Starting phenix.real_space_refine on Fri Mar 15 01:04:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd8_6640/03_2024/3jd8_6640_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd8_6640/03_2024/3jd8_6640.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd8_6640/03_2024/3jd8_6640.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd8_6640/03_2024/3jd8_6640.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd8_6640/03_2024/3jd8_6640_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd8_6640/03_2024/3jd8_6640_updated.pdb" } resolution = 4.43 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= 0.005 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 2193 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 42 5.16 5 C 5075 2.51 5 N 1336 2.21 5 O 1597 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 30": "OE1" <-> "OE2" Residue "A GLU 143": "OE1" <-> "OE2" Residue "A ARG 518": "NH1" <-> "NH2" Residue "A PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 584": "OE1" <-> "OE2" Residue "A GLU 730": "OE1" <-> "OE2" Residue "A GLU 1188": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8050 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 7695 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1133, 7694 Classifications: {'peptide': 1133} Incomplete info: {'truncation_to_alanine': 341} Link IDs: {'CIS': 5, 'PCIS': 3, 'PTRANS': 56, 'TRANS': 1068} Chain breaks: 2 Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 1271 Unresolved non-hydrogen angles: 1643 Unresolved non-hydrogen dihedrals: 1110 Unresolved non-hydrogen chiralities: 105 Planarities with less than four sites: {'GLN:plan1': 14, 'HIS:plan': 6, 'TYR:plan': 15, 'ASN:plan1': 14, 'TRP:plan': 9, 'ASP:plan': 20, 'PHE:plan': 37, 'GLU:plan': 10, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 716 Conformer: "B" Number of residues, atoms: 1133, 7694 Classifications: {'peptide': 1133} Incomplete info: {'truncation_to_alanine': 341} Link IDs: {'CIS': 5, 'PCIS': 3, 'PTRANS': 56, 'TRANS': 1068} Chain breaks: 2 Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 1271 Unresolved non-hydrogen angles: 1643 Unresolved non-hydrogen dihedrals: 1110 Unresolved non-hydrogen chiralities: 105 Planarities with less than four sites: {'GLN:plan1': 14, 'HIS:plan': 6, 'TYR:plan': 15, 'ASN:plan1': 14, 'TRP:plan': 9, 'ASP:plan': 20, 'PHE:plan': 37, 'GLU:plan': 10, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 716 bond proxies already assigned to first conformer: 7835 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 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: "F" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 182 Unusual residues: {'CLR': 1, 'NAG': 11} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 8.62, per 1000 atoms: 1.07 Number of scatterers: 8050 At special positions: 0 Unit cell: (84.9251, 97.9905, 169.85, 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 42 16.00 O 1597 8.00 N 1336 7.00 C 5075 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 25 " - pdb=" SG CYS A 74 " distance=2.05 Simple disulfide: pdb=" SG CYS A 31 " - pdb=" SG CYS A 42 " distance=2.05 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 109 " distance=2.05 Simple disulfide: pdb=" SG CYS A 75 " - pdb=" SG CYS A 113 " distance=2.06 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 238 " distance=2.04 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 160 " distance=2.04 Simple disulfide: pdb=" SG CYS A 177 " - pdb=" SG CYS A 184 " distance=2.08 Simple disulfide: pdb=" SG CYS A 227 " - pdb=" SG CYS A 243 " distance=1.91 Simple disulfide: pdb=" SG CYS A 240 " - pdb=" SG CYS A 247 " distance=1.79 Simple disulfide: pdb=" SG CYS A 468 " - pdb=" SG CYS A 479 " distance=2.10 Simple disulfide: pdb=" SG CYS A 516 " - pdb=" SG CYS A 533 " distance=2.07 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 ALPHA1-6 " BMA F 3 " - " MAN F 4 " BETA1-4 " NAG A1318 " - " NAG A1319 " " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " NAG-ASN " NAG A1303 " - " ASN A 158 " " NAG A1309 " - " ASN A 572 " " NAG A1316 " - " ASN A 122 " " NAG A1317 " - " ASN A 70 " " NAG A1319 " - " ASN A 185 " " NAG A1320 " - " ASN A1064 " " NAG A1322 " - " ASN A 135 " " NAG A1324 " - " ASN A 459 " " NAG B 1 " - " ASN A 222 " " NAG C 1 " - " ASN A 524 " " NAG D 1 " - " ASN A 557 " " NAG E 1 " - " ASN A 598 " Time building additional restraints: 3.54 Conformation dependent library (CDL) restraints added in 1.3 seconds 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2118 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 43 helices and 4 sheets defined 52.1% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.25 Creating SS restraints... Processing helix chain 'A' and