEU cc_start: 0.8289 (tm) cc_final: 0.7720 (mt) REVERT: A 1158 VAL cc_start: 0.8953 (t) cc_final: 0.8711 (m) outliers start: 27 outliers final: 11 residues processed: 112 average time/residue: 1.1125 time to fit residues: 135.2752 Evaluate side-chains 99 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 87 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 497 HIS Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 688 GLU Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1161 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 0.7980 chunk 81 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 GLN ** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 530 HIS A 553 GLN ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 793 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9948 Z= 0.284 Angle : 0.752 13.742 13543 Z= 0.354 Chirality : 0.047 0.302 1576 Planarity : 0.005 0.049 1698 Dihedral : 15.366 177.057 1800 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.73 % Favored : 93.01 % Rotamer: Outliers : 3.19 % Allowed : 14.38 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -0.92 (0.24), residues: 1194 helix: 0.57 (0.20), residues: 628 sheet: -1.04 (0.58), residues: 88 loop : -2.16 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 949 HIS 0.007 0.001 HIS A1042 PHE 0.013 0.001 PHE A1224 TYR 0.020 0.002 TYR A1037 ARG 0.004 0.000 ARG A 958 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 96 time to evaluate : 0.963 Fit side-chains revert: symmetry clash REVERT: A 192 TYR cc_start: 0.7496 (t80) cc_final: 0.7204 (t80) REVERT: A 241 GLN cc_start: 0.7116 (tm-30) cc_final: 0.6576 (tm-30) REVERT: A 260 TRP cc_start: 0.5714 (m-10) cc_final: 0.5168 (m-90) REVERT: A 586 GLU cc_start: 0.6909 (tp30) cc_final: 0.6601 (tp30) REVERT: A 666 SER cc_start: 0.8973 (OUTLIER) cc_final: 0.8543 (p) outliers start: 32 outliers final: 18 residues processed: 113 average time/residue: 1.0883 time to fit residues: 133.3778 Evaluate side-chains 110 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 91 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 497 HIS Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 955 SER Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1069 MET Chi-restraints excluded: chain A residue 1105 SER Chi-restraints excluded: chain A residue 1114 MET Chi-restraints excluded: chain A residue 1142 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 65 optimal weight: 1.9990 chunk 1 optimal weight: 20.0000 chunk 85 optimal weight: 0.5980 chunk 47 optimal weight: 0.0570 chunk 98 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 38 optimal weight: 0.0980 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 790 GLN A 793 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9948 Z= 0.202 Angle : 0.698 12.379 13543 Z= 0.331 Chirality : 0.045 0.288 1576 Planarity : 0.004 0.049 1698 Dihedral : 14.590 178.614 1799 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.89 % Favored : 93.86 % Rotamer: Outliers : 2.61 % Allowed : 15.25 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -0.58 (0.24), residues: 1194 helix: 0.80 (0.21), residues: 627 sheet: -0.90 (0.59), residues: 88 loop : -1.92 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 949 HIS 0.007 0.001 HIS A1042 PHE 0.012 0.001 PHE A 370 TYR 0.016 0.001 TYR A 506 ARG 0.003 0.000 ARG A 615 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 102 time to evaluate : 1.005 Fit side-chains revert: symmetry clash REVERT: A 192 TYR cc_start: 0.7497 (t80) cc_final: 0.7161 (t80) REVERT: A 260 TRP cc_start: 0.5701 (m-10) cc_final: 0.5156 (m-90) REVERT: A 586 GLU cc_start: 0.6909 (tp30) cc_final: 0.6600 (tp30) REVERT: A 666 SER cc_start: 0.9099 (OUTLIER) cc_final: 0.8679 (p) outliers start: 26 outliers final: 15 residues processed: 116 average time/residue: 1.0246 time to fit residues: 129.4862 Evaluate side-chains 104 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 88 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 497 HIS Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1069 MET Chi-restraints excluded: chain A residue 1105 SER Chi-restraints excluded: chain A residue 1114 MET Chi-restraints excluded: chain A residue 1142 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 