Starting phenix.real_space_refine on Thu Feb 15 05:13:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ap1_15556/02_2024/8ap1_15556_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ap1_15556/02_2024/8ap1_15556.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ap1_15556/02_2024/8ap1_15556.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ap1_15556/02_2024/8ap1_15556.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ap1_15556/02_2024/8ap1_15556_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ap1_15556/02_2024/8ap1_15556_updated.pdb" } resolution = 3.47 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= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 60 5.49 5 Mg 1 5.21 5 S 35 5.16 5 C 7001 2.51 5 N 1939 2.21 5 O 2185 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 515": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11221 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2781 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 319} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 7275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 918, 7275 Classifications: {'peptide': 918} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 44, 'TRANS': 873} Chain breaks: 3 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 62 Chain: "N" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 561 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "T" Number of atoms: 539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 539 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' DC:plan2': 1, ' DC:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.29, per 1000 atoms: 0.56 Number of scatterers: 11221 At special positions: 0 Unit cell: (104.88, 110.96, 113.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 35 16.00 P 60 15.00 Mg 1 11.99 O 2185 8.00 N 1939 7.00 C 7001 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.64 Conformation dependent library (CDL) restraints added in 1.9 seconds 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2382 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 56 helices and 9 sheets defined 49.7% alpha, 7.2% beta 21 base pairs and 37 stacking pairs defined. Time for finding SS restraints: 5.17 Creating SS restraints... Processing helix chain 'B' and resid 8 through 11 No H-bonds generated for 'chain 'B' and resid 8 through 11' Processing helix chain 'B' and resid 26 through 36 Processing helix chain 'B' and resid 38 through 40 No H-bonds generated for 'chain 'B' and resid 38 through 40' Processing helix chain 'B' and resid 45 through 47 No H-bonds generated for 'chain 'B' and resid 45 through 47' Processing helix chain 'B' and resid 59 through 68 Processing helix chain 'B' and resid 80 through 89 removed outlier: 3.630A pdb=" N PHE B 85 " --> pdb=" O SER B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 112 removed outlier: 4.119A pdb=" N SER B 109 " --> pdb=" O TRP B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 156 removed outlier: 3.843A pdb=" N GLY B 155 " --> pdb=" O LEU B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 163 No H-bonds generated for 'chain 'B' and resid 161 through 163' Processing helix chain 'B' and resid 174 through 180 Processing helix chain 'B' and resid 191 through 199 Processing helix chain 'B' and resid 211 through 214 Processing helix chain 'B' and resid 218 through 224 removed outlier: 4.004A pdb=" N GLU B 222 " --> pdb=" O SER B 218 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU B 223 " --> pdb=" O GLN B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 267 Processing helix chain 'B' and resid 278 through 280 No H-bonds generated for 'chain 'B' and resid 278 through 280' Processing helix chain 'B' and resid 285 through 291 Processing helix chain 'B' and resid 298 through 300 No H-bonds generated for 'chain 'B' and resid 298 through 300' Processing helix chain 'B' and resid 303 through 305 No H-bonds generated for 'chain 'B' and resid 303 through 305' Processing helix chain 'B' and resid 308 through 319 Processing helix chain 'A' and resid 388 through 394 Processing helix chain 'A' and resid 398 through 421 removed