resid 53 through 62 removed outlier: 5.026A pdb=" N ASP A 57 " --> pdb=" O ASP A 54 " (cutoff:3.500A) 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 94 removed outlier: 4.508A pdb=" N GLN A 88 " --> pdb=" O LYS A 84 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N LEU A 89 " --> pdb=" O ASP A 85 " (cutoff:3.500A) Proline residue: A 90 - end of helix Processing helix chain 'A' and resid 98 through 113 Processing helix chain 'A' and resid 117 through 120 No H-bonds generated for 'chain 'A' and resid 117 through 120' Processing helix chain 'A' and resid 150 through 160 Processing helix chain 'A' and resid 172 through 176 Processing helix chain 'A' and resid 186 through 193 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 261 through 287 Processing helix chain 'A' and resid 331 through 349 removed outlier: 4.173A pdb=" N ASN A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 369 Processing helix chain 'A' and resid 388 through 399 Processing helix chain 'A' and resid 433 through 435 No H-bonds generated for 'chain 'A' and resid 433 through 435' Processing helix chain 'A' and resid 437 through 451 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 488 Processing helix chain 'A' and resid 492 through 496 Processing helix chain 'A' and resid 511 through 516 Processing helix chain 'A' and resid 543 through 545 No H-bonds generated for 'chain 'A' and resid 543 through 545' 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 574 through 593 removed outlier: 3.534A pdb=" N ARG A 579 " --> pdb=" O GLU A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 616 removed outlier: 4.051A pdb=" N LEU A 613 " --> pdb=" O ILE A 609 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN A 614 " --> pdb=" O GLU A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 637 removed outlier: 3.882A pdb=" N THR A 623 " --> pdb=" O SER A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 665 Processing helix chain 'A' and resid 676 through 697 Proline residue: A 681 - end of helix removed outlier: 4.523A pdb=" N LEU A 684 " --> pdb=" O LEU A 680 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ILE A 685 " --> pdb=" O PRO A 681 " (cutoff:3.500A) Proline residue: A 691 - end of helix removed outlier: 3.797A pdb=" N VAL A 694 " --> pdb=" O ILE A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 713 removed outlier: 3.869A pdb=" N ASP A 712 " --> pdb=" O ALA A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 733 removed outlier: 3.514A pdb=" N ARG A 726 " --> pdb=" O GLN A 722 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL A 731 " --> pdb=" O VAL A 727 " (cutoff:3.500A) Proline residue: A 733 - end of helix Processing helix chain 'A' and resid 742 through 771 removed outlier: 3.521A pdb=" N VAL A 753 " --> pdb=" O GLY A 749 " (cutoff:3.500A) Proline residue: A 755 - end of helix removed outlier: 4.352A pdb=" N SER A 761 " --> pdb=" O VAL A 757 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE A 763 " --> pdb=" O THR A 759 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA A 764 " --> pdb=" O PHE A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 829 Proline residue: A 827 - end of helix Processing helix chain 'A' and resid 832 through 850 Proline residue: A 836 - end of helix Processing helix chain 'A' and resid 865 through 875 Processing helix chain 'A' and resid 894 through 911 Processing helix chain 'A' and resid 931 through 939 Proline residue: A 939 - end of helix Processing helix chain 'A' and resid 987 through 994 removed outlier: 3.527A pdb=" N GLN A 991 " --> pdb=" O LYS A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1004 Processing helix chain 'A' and resid 1048 through 1068 Processing helix chain 'A' and resid 1085 through 1091 removed outlier: 4.429A pdb=" N GLN A1090 " --> pdb=" O VAL A1086 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N TYR A1091 " --> pdb=" O PHE A1087 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1112 Processing helix chain 'A' and resid 1122 through 1143 removed outlier: 3.595A pdb=" N THR A1130 " --> pdb=" O ILE A1126 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA A1132 " --> pdb=" O CYS A1128 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU A1135 " --> pdb=" O ILE A1131 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASN A1137 " --> pdb=" O MET A1133 " (cutoff:3.500A) Processing helix chain 'A' and resid 1151 through 1173 removed outlier: 3.828A pdb=" N VAL A1155 " --> pdb=" O ALA A1151 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N HIS A1170 " --> pdb=" O GLU A1166 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE A1171 " --> pdb=" O PHE A1167 " (cutoff:3.500A) Processing helix chain 'A' and resid 1185 through 1212 