Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 16:44:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd8_6640/04_2023/3jd8_6640_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd8_6640/04_2023/3jd8_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_6640/04_2023/3jd8_6640.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd8_6640/04_2023/3jd8_6640.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd8_6640/04_2023/3jd8_6640_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd8_6640/04_2023/3jd8_6640_updated.pdb" } resolution = 4.43 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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-1.21rc1-4938/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 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 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 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 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 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 chiralities: 11 Time building chain proxies: 9.13, per 1000 atoms: 1.13 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: 4.28 Conformation dependent library (CDL) restraints added in 1.6 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: 1.42 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: 2.43 Time building geometry restraints manager: 4.57 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 - 17.95: 4205 17.95 - 35.91: 278 35.91 - 53.86: 111 53.86 - 71.82: 45 71.82 - 89.77: 14 Dihedral angle restraints: 4653 sinusoidal: 1370 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 4650 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: 0.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 2.540 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 30.980 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.280 ------------------------------------------------------------------------------- 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 : 16.872 89.775 2502 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 % 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 *********************** 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 : 0.996 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 outliers start: 76 outliers final: 25 residues processed: 290 average time/residue: 0.2198 time to fit residues: 84.0227 Evaluate side-chains 174 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 149 time to evaluate : 0.984 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 3 residues processed: 25 average time/residue: 0.1340 time to fit residues: 6.2439 ------------------------------------------------------------------------------- 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: 0.0070 chunk 85 optimal weight: 20.0000 chunk 47 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 chunk 57 optimal weight: 0.3980 chunk 45 optimal weight: 2.9990 chunk 88 optimal weight: 9.9990 chunk 34 optimal weight: 0.8980 chunk 53 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 overall best weight: 1.4602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6670 moved from start: 0.4379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.093 8195 Z= 0.362 Angle : 1.069 15.060 11234 Z= 0.523 Chirality : 0.062 0.717 1411 Planarity : 0.006 0.073 1453 Dihedral : 6.394 45.189 1193 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 20.38 Ramachandran Plot: Outliers : 1.95 % Allowed : 8.96 % Favored : 89.09 % Rotamer Outliers : 0.16 % 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 (0.25), residues: 1127 helix: 0.18 (0.22), residues: 566 sheet: -0.05 (0.57), residues: 82 loop : -3.07 (0.28), residues: 479 *********************** 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 193 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 192 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 193 average time/residue: 0.1738 time to fit residues: 47.7278 Evaluate side-chains 136 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 0.949 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2285 ------------------------------------------------------------------------------- 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: 10.0000 chunk 31 optimal weight: 10.0000 chunk 85 optimal weight: 20.0000 chunk 69 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 102 optimal weight: 20.0000 chunk 111 optimal weight: 0.8980 chunk 91 optimal weight: 10.0000 chunk 101 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 82 optimal weight: 0.9980 overall best weight: 4.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 200 GLN ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 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** A 593 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.5602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.062 8195 Z= 0.355 Angle : 0.970 13.997 11234 Z= 0.469 Chirality : 0.053 0.528 1411 Planarity : 0.008 0.201 1453 Dihedral : 5.961 45.457 1193 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 21.25 Ramachandran Plot: Outliers : 1.51 % Allowed : 9.32 % Favored : 89.17 % Rotamer Outliers : 0.00 % 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: -1.18 (0.26), residues: 1127 helix: 0.59 (0.23), residues: 571 sheet: -0.52 (0.60), residues: 78 loop : -2.62 (0.28), residues: 478 *********************** 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 155 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.1799 time to fit residues: 40.1699 Evaluate side-chains 123 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 0.958 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2625 ------------------------------------------------------------------------------- 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: 