outlier: 4.625A pdb=" N ASP A 414 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG A 415 " --> pdb=" O PHE A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 440 Processing helix chain 'A' and resid 449 through 477 removed outlier: 3.525A pdb=" N TRP A 455 " --> pdb=" O ASN A 451 " (cutoff:3.500A) Proline residue: A 463 - end of helix Processing helix chain 'A' and resid 492 through 495 No H-bonds generated for 'chain 'A' and resid 492 through 495' Processing helix chain 'A' and resid 497 through 500 No H-bonds generated for 'chain 'A' and resid 497 through 500' Processing helix chain 'A' and resid 505 through 518 Processing helix chain 'A' and resid 531 through 557 Processing helix chain 'A' and resid 594 through 611 removed outlier: 4.650A pdb=" N ARG A 599 " --> pdb=" O SER A 595 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE A 600 " --> pdb=" O ILE A 596 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLN A 610 " --> pdb=" O SER A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 660 removed outlier: 3.556A pdb=" N ASN A 660 " --> pdb=" O ILE A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 716 removed outlier: 3.684A pdb=" N ASN A 716 " --> pdb=" O ALA A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 730 Processing helix chain 'A' and resid 739 through 750 Processing helix chain 'A' and resid 776 through 812 removed outlier: 3.571A pdb=" N ALA A 812 " --> pdb=" O GLU A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 848 Processing helix chain 'A' and resid 858 through 872 removed outlier: 4.407A pdb=" N LEU A 862 " --> pdb=" O GLY A 858 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N LYS A 863 " --> pdb=" O PRO A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 899 removed outlier: 5.370A pdb=" N GLN A 892 " --> pdb=" O GLU A 888 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N ASP A 893 " --> pdb=" O SER A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 909 No H-bonds generated for 'chain 'A' and resid 907 through 909' Processing helix chain 'A' and resid 914 through 928 removed outlier: 4.335A pdb=" N ALA A 919 " --> pdb=" O TRP A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 935 No H-bonds generated for 'chain 'A' and resid 933 through 935' Processing helix chain 'A' and resid 949 through 958 removed outlier: 3.581A pdb=" N TYR A 954 " --> pdb=" O GLY A 950 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 967 Processing helix chain 'A' and resid 978 through 994 Processing helix chain 'A' and resid 1000 through 1003 No H-bonds generated for 'chain 'A' and resid 1000 through 1003' Processing helix chain 'A' and resid 1014 through 1020 Processing helix chain 'A' and resid 1026 through 1040 removed outlier: 3.643A pdb=" N SER A1038 " --> pdb=" O ALA A1034 " (cutoff:3.500A) Proline residue: A1039 - end of helix Processing helix chain 'A' and resid 1049 through 1064 removed outlier: 3.720A pdb=" N TYR A1053 " --> pdb=" O ASP A1049 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N GLU A1064 " --> pdb=" O SER A1060 " (cutoff:3.500A) Processing helix chain 'A' and resid 1068 through 1085 removed outlier: 3.730A pdb=" N ILE A1072 " --> pdb=" O SER A1068 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS A1085 " --> pdb=" O LYS A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1091 through 1093 No H-bonds generated for 'chain 'A' and resid 1091 through 1093' Processing helix chain 'A' and resid 1150 through 1180 removed outlier: 3.916A pdb=" N LYS A1154 " --> pdb=" O ALA A1150 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU A1157 " --> pdb=" O GLN A1153 " (cutoff:3.500A) Proline residue: A1158 - end of helix removed outlier: 3.768A pdb=" N ILE A1162 " --> pdb=" O PRO A1158 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1213 Processing helix chain 'A' and resid 1218 through 1228 Processing helix chain 'A' and resid 1243 through 1258 removed outlier: 4.194A pdb=" N ILE A1248 " --> pdb=" O LEU A1244 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE A1249 " --> pdb=" O ALA A1245 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU A1255 " --> pdb=" O ILE A1251 