removed outlier: 3.643A pdb=" N HIS A1193 " --> pdb=" O GLU A1189 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER A1196 " --> pdb=" O ALA A1192 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N SER A1197 " --> pdb=" O HIS A1193 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE A1202 " --> pdb=" O VAL A1198 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR A1203 " --> pdb=" O PHE A1199 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL A1211 " --> pdb=" O PHE A1207 " (cutoff:3.500A) Processing helix chain 'A' and resid 1220 through 1250 removed outlier: 3.773A pdb=" N TYR A1225 " --> pdb=" O PHE A1221 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ARG A1227 " --> pdb=" O ILE A1223 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR A1229 " --> pdb=" O TYR A1225 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU A1230 " --> pdb=" O PHE A1226 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU A1241 " --> pdb=" O ALA A1237 " (cutoff:3.500A) Proline residue: A1245 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 126 through 130 Processing sheet with id= B, first strand: chain 'A' and resid 204 through 209 removed outlier: 3.552A pdb=" N LEU A 144 " --> pdb=" O THR A 204 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N GLN A 145 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N VAL A 123 " --> pdb=" O GLN A 145 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N TYR A 147 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N LEU A 121 " --> pdb=" O TYR A 147 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 561 through 567 Processing sheet with id= D, first strand: chain 'A' and resid 454 through 457 390 hydrogen bonds defined for protein. 1125 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: 2.44 Time building geometry restraints manager: 3.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.44: 3489 1.44 - 1.67: 4645 1.67 - 1.90: 60 1.90 - 2.13: 0 2.13 - 2.36: 1 Bond restraints: 8195 Sorted by residual: bond pdb=" C VAL A 959 " pdb=" N PRO A 984 " ideal model delta sigma weight residual 1.334 2.360 -1.026 2.34e-02 1.83e+03 1.92e+03 bond pdb=" C SER A 940 " pdb=" N SER A 941 " ideal model delta sigma weight residual 1.332 1.657 -0.325 1.40e-02 5.10e+03 5.38e+02 bond pdb=" C LEU A 469 " pdb=" N ALA A 470 " ideal model delta sigma weight residual 1.334 1.216 0.118 1.26e-02 6.30e+03 8.77e+01 bond pdb=" C LEU A1060 " pdb=" N ILE A1061 " ideal model delta sigma weight residual 1.334 1.441 -0.107 1.25e-02 6.40e+03 7.33e+01 bond pdb=" C GLN A 881 " pdb=" N TYR A 882 " ideal model delta sigma weight residual 1.331 1.221 0.111 1.33e-02 5.65e+03 6.93e+01 ... (remaining 8190 not shown) Histogram of bond angle deviations from ideal: 86.79 - 98.15: 2 98.15 - 109.50: 951 109.50 - 120.86: 7447 120.86 - 132.22: 2814 132.22 - 143.58: 20 Bond angle restraints: 11234 Sorted by residual: angle pdb=" CA VAL A 959 " pdb=" C VAL A 959 " pdb=" N PRO A 984 " ideal model delta sigma weight residual 118.88 86.79 32.09 1.54e+00 4.22e-01 4.34e+02 angle pdb=" O VAL A 959 " pdb=" C VAL A 959 " pdb=" N PRO A 984 " ideal model delta sigma weight residual 121.10 143.58 -22.48 1.14e+00 7.69e-01 3.89e+02 angle pdb=" C VAL A 959 " pdb=" N PRO A 984 " pdb=" CA PRO A 984 " ideal model delta sigma weight residual 119.84 98.82 21.02 1.25e+00 6.40e-01 2.83e+02 angle pdb=" N GLN A 881 " pdb=" CA GLN A 881 " pdb=" C GLN A 881 " ideal model delta sigma weight residual 108.86 123.53 -14.67 1.41e+00 5.03e-01 1.08e+02 angle pdb=" N PHE A 995 " pdb=" CA PHE A 995 " pdb=" C PHE A 995 " ideal model delta sigma weight residual 108.34 121.88 -13.54 1.31e+00 5.83e-01 1.07e+02 ... (remaining 11229 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.43: 4839 24.43 - 48.86: 238 48.86 - 73.28: 96 73.28 - 97.71: 23 97.71 - 122.14: 11 Dihedral angle restraints: 5207 sinusoidal: 1924 harmonic: 3283 Sorted by residual: 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 93.00 13.01 79.99 1 1.00e+01 1.00e-02 7.93e+01 dihedral pdb=" C SER A 602 " pdb=" N SER A 602 " pdb=" CA SER A 602 " pdb=" CB SER A 602 " ideal model delta harmonic sigma weight residual -122.60 -102.74 -19.86 0 2.50e+00 1.60e-01 6.31e+01 dihedral pdb=" CA SER A 602 " pdb=" C SER A 602 " pdb=" N PHE A 603 " pdb=" CA PHE A 603 " ideal model delta harmonic sigma weight residual 180.00 -142.67 -37.33 0 5.00e+00 4.00e-02 5.57e+01 ... (remaining 5204 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.409: 1394 0.409 - 0.817: 10 0.817 - 1.226: 4 1.226 - 1.634: 2 1.634 - 2.043: 1 Chirality restraints: 1411 Sorted by residual: chirality pdb=" C1 NAG A1318 " pdb=" C2 NAG A1318 " pdb=" O5 NAG A1318 " pdb=" O4 NAG A1319 " both_signs ideal model delta sigma weight