5.9990 chunk 77 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 11 optimal weight: 20.0000 chunk 49 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 chunk 109 optimal weight: 7.9990 chunk 97 optimal weight: 6.9990 chunk 29 optimal weight: 30.0000 chunk 90 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 200 GLN ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 GLN A 452 ASN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.6507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.067 8195 Z= 0.347 Angle : 0.917 10.408 11234 Z= 0.452 Chirality : 0.052 0.432 1411 Planarity : 0.006 0.092 1453 Dihedral : 6.064 56.954 1193 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 21.25 Ramachandran Plot: Outliers : 1.24 % Allowed : 9.32 % Favored : 89.44 % Rotamer Outliers : 0.00 % 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: -1.06 (0.26), residues: 1127 helix: 0.57 (0.22), residues: 582 sheet: -1.62 (0.53), residues: 81 loop : -2.22 (0.30), residues: 464 *********************** 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 145 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.1644 time to fit residues: 34.9412 Evaluate side-chains 116 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 0.985 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3134 ------------------------------------------------------------------------------- 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: 20.0000 chunk 81 optimal weight: 9.9990 chunk 45 optimal weight: 7.9990 chunk 93 optimal weight: 4.9990 chunk 75 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 55 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 27 optimal weight: 20.0000 chunk 36 optimal weight: 7.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1137 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.7045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 8195 Z= 0.287 Angle : 0.848 9.921 11234 Z= 0.409 Chirality : 0.049 0.396 1411 Planarity : 0.005 0.062 1453 Dihedral : 5.589 43.948 1193 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 20.71 Ramachandran Plot: Outliers : 1.24 % Allowed : 8.96 % Favored : 89.80 % Rotamer Outliers : 0.00 % 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: 0.76 (0.22), residues: 589 sheet: -1.92 (0.53), residues: 87 loop : -2.21 (0.30), residues: 451 *********************** 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 138 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.1691 time to fit residues: 34.1118 Evaluate side-chains 108 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.970 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3031 ------------------------------------------------------------------------------- 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: 0.8980 chunk 21 optimal weight: 7.9990 chunk 64 optimal weight: 30.0000 chunk 26 optimal weight: 0.1980 chunk 109 optimal weight: 7.9990 chunk 90 optimal weight: 40.0000 chunk 50 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 200 GLN ** 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** ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.7395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 8195 Z= 0.227 Angle : 0.797 9.456 11234 Z= 0.381 Chirality : 0.047 0.369 1411 Planarity : 0.005 0.061 1453 Dihedral : 5.335 39.490 1193 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 1.24 % Allowed : 8.16 % Favored : 90.59 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.47 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.26), residues: 1127 helix: 0.95 (0.22), residues: 588 sheet: -2.09 (0.50), residues: 87 loop : -2.27 (0.30), residues: 452 *********************** 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 : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.1655 time to fit residues: 31.9651 Evaluate side-chains 102 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.966 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2543 ------------------------------------------------------------------------------- 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: 6.9990 chunk 62 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 92 optimal weight: 9.9990 chunk 108 optimal weight: 3.9990 chunk 68 optimal weight: 20.0000 chunk 66 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 43 optimal weight: 20.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.7663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 8195 Z= 0.227 Angle : 0.804 10.607 11234 Z= 0.380 Chirality : 0.047 0.356 1411 Planarity : 0.005 0.059 1453 Dihedral : 5.274 36.858 1193 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 18.29 Ramachandran Plot: Outliers : 1.15 % Allowed : 8.16 % Favored : 90.68 % Rotamer Outliers : 0.00 % 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: -0.82 (0.26), residues: 1127 helix: 0.99 (0.22), residues: 586 sheet: -2.21 (0.48), residues: 87 loop : -2.31 (0.29), residues: 454 *********************** 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 125 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.1542 time to fit residues: 29.0373 Evaluate side-chains 103 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 0.974 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2933 ------------------------------------------------------------------------------- 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: 7.9990 chunk 32 optimal weight: 0.5980 chunk 21 optimal weight: 7.9990 chunk 69 optimal weight: 8.9990 chunk 74 optimal weight: 30.0000 chunk 53 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 85 optimal weight: 0.0020 chunk 99 optimal weight: 6.9990 chunk 104 optimal weight: 0.9990 chunk 95 optimal weight: 8.9990 overall best weight: 2.