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N SER A1256 " --> pdb=" O ARG A1252 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ARG A1257 " --> pdb=" O LYS A1253 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LYS A1258 " --> pdb=" O ASP A1254 " (cutoff:3.500A) Processing helix chain 'A' and resid 1265 through 1279 removed outlier: 3.788A pdb=" N GLU A1272 " --> pdb=" O GLU A1268 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS A1274 " --> pdb=" O TYR A1270 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG A1275 " --> pdb=" O PHE A1271 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU A1277 " --> pdb=" O LYS A1273 " (cutoff:3.500A) Processing helix chain 'A' and resid 1284 through 1291 Processing helix chain 'A' and resid 1297 through 1302 Processing helix chain 'A' and resid 1340 through 1345 removed outlier: 3.527A pdb=" N LEU A1343 " --> pdb=" O VAL A1340 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN A1345 " --> pdb=" O VAL A1342 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 203 through 207 removed outlier: 6.597A pdb=" N LEU B 244 " --> pdb=" O ILE B 205 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ILE B 207 " --> pdb=" O ILE B 242 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ILE B 242 " --> pdb=" O ILE B 207 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLN B 72 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ASP B 52 " --> pdb=" O GLN B 72 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N SER B 74 " --> pdb=" O ASP B 52 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N GLN B 96 " --> pdb=" O LEU B 75 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 528 through 530 Processing sheet with id= C, first strand: chain 'A' and resid 614 through 619 Processing sheet with id= D, first strand: chain 'A' and resid 817 through 819 removed outlier: 3.511A pdb=" N LEU A 818 " --> pdb=" O TRP A 734 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 822 through 824 Processing sheet with id= F, first strand: chain 'A' and resid 942 through 945 Processing sheet with id= G, first strand: chain 'A' and resid 1109 through 1111 Processing sheet with id= H, first strand: chain 'A' and resid 1128 through 1131 Processing sheet with id= I, first strand: chain 'A' and resid 1233 through 1237 420 hydrogen bonds defined for protein. 1224 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 47 hydrogen bonds 94 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 37 stacking parallelities Total time for adding SS restraints: 4.69 Time building geometry restraints manager: 4.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2700 1.33 - 1.45: 2486 1.45 - 1.57: 6236 1.57 - 1.69: 115 1.69 - 1.81: 59 Bond restraints: 11596 Sorted by residual: bond pdb=" C2' DT T 34 " pdb=" C1' DT T 34 " ideal model delta sigma weight residual 1.525 1.394 0.131 2.00e-02 2.50e+03 4.27e+01 bond pdb=" O3' DG T 8 " pdb=" P DC T 9 " ideal model delta sigma weight residual 1.607 1.520 0.087 1.50e-02 4.44e+03 3.35e+01 bond pdb=" N ILE B 112 " pdb=" CA ILE B 112 " ideal model delta sigma weight residual 1.452 1.499 -0.047 1.18e-02 7.18e+03 1.57e+01 bond pdb=" C2' DA T 17 " pdb=" C1' DA T 17 " ideal model delta sigma weight residual 1.525 1.596 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" N ILE A 665 " pdb=" CA ILE A 665 " ideal model delta sigma weight residual 1.461 1.497 -0.036 1.17e-02 7.31e+03 9.62e+00 ... (remaining 11591 not shown) Histogram of bond angle deviations from ideal: 98.60 - 105.70: 483 105.70 - 112.81: 6285 112.81 - 119.92: 3977 119.92 - 127.02: 4914 127.02 - 134.13: 288 Bond angle restraints: 15947 Sorted by residual: angle pdb=" O3' DT T 34 " pdb=" C3' DT T 34 " pdb=" C2' DT T 34 " ideal model delta sigma weight residual 111.50 101.12 10.38 1.50e+00 4.44e-01 4.78e+01 angle pdb=" O3' DT T 16 " pdb=" P DA T 17 " pdb=" OP2 DA T 17 " ideal model delta sigma weight residual 108.00 123.94 -15.94 3.00e+00 1.11e-01 2.82e+01 angle pdb=" C3' DA T 17 " pdb=" O3' DA T 17 " pdb=" P DC T 18 " ideal model delta sigma weight residual 120.20 112.40 7.80 1.50e+00 4.44e-01 2.71e+01 angle pdb=" N ILE A 665 " pdb=" CA