residual False -2.40 -0.84 -1.56 2.00e-02 2.50e+03 6.11e+03 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.87 -1.53 2.00e-02 2.50e+03 5.85e+03 chirality pdb=" C1 BMA F 3 " pdb=" O4 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-02 2.50e+03 4.95e+02 ... (remaining 1408 not shown) Planarity restraints: 1465 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 572 " 0.132 2.00e-02 2.50e+03 2.94e-01 1.08e+03 pdb=" CG ASN A 572 " -0.081 2.00e-02 2.50e+03 pdb=" OD1 ASN A 572 " 0.155 2.00e-02 2.50e+03 pdb=" ND2 ASN A 572 " -0.530 2.00e-02 2.50e+03 pdb=" C1 NAG A1309 " 0.323 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " -0.329 2.00e-02 2.50e+03 2.85e-01 1.02e+03 pdb=" C7 NAG D 1 " 0.074 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " -0.046 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " 0.501 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " -0.200 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " -0.308 2.00e-02 2.50e+03 2.59e-01 8.41e+02 pdb=" C7 NAG D 2 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " -0.188 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " 0.446 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " -0.030 2.00e-02 2.50e+03 ... (remaining 1462 not shown) Histogram of nonbonded interaction distances: 1.34 - 2.05: 40 2.05 - 2.76: 1323 2.76 - 3.47: 12474 3.47 - 4.19: 18775 4.19 - 4.90: 31123 Nonbonded interactions: 63735 Sorted by model distance: nonbonded pdb=" O TRP A 942 " pdb=" CB CYS A1011 " model vdw 1.335 3.440 nonbonded pdb=" CD2 LEU A 656 " pdb=" CB PRO A 755 " model vdw 1.371 3.860 nonbonded pdb=" CG1 VAL A 727 " pdb=" CG1 VAL A1165 " model vdw 1.411 3.880 nonbonded pdb=" CD2 LEU A 680 " pdb=" CE2 TYR A1229 " model vdw 1.470 3.760 nonbonded pdb=" O LEU A 656 " pdb=" CD1 LEU A 751 " model vdw 1.483 3.460 ... (remaining 63730 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 'C' selection = chain 'E' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 2.170 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 29.730 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6492 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 : 0.015 1.026 8195 Z= 1.007 Angle : 1.564 32.094 11234 Z= 1.019 Chirality : 0.128 2.043 1411 Planarity : 0.016 0.285 1453 Dihedral : 18.261 122.138 3056 Min Nonbonded Distance : 1.335 Molprobity Statistics. All-atom Clashscore : 78.13 Ramachandran Plot: Outliers : 8.36 % Allowed : 11.91 % Favored : 79.73 % Rotamer: Outliers : 11.82 % Allowed : 8.55 % Favored : 79.63 % Cbeta Deviations : 0.47 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.47 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -3.27 (0.23), residues: 1125 helix: -1.35 (0.20), residues: 546 sheet: -0.69 (0.56), residues: 85 loop : -3.45 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.004 TRP A 27 HIS 0.007 0.001 HIS A 441 PHE 0.025 0.003 PHE A 203 TYR 0.030 0.003 TYR A 147 ARG 0.011 0.001 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 248 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.7348 (mttm) cc_final: 0.7017 (mmtm) REVERT: A 467 ILE cc_start: 0.8263 (pt) cc_final: 0.7808 (mm) REVERT: A 523 LEU cc_start: 0.7793 (mt) cc_final: 0.7582 (tp) REVERT: A 541 VAL cc_start: 0.7976 (t) cc_final: 0.7669 (t) REVERT: A 588 ILE cc_start: 0.8360 (mt) cc_final: 0.7486 (tp) REVERT: A 678 ILE cc_start: 0.8283 (mt) cc_final: 0.8069 (mt) REVERT: A 722 GLN cc_start: 0.8864 (OUTLIER) cc_final: 0.8096 (tm-30) REVERT: A 760 PHE cc_start: 0.8994 (OUTLIER) cc_final: 0.8694 (t80) REVERT: A 1048 SER cc_start: 0.4564 (p) cc_final: 0.3996 (p) REVERT: A 1072 ASN cc_start: 0.4586 (OUTLIER) cc_final: 0.3909 (t0) REVERT: A 1094 ILE cc_start: 0.9160 (mm) cc_final: 0.8781 (mm) outliers start: 76 outliers final: 25 residues processed: 290 average time/residue: 0.2059 time to fit residues: 79.0908 Evaluate side-chains 180 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 152 time to evaluate : 0.916 ------------------------------------------------------------------------------- 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: 0.0030 chunk 85 optimal weight: 20.0000 chunk 47 optimal weight: 0.9980 chunk 29 optimal weight: 9.9990 chunk 57 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 88 optimal weight: 9.9990 chunk 34 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 overall best weight: 1.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN A 150 GLN A 154 ASN ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 397 GLN ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 HIS ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6669 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 8195 Z= 0.371 Angle : 1.088 15.504 11234 Z= 0.536 Chirality : 0.065 0.776 1411 Planarity : 0.006 0.100 1453 Dihedral : 11.719 114.954 1747 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 20.45 Ramachandran Plot: Outliers : 2.04 % Allowed : 9.14 % Favored : 88.82 % Rotamer: Outliers : 0.31 % Allowed : 2.02 % Favored : 97.