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.7940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.067 8195 Z= 0.239 Angle : 0.824 13.024 11234 Z= 0.390 Chirality : 0.047 0.339 1411 Planarity : 0.005 0.057 1453 Dihedral : 5.261 35.790 1193 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 18.56 Ramachandran Plot: Outliers : 0.98 % Allowed : 8.25 % Favored : 90.77 % Rotamer Outliers : 0.00 % 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: -0.82 (0.26), residues: 1127 helix: 0.98 (0.22), residues: 592 sheet: -2.32 (0.48), residues: 87 loop : -2.31 (0.30), residues: 448 *********************** 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 : 1.035 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.1561 time to fit residues: 30.0612 Evaluate side-chains 95 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 1.061 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4219 ------------------------------------------------------------------------------- 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: 2.9990 chunk 61 optimal weight: 9.9990 chunk 44 optimal weight: 20.0000 chunk 79 optimal weight: 20.0000 chunk 31 optimal weight: 10.0000 chunk 91 optimal weight: 0.0020 chunk 95 optimal weight: 9.9990 chunk 66 optimal weight: 0.5980 chunk 107 optimal weight: 8.9990 chunk 65 optimal weight: 10.0000 overall best weight: 2.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 397 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.8248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 8195 Z= 0.231 Angle : 0.811 11.815 11234 Z= 0.382 Chirality : 0.048 0.326 1411 Planarity : 0.005 0.057 1453 Dihedral : 5.148 33.894 1193 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 19.03 Ramachandran Plot: Outliers : 0.89 % Allowed : 9.23 % Favored : 89.88 % Rotamer Outliers : 0.00 % 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: -0.77 (0.26), residues: 1127 helix: 1.08 (0.22), residues: 590 sheet: -2.45 (0.46), residues: 100 loop : -2.31 (0.31), residues: 437 *********************** 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 123 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 0.914 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.1808 time to fit residues: 33.9819 Evaluate side-chains 93 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 1.018 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4202 ------------------------------------------------------------------------------- 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: 9.9990 chunk 74 optimal weight: 30.0000 chunk 112 optimal weight: 6.9990 chunk 103 optimal weight: 9.9990 chunk 89 optimal weight: 10.0000 chunk 9 optimal weight: 0.1980 chunk 69 optimal weight: 10.0000 chunk 54 optimal weight: 6.9990 chunk 71 optimal weight: 50.0000 chunk 95 optimal weight: 8.9990 chunk 27 optimal weight: 20.0000 overall best weight: 6.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 397 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 ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.8773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.083 8195 Z= 0.390 Angle : 0.920 9.282 11234 Z= 0.455 Chirality : 0.052 0.302 1411 Planarity : 0.006 0.057 1453 Dihedral : 5.670 36.256 1193 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 25.42 Ramachandran Plot: Outliers : 0.80 % Allowed : 10.56 % Favored : 88.64 % Rotamer Outliers : 0.00 % 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: -1.33 (0.26), residues: 1127 helix: 0.48 (0.22), residues: 597 sheet: -2.70 (0.45), residues: 102 loop : -2.37 (0.31), residues: 428 ********************** 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 118 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.1524 time to fit residues: 28.0666 Evaluate side-chains 90 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.893 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1903 ------------------------------------------------------------------------------- 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: 10.0000 chunk 13 optimal weight: 5.9990 chunk 24 optimal weight: 20.0000 chunk 89 optimal weight: 8.9990 chunk 37 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 11 optimal weight: 0.0030 chunk 16 optimal weight: 20.0000 chunk 78 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 64 optimal weight: 30.0000 overall best weight: 4.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 553 GLN ** 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 = 0.3616 r_free = 0.3616 target = 0.075673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.061632 restraints weight = 53909.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.062706 restraints weight = 39149.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.063482 restraints weight = 30992.847| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3341 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3341 r_free = 0.3341 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3341 r_free = 0.3341 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3341 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.8997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 8195 Z= 0.291 Angle : 0.832 9.457 11234 Z= 0.404 Chirality : 0.049 0.306 1411 Planarity : 0.005 0.056 1453 Dihedral : 5.492 35.218 1193 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 23.07 Ramachandran Plot: Outliers : 0.80 % Allowed : 9.85 % Favored : 89.35 % Rotamer Outliers : 0.00 % 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: -1.21 (0.26), residues: 1127 helix: 0.64 (0.22), residues: 595 sheet: -2.67 (0.44), residues: 113 loop : -2.37 (0.31), residues: 419 =============================================================================== Job complete usr+sys time: 1648.35 seconds wall clock time: 30 minutes 56.84 seconds (1856.84 seconds total)