103 optimal weight: 0.3980 chunk 22 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 115 optimal weight: 0.6980 chunk 95 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 38 optimal weight: 0.5980 chunk 60 optimal weight: 0.6980 chunk 111 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 GLN A 145 GLN ** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 793 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9948 Z= 0.181 Angle : 0.665 10.644 13543 Z= 0.316 Chirality : 0.044 0.309 1576 Planarity : 0.004 0.050 1698 Dihedral : 13.177 179.167 1796 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.14 % Favored : 93.60 % Rotamer: Outliers : 2.90 % Allowed : 15.73 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: 1194 helix: 1.06 (0.21), residues: 626 sheet: -0.79 (0.59), residues: 88 loop : -1.76 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 949 HIS 0.007 0.001 HIS A1042 PHE 0.014 0.001 PHE A 209 TYR 0.015 0.001 TYR A 570 ARG 0.003 0.000 ARG A 615 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 93 time to evaluate : 1.196 Fit side-chains revert: symmetry clash REVERT: A 192 TYR cc_start: 0.7576 (t80) cc_final: 0.7259 (t80) REVERT: A 241 GLN cc_start: 0.6886 (tm-30) cc_final: 0.6437 (tm-30) REVERT: A 260 TRP cc_start: 0.5455 (m-10) cc_final: 0.4942 (m-90) REVERT: A 586 GLU cc_start: 0.6929 (tp30) cc_final: 0.6631 (tp30) REVERT: A 666 SER cc_start: 0.9118 (OUTLIER) cc_final: 0.8705 (p) REVERT: A 955 SER cc_start: 0.7601 (OUTLIER) cc_final: 0.7186 (t) REVERT: A 1069 MET cc_start: 0.9024 (OUTLIER) cc_final: 0.8716 (mtt) outliers start: 29 outliers final: 15 residues processed: 110 average time/residue: 1.1122 time to fit residues: 133.7421 Evaluate side-chains 106 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 88 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 497 HIS Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 551 ASP Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 955 SER Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1069 MET Chi-restraints excluded: chain A residue 1105 SER Chi-restraints excluded: chain A residue 1142 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 12 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 114 optimal weight: 0.0370 chunk 71 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 45 optimal weight: 5.9990 overall best weight: 1.3062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 GLN A 145 GLN ** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 793 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9948 Z= 0.270 Angle : 0.704 10.213 13543 Z= 0.335 Chirality : 0.046 0.313 1576 Planarity : 0.005 0.050 1698 Dihedral : 12.813 177.271 1796 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.40 % Favored : 93.35 % Rotamer: Outliers : 2.32 % Allowed : 16.70 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.25), residues: 1194 helix: 1.00 (0.21), residues: 627 sheet: -0.79 (0.59), residues: 88 loop : -1.76 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 949 HIS 0.006 0.001 HIS A1042 PHE 0.013 0.001 PHE A1167 TYR 0.020 0.002 TYR A1037 ARG 0.006 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 95 time to evaluate : 0.930 Fit side-chains revert: symmetry clash REVERT: A 192 TYR cc_start: 0.7610 (t80) cc_final: 0.7357 (t80) REVERT: A 241 GLN cc_start: 0.6861 (tm-30) cc_final: 0.6384 (tm-30) REVERT: A 260 TRP cc_start: 0.5618 (m-10) cc_final: 0.5089 (m-90) REVERT: A 586 GLU cc_start: 0.6936 (tp30) cc_final: 0.6628 (tp30) REVERT: A 666 SER cc_start: 0.9141 (OUTLIER) cc_final: 0.8711 (p) REVERT: A 955 SER cc_start: 0.7663 (OUTLIER) cc_final: 0.7236 (t) REVERT: A 1228 MET cc_start: 0.8768 (mtp) cc_final: 0.8419 (mmm) outliers start: 23 outliers final: 19 residues processed: 105 average time/residue: 1.0702 time to fit residues: 122.4350 Evaluate side-chains 112 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 91 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 497 HIS Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 551 ASP Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 955 SER Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1069 MET Chi-restraints excluded: chain A residue 1105 SER Chi-restraints