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.47 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -1.71 (0.26), residues: 1127 helix: 0.21 (0.22), residues: 571 sheet: 0.19 (0.60), residues: 73 loop : -3.13 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.005 TRP A 381 HIS 0.010 0.002 HIS A1042 PHE 0.052 0.003 PHE A 760 TYR 0.036 0.003 TYR A 56 ARG 0.010 0.001 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 190 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.7265 (mttm) cc_final: 0.7038 (mptt) REVERT: A 106 ASN cc_start: 0.8607 (m110) cc_final: 0.8390 (m-40) REVERT: A 632 PHE cc_start: 0.8723 (t80) cc_final: 0.8487 (t80) REVERT: A 720 LEU cc_start: 0.9170 (mt) cc_final: 0.8890 (mt) REVERT: A 722 GLN cc_start: 0.8981 (tp40) cc_final: 0.8724 (tm-30) REVERT: A 1099 ILE cc_start: 0.8649 (mm) cc_final: 0.8349 (mm) REVERT: A 1156 ASN cc_start: 0.6157 (t0) cc_final: 0.5309 (t0) REVERT: A 1166 GLU cc_start: 0.7444 (tm-30) cc_final: 0.7090 (tt0) REVERT: A 1225 TYR cc_start: 0.6462 (t80) cc_final: 0.6164 (t80) outliers start: 2 outliers final: 0 residues processed: 192 average time/residue: 0.1641 time to fit residues: 44.5944 Evaluate side-chains 138 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 0.922 ------------------------------------------------------------------------------- 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: 5.9990 chunk 31 optimal weight: 0.9980 chunk 85 optimal weight: 30.0000 chunk 69 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 chunk 111 optimal weight: 0.8980 chunk 91 optimal weight: 20.0000 chunk 101 optimal weight: 8.9990 chunk 35 optimal weight: 9.9990 chunk 82 optimal weight: 0.8980 overall best weight: 2.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 ASN ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 moved from start: 0.5436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 8195 Z= 0.291 Angle : 0.911 17.137 11234 Z= 0.437 Chirality : 0.054 0.623 1411 Planarity : 0.006 0.091 1453 Dihedral : 9.901 102.949 1747 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 18.90 Ramachandran Plot: Outliers : 1.51 % Allowed : 9.32 % Favored : 89.17 % Rotamer: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.47 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.04 (0.26), residues: 1127 helix: 0.75 (0.23), residues: 563 sheet: -0.18 (0.64), residues: 80 loop : -2.63 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP A 583 HIS 0.006 0.002 HIS A1239 PHE 0.039 0.003 PHE A 760 TYR 0.022 0.002 TYR A 594 ARG 0.008 0.001 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.7435 (mttm) cc_final: 0.7099 (tmtt) REVERT: A 630 ILE cc_start: 0.9366 (pt) cc_final: 0.9127 (pt) REVERT: A 632 PHE cc_start: 0.8895 (t80) cc_final: 0.8639 (t80) REVERT: A 722 GLN cc_start: 0.9137 (tp40) cc_final: 0.8843 (tm-30) REVERT: A 1081 TYR cc_start: 0.6436 (t80) cc_final: 0.6139 (t80) REVERT: A 1084 PHE cc_start: 0.8148 (p90) cc_final: 0.7844 (p90) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.1615 time to fit residues: 37.9718 Evaluate side-chains 120 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.772 ------------------------------------------------------------------------------- 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: 8.9990 chunk 77 optimal weight: 20.0000 chunk 53 optimal weight: 8.9990 chunk 11 optimal weight: 30.0000 chunk 49 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 103 optimal weight: 9.9990 chunk 109 optimal weight: 20.0000 chunk 97 optimal weight: 5.9990 chunk 29 optimal weight: 30.0000 chunk 90 optimal weight: 7.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 ASN ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 GLN ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1137 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.6711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 8195 Z= 0.427 Angle : 1.018 13.655 11234 Z= 0.500 Chirality : 0.054 0.485 1411 Planarity : 0.006 0.075 1453 Dihedral : 9.834 93.493 1747 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 25.69 Ramachandran Plot: Outliers : 1.24 % Allowed : 10.47 % Favored : 88.29 % Rotamer: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.47 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.27 (0.26), residues: 1127 helix: 0.36 (0.22), residues: 584 sheet: -1.77 (0.52), residues: 89 loop : -2.26 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.005 TRP A 583 HIS 0.010 0.003 HIS A 398 PHE 0.032 0.003 PHE A1224 TYR 0.032 0.003 TYR A 102 ARG 0.012 0.002 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.7590 (mttm) cc_final: 0.7292 (mttt) REVERT: A 542 PHE cc_start: 0.7234 (m-80) cc_final: 0.7030 (m-80) REVERT: A 544 TRP cc_start: 0.8406 (p90) cc_final: 0.7712 (p90) REVERT: A 720 LEU cc_start: 0.9236 (mt) cc_final: 0.8940 (mm) REVERT: A 760 PHE cc_start: 0.8292 (m-80) cc_final: 0.8001 (t80) REVERT: A 1084 PHE cc_start: 0.8544 (p90) cc_final: 0.8338 (p90) REVERT: A 1191 LEU cc_start: 0.8794 (tp) cc_final: 0.8467 (tt) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.1613 time to fit residues: 33.5844 Evaluate side-chains 108 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.665 ------------------------------------------------------------------------------- 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: 0.9990 chunk 1 optimal weight: 8.9990 chunk 81 optimal weight: 0.9980 chunk 45 optimal weight: 8.9990 chunk 93 optimal weight: 1.9990 chunk 75 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 55 optimal weight: 7.9990 chunk 98 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 ASN ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 ASN ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 553 GLN A 593 ASN A1137 ASN ** A1170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.6993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8195 Z= 0.254 Angle : 0.833 10.996 11234 Z= 0.397 Chirality : 0.050 0.508 1411 Planarity : 0.005 0.064 1453 Dihedral : 9.013 82.641 1747 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 1.24 % Allowed : 7.81 % Favored : 90.95 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.47 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.26), residues: 1127 helix: 0.83 (0.22), residues: 581 sheet: -1.83 (0.52), residues: 89 loop : -2.30 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.004 TRP A 189 HIS 0.008 0.002 HIS A1042 PHE 0.026 0.002 PHE A 760 TYR 0.041 0.002 TYR A1037 ARG 0.011 0.001 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.7513 (mttm) cc_final: 0.7171 (mttt) REVERT: A 544 TRP cc_start: 0.8203 (p90) cc_final: 0.7601 (p90) REVERT: A 722 GLN cc_start: 0.8928 (tp40) cc_final: 0.8561 (tm-30) REVERT: A 1055 LEU cc_start: 0.8630 (tt) cc_final: 0.8427 (tp) REVERT: A 1157 LEU cc_start: 0.7760 (mm) cc_final: 0.7525 (mm) REVERT: A 1191 LEU cc_start: 0.8626 (tp) cc_final: 0.8353 (tt) REVERT: A 1228 MET cc_start: 0.8065 (ppp) cc_final: 0.6846 (ppp) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.1604 time to fit residues: 33.2103 Evaluate side-chains 117 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.880 ------------------------------------------------------------------------------- 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: 8.9990 chunk 64 optimal weight: 30.0000 chunk 26 optimal weight: 3.9990 chunk 109 optimal weight: 20.0000 chunk 90 optimal weight: 20.0000 chunk 50 optimal weight: 9.9990 chunk 9 optimal weight: 7.9990 chunk 36 optimal weight: 9.9990 chunk 57 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.7470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 8195 Z= 0.312 Angle : 0.838 10.625 11234 Z= 0.409 Chirality : 0.049 0.472 1411 Planarity : 0.005 0.069 1453 Dihedral : 8.546 66.117 1747 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 21.99 Ramachandran Plot: Outliers : 1.06 % Allowed : 9.23 % Favored : 89.71 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.47 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.97 (0.26), residues: 1127 helix: 0.76 (0.22), residues: 583 sheet: -2.01 (0.51), residues: 87 loop : -2.27 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP A 583 HIS 0.005 0.002 HIS A 398 PHE 0.022 0.002 PHE A 760 TYR 0.023 0.002 TYR A 102 ARG 0.007 0.001 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.7646 (mttm) cc_final: 0.7323 (mttt) REVERT: A 190 ILE cc_start: 0.9009 (mm) cc_final: 0.8775 (mm) REVERT: A 390 LEU cc_start: 0.8565 (pp) cc_final: 0.7445 (pp) REVERT: A 544 TRP cc_start: 0.7993 (p90) cc_final: 0.7327 (p90) REVERT: A 1157 LEU cc_start: 0.7570 (mm) cc_final: 0.7307 (mm) REVERT: A 1228 MET cc_start: 0.8121 (ppp) cc_final: 0.6869 (ppp) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.1653 time to fit residues: 31.3968 Evaluate side-chains 98 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.923 ------------------------------------------------------------------------------- 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: 4.9990 chunk 62 optimal weight: 4.9990 chunk 79 optimal weight: 20.0000 chunk 61 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 108 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 GLN ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.7789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8195 Z= 0.277 Angle : 0.834 11.840 11234 Z= 0.409 Chirality : 0.049 0.479 1411 Planarity : 0.005 0.059 1453 Dihedral : 8.316 54.738 1747 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 20.04 Ramachandran Plot: Outliers : 1.06 % Allowed : 8.70 % Favored : 90.24 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.47 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.99 (0.26), residues: 1127 helix: 0.84 (0.22), residues: 581 sheet: -2.17 (0.49), residues: 87 loop : -2.38 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 544 HIS 0.006 0.002 HIS A1042 PHE 0.023 0.002 PHE A 101 TYR 0.037 0.002 TYR A 594 ARG 0.004 0.001 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.7638 (mttm) cc_final: 0.7318 (mttt) REVERT: A 190 ILE cc_start: 0.9020 (mm) cc_final: 0.8787 (mm) REVERT: A 542 PHE cc_start: 0.7649 (m-80) cc_final: 0.7328 (m-80) REVERT: A 544 TRP cc_start: 0.7885 (p90) cc_final: 0.7326 (p90) REVERT: A 722 GLN cc_start: 0.8744 (tp40) cc_final: 0.8510 (tm-30) REVERT: A 1134 VAL cc_start: 0.8093 (t) cc_final: 0.7648 (m) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.1586 time to fit residues: 30.1815 Evaluate side-chains 105 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.900 ------------------------------------------------------------------------------- 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: 8.9990 chunk 32 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 69 optimal weight: 0.4980 chunk 74 optimal weight: 40.0000 chunk 53 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 85 optimal weight: 8.9990 chunk 99 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 95 optimal weight: 0.0470 overall best weight: 3.1084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.8002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8195 Z= 0.259 Angle : 0.812 12.477 11234 Z= 0.395 Chirality : 0.049 0.468 1411 Planarity : 0.005 0.057 1453 Dihedral : 8.189 54.389 1747 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 19.37 Ramachandran Plot: Outliers : 0.89 % Allowed : 8.61 % Favored : 90.51 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.47 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.95 (0.26), residues: 1127 helix: 0.84 (0.22), residues: 587 sheet: -2.18 (0.48), residues: 87 loop : -2.34 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 544 HIS 0.005 0.001 HIS A1042 PHE 0.044 0.002 PHE A 590 TYR 0.035 0.002 TYR A 594 ARG 0.004 0.001 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.7640 (mttm) cc_final: 0.7319 (mttt) REVERT: A 190 ILE cc_start: 0.9020 (mm) cc_final: 0.8779 (mm) REVERT: A 542 PHE cc_start: 0.7568 (m-80) cc_final: 0.7299 (m-80) REVERT: A 544 TRP cc_start: 0.7860 (p90) cc_final: 0.7285 (p90) REVERT: A 1134 VAL cc_start: 0.8208 (t) cc_final: 0.7509 (m) REVERT: A 1170 HIS cc_start: 0.7144 (m-70) cc_final: 0.5771 (m-70) REVERT: A 1228 MET cc_start: 0.8664 (ppp) cc_final: 0.7364 (ptt) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.1688 time to fit residues: 31.4157 Evaluate side-chains 107 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 0.829 ------------------------------------------------------------------------------- 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: 0.9990 chunk 104 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 44 optimal weight: 10.0000 chunk 79 optimal weight: 20.0000 chunk 31 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 95 optimal weight: 8.9990 chunk 66 optimal weight: 0.9990 chunk 107 optimal weight: 20.0000 chunk 65 optimal weight: 6.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.8143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8195 Z= 0.215 Angle : 0.764 13.181 11234 Z= 0.369 Chirality : 0.048 0.471 1411 Planarity : 0.005 0.057 1453 Dihedral : 7.909 59.219 1747 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.89 % Allowed : 7.54 % Favored : 91.57 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.47 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.78 (0.26), residues: 1127 helix: 0.98 (0.22), residues: 591 sheet: -2.16 (0.48), residues: 88 loop : -2.28 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 544 HIS 0.005 0.001 HIS A1239 PHE 0.019 0.002 PHE A 590 TYR 0.033 0.002 TYR A 594 ARG 0.003 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 0.882 Fit side-chains revert: symmetry clash REVERT: A 38 LYS cc_start: 0.7589 (mttm) cc_final: 0.7286 (mttt) REVERT: A 190 ILE cc_start: 0.8967 (mm) cc_final: 0.8753 (mm) REVERT: A 542 PHE cc_start: 0.7510 (m-80) cc_final: 0.7223 (m-80) REVERT: A 544 TRP cc_start: 0.7761 (p90) cc_final: 0.7188 (p90) REVERT: A 726 ARG cc_start: 0.7565 (mmp80) cc_final: 