excluded: chain A residue 1142 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 68 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 22 optimal weight: 0.0270 chunk 72 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 10 optimal weight: 20.0000 chunk 90 optimal weight: 0.6980 chunk 104 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 GLN ** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 793 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9948 Z= 0.181 Angle : 0.670 9.624 13543 Z= 0.317 Chirality : 0.044 0.293 1576 Planarity : 0.004 0.050 1698 Dihedral : 12.404 179.372 1796 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.23 % Favored : 93.52 % Rotamer: Outliers : 2.80 % Allowed : 16.22 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -0.14 (0.25), residues: 1194 helix: 1.14 (0.21), residues: 628 sheet: -0.77 (0.58), residues: 88 loop : -1.65 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 949 HIS 0.007 0.001 HIS A1042 PHE 0.012 0.001 PHE A 93 TYR 0.015 0.001 TYR A 570 ARG 0.007 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 94 time to evaluate : 0.944 Fit side-chains revert: symmetry clash REVERT: A 145 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.7204 (pt0) REVERT: A 192 TYR cc_start: 0.7564 (t80) cc_final: 0.7311 (t80) REVERT: A 241 GLN cc_start: 0.6978 (OUTLIER) cc_final: 0.6575 (tm-30) REVERT: A 260 TRP cc_start: 0.5334 (m-10) cc_final: 0.4835 (m-90) REVERT: A 586 GLU cc_start: 0.6933 (tp30) cc_final: 0.6640 (tp30) REVERT: A 666 SER cc_start: 0.9122 (OUTLIER) cc_final: 0.8710 (p) REVERT: A 955 SER cc_start: 0.7689 (OUTLIER) cc_final: 0.7280 (t) REVERT: A 1069 MET cc_start: 0.9018 (OUTLIER) cc_final: 0.8711 (mtt) outliers start: 28 outliers final: 14 residues processed: 109 average time/residue: 1.0566 time to fit residues: 125.5086 Evaluate side-chains 109 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 90 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 497 HIS Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 955 SER Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1069 MET Chi-restraints excluded: chain A residue 1105 SER Chi-restraints excluded: chain A residue 1142 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 0.6980 chunk 109 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 46 optimal weight: 0.0870 chunk 83 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 101 optimal weight: 0.5980 chunk 70 optimal weight: 0.8980 chunk 113 optimal weight: 5.9990 chunk 68 optimal weight: 0.6980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 GLN ** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 793 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9948 Z= 0.180 Angle : 0.666 9.921 13543 Z= 0.314 Chirality : 0.044 0.306 1576 Planarity : 0.004 0.050 1698 Dihedral : 12.060 179.094 1796 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.31 % Favored : 93.52 % Rotamer: Outliers : 2.22 % Allowed : 17.08 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -0.04 (0.25), residues: 1194 helix: 1.23 (0.21), residues: 628 sheet: -0.74 (0.58), residues: 88 loop : -1.62 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 949 HIS 0.007 0.001 HIS A1042 PHE 0.014 0.001 PHE A 209 TYR 0.014 0.001 TYR A 570 ARG 0.007 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 97 time to evaluate : 1.079 Fit side-chains revert: symmetry clash REVERT: A 145 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.7170 (pt0) REVERT: A 192 TYR cc_start: 0.7545 (t80) cc_final: 0.7306 (t80) REVERT: A 241 GLN cc_start: 0.6979 (OUTLIER) cc_final: 0.6587 (tm-30) REVERT: A 586 GLU cc_start: 0.6952 (tp30) cc_final: 0.6642 (tp30) REVERT: A 666 SER cc_start: 0.9125 (OUTLIER) cc_final: 0.8715 (p) REVERT: A 955 SER cc_start: 0.7654 (OUTLIER) cc_final: 0.7234 (t) REVERT: A 1069 MET cc_start: 0.9010 (OUTLIER) cc_final: 0.8677 (mtt) REVERT: A 1228 MET cc_start: 0.8736 (mtp) cc_final: 0.8458 (mmm) outliers start: 22 outliers final: 13 residues processed: 108 average time/residue: 1.0614 time to fit residues: 124.9984 Evaluate side-chains 109 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 91 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 497 HIS Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 