0.7023 (mmp80) REVERT: A 1101 ASN cc_start: 0.7162 (m110) cc_final: 0.6902 (m110) REVERT: A 1134 VAL cc_start: 0.8271 (t) cc_final: 0.7652 (m) REVERT: A 1157 LEU cc_start: 0.7838 (mm) cc_final: 0.7611 (mm) REVERT: A 1170 HIS cc_start: 0.6696 (m-70) cc_final: 0.6079 (m-70) REVERT: A 1203 THR cc_start: 0.8384 (t) cc_final: 0.7980 (p) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.1649 time to fit residues: 32.0664 Evaluate side-chains 119 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.919 ------------------------------------------------------------------------------- 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: 8.9990 chunk 74 optimal weight: 40.0000 chunk 112 optimal weight: 20.0000 chunk 103 optimal weight: 3.9990 chunk 89 optimal weight: 8.9990 chunk 9 optimal weight: 20.0000 chunk 69 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 71 optimal weight: 50.0000 chunk 95 optimal weight: 0.0670 chunk 27 optimal weight: 20.0000 overall best weight: 2.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 ASN ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 GLN ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.8382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 8195 Z= 0.250 Angle : 0.766 12.184 11234 Z= 0.376 Chirality : 0.048 0.457 1411 Planarity : 0.005 0.056 1453 Dihedral : 7.759 55.520 1747 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 18.49 Ramachandran Plot: Outliers : 0.98 % Allowed : 8.25 % Favored : 90.77 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.47 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.77 (0.26), residues: 1127 helix: 1.03 (0.22), residues: 584 sheet: -2.20 (0.46), residues: 99 loop : -2.27 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 544 HIS 0.005 0.001 HIS A 398 PHE 0.021 0.002 PHE A 101 TYR 0.030 0.002 TYR A 594 ARG 0.003 0.001 ARG A 116 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.7603 (mttm) cc_final: 0.7284 (mttt) REVERT: A 190 ILE cc_start: 0.8921 (mm) cc_final: 0.8719 (mm) REVERT: A 542 PHE cc_start: 0.7586 (m-80) cc_final: 0.7304 (m-80) REVERT: A 544 TRP cc_start: 0.7763 (p90) cc_final: 0.7239 (p90) REVERT: A 1101 ASN cc_start: 0.7144 (m110) cc_final: 0.6803 (m110) REVERT: A 1157 LEU cc_start: 0.8052 (mm) cc_final: 0.7690 (mm) REVERT: A 1203 THR cc_start: 0.8462 (t) cc_final: 0.8014 (p) REVERT: A 1229 TYR cc_start: 0.6963 (t80) cc_final: 0.6519 (t80) REVERT: A 1232 MET cc_start: 0.8439 (ppp) cc_final: 0.8198 (ppp) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.1704 time to fit residues: 30.9243 Evaluate side-chains 105 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.891 ------------------------------------------------------------------------------- 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: 30.0000 chunk 13 optimal weight: 10.0000 chunk 24 optimal weight: 20.0000 chunk 89 optimal weight: 7.9990 chunk 37 optimal weight: 0.6980 chunk 92 optimal weight: 8.9990 chunk 11 optimal weight: 5.9990 chunk 16 optimal weight: 0.0370 chunk 78 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 64 optimal weight: 30.0000 overall best weight: 3.9464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 ASN ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.076890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.062128 restraints weight = 51194.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.063122 restraints weight = 39228.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 17)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.063641 restraints weight = 31962.177| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3358 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3358 r_free = 0.3358 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3358 r_free = 0.3358 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3358 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.8676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 8195 Z= 0.276 Angle : 0.781 11.887 11234 Z= 0.386 Chirality : 0.048 0.447 1411 Planarity : 0.005 0.057 1453 Dihedral : 7.802 54.106 1747 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 19.30 Ramachandran Plot: Outliers : 0.98 % Allowed : 8.34 % Favored : 90.68 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.47 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.86 (0.26), residues: 1127 helix: 0.88 (0.22), residues: 588 sheet: -2.24 (0.46), residues: 99 loop : -2.19 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 544 HIS 0.005 0.001 HIS A 398 PHE 0.022 0.002 PHE A 101 TYR 0.031 0.002 TYR A 594 ARG 0.004 0.001 ARG A 518 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1642.24 seconds wall clock time: 30 minutes 29.99 seconds (1829.99 seconds total)