551 ASP Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 955 SER Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1069 MET Chi-restraints excluded: chain A residue 1105 SER Chi-restraints excluded: chain A residue 1142 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 53 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 118 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 94 optimal weight: 0.0870 chunk 9 optimal weight: 8.9990 chunk 72 optimal weight: 0.7980 chunk 57 optimal weight: 0.0970 chunk 74 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 overall best weight: 0.5956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 793 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9948 Z= 0.180 Angle : 0.667 12.569 13543 Z= 0.313 Chirality : 0.044 0.322 1576 Planarity : 0.004 0.050 1698 Dihedral : 11.591 179.225 1796 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.14 % Favored : 93.60 % Rotamer: Outliers : 1.93 % Allowed : 17.66 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: 0.08 (0.25), residues: 1194 helix: 1.32 (0.21), residues: 629 sheet: -0.69 (0.58), residues: 88 loop : -1.57 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 949 HIS 0.007 0.001 HIS A1042 PHE 0.016 0.001 PHE A1167 TYR 0.014 0.001 TYR A 570 ARG 0.007 0.000 ARG A 161 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 100 time to evaluate : 1.113 Fit side-chains revert: symmetry clash REVERT: A 145 GLN cc_start: 0.8049 (OUTLIER) cc_final: 0.6877 (pt0) REVERT: A 192 TYR cc_start: 0.7557 (t80) cc_final: 0.7336 (t80) REVERT: A 241 GLN cc_start: 0.7028 (OUTLIER) cc_final: 0.6622 (tm-30) REVERT: A 586 GLU cc_start: 0.6999 (tp30) cc_final: 0.6683 (tp30) REVERT: A 666 SER cc_start: 0.9121 (OUTLIER) cc_final: 0.8715 (p) REVERT: A 955 SER cc_start: 0.7708 (OUTLIER) cc_final: 0.7299 (t) REVERT: A 1069 MET cc_start: 0.8987 (OUTLIER) cc_final: 0.8651 (mtt) REVERT: A 1234 LEU cc_start: 0.7901 (tt) cc_final: 0.7660 (tp) outliers start: 19 outliers final: 13 residues processed: 111 average time/residue: 1.0350 time to fit residues: 125.7469 Evaluate side-chains 112 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 94 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 497 HIS Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 955 SER Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1069 MET Chi-restraints excluded: chain A residue 1105 SER Chi-restraints excluded: chain A residue 1142 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 87 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 94 optimal weight: 0.0980 chunk 39 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 chunk 11 optimal weight: 10.0000 chunk 17 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 5 optimal weight: 0.0570 chunk 68 optimal weight: 2.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 GLN ** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 793 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.161444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.122158 restraints weight = 31735.276| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 6.31 r_work: 0.2810 rms_B_bonded: 5.87 restraints_weight: 2.0000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2771 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2771 r_free = 0.2771 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2771 r_free = 0.2771 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2771 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9948 Z= 0.173 Angle : 0.657 10.788 13543 Z= 0.309 Chirality : 0.043 0.292 1576 Planarity : 0.004 0.050 1698 Dihedral : 11.052 179.479 1796 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.31 % Favored : 93.43 % Rotamer: Outliers : 1.93 % Allowed : 17.95 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: 0.17 (0.25), residues: 1194 helix: 1.39 (0.21), residues: 628 sheet: -0.61 (0.58), residues: 88 loop : -1.50 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 949 HIS 0.007 0.001 HIS A1042 PHE 0.015 0.001 PHE A 209 TYR 0.014 0.001 TYR A 570 ARG 0.007 0.000 ARG A 161 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3148.62 seconds wall clock time: 57 minutes 10.81 seconds (3430.81 seconds total)