ILE A 665 " pdb=" C ILE A 665 " ideal model delta sigma weight residual 110.42 115.35 -4.93 9.60e-01 1.09e+00 2.63e+01 angle pdb=" C5' DA N 129 " pdb=" C4' DA N 129 " pdb=" O4' DA N 129 " ideal model delta sigma weight residual 109.40 117.01 -7.61 1.50e+00 4.44e-01 2.57e+01 ... (remaining 15942 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.84: 6539 34.84 - 69.69: 308 69.69 - 104.53: 10 104.53 - 139.37: 4 139.37 - 174.21: 4 Dihedral angle restraints: 6865 sinusoidal: 3191 harmonic: 3674 Sorted by residual: dihedral pdb=" O3B GTP A1402 " pdb=" O3A GTP A1402 " pdb=" PB GTP A1402 " pdb=" PA GTP A1402 " ideal model delta sinusoidal sigma weight residual 291.08 131.99 159.09 1 2.00e+01 2.50e-03 4.64e+01 dihedral pdb=" O2G GTP A1402 " pdb=" O3B GTP A1402 " pdb=" PG GTP A1402 " pdb=" PB GTP A1402 " ideal model delta sinusoidal sigma weight residual 177.30 -25.73 -156.97 1 2.00e+01 2.50e-03 4.61e+01 dihedral pdb=" C5' GTP A1402 " pdb=" O5' GTP A1402 " pdb=" PA GTP A1402 " pdb=" O3A GTP A1402 " ideal model delta sinusoidal sigma weight residual 69.27 -150.39 -140.34 1 2.00e+01 2.50e-03 4.25e+01 ... (remaining 6862 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 1715 0.117 - 0.235: 36 0.235 - 0.352: 4 0.352 - 0.469: 3 0.469 - 0.586: 1 Chirality restraints: 1759 Sorted by residual: chirality pdb=" C1' DT T 34 " pdb=" O4' DT T 34 " pdb=" C2' DT T 34 " pdb=" N1 DT T 34 " both_signs ideal model delta sigma weight residual False 2.47 1.88 0.59 2.00e-01 2.50e+01 8.59e+00 chirality pdb=" P DA T 17 " pdb=" OP1 DA T 17 " pdb=" OP2 DA T 17 " pdb=" O5' DA T 17 " both_signs ideal model delta sigma weight residual True 2.35 -2.81 -0.47 2.00e-01 2.50e+01 5.48e+00 chirality pdb=" P DC T 18 " pdb=" OP1 DC T 18 " pdb=" OP2 DC T 18 " pdb=" O5' DC T 18 " both_signs ideal model delta sigma weight residual True 2.35 -2.79 -0.45 2.00e-01 2.50e+01 4.96e+00 ... (remaining 1756 not shown) Planarity restraints: 1835 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 932 " -0.046 5.00e-02 4.00e+02 6.99e-02 7.82e+00 pdb=" N PRO A 933 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO A 933 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 933 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 852 " -0.014 2.00e-02 2.50e+03 1.66e-02 6.93e+00 pdb=" CG TRP A 852 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP A 852 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP A 852 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 852 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP A 852 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 852 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 852 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 852 " -0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP A 852 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 668 " -0.011 2.00e-02 2.50e+03 2.29e-02 5.27e+00 pdb=" C VAL A 668 " 0.040 2.00e-02 2.50e+03 pdb=" O VAL A 668 " -0.015 2.00e-02 2.50e+03 pdb=" N GLN A 669 " -0.013 2.00e-02 2.50e+03 ... (remaining 1832 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 90 2.60 - 3.17: 9083 3.17 - 3.75: 16852 3.75 - 4.32: 24232 4.32 - 4.90: 39626 Nonbonded interactions: 89883 Sorted by model distance: nonbonded pdb="MG MG A1401 " pdb=" O1B GTP A1402 " model vdw 2.023 2.170 nonbonded pdb=" OD1 ASP A 945 " pdb="MG MG A1401 " model vdw 2.025 2.170 nonbonded pdb=" OD2 ASP A1189 " pdb="MG MG A1401 " model vdw 2.107 2.170 nonbonded pdb="MG MG A1401 " pdb=" O2G GTP A1402 " model vdw 2.111 2.170 nonbonded pdb=" O GLY A 946 " pdb="MG MG A1401 " model vdw 2.122 2.170 ... (remaining 89878 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.630 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 36.140 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.131 11596 Z= 0.304 Angle : 0.762 15.941 15947 Z= 0.438 Chirality : 0.053 0.586 1759 Planarity : 0.005 0.070 1835 Dihedral : 18.362 174.214 4483 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.27 % Allowed : 1.10 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.24), residues: 1247 helix: 0.95 (0.21), residues: 633 sheet: -0.19 (0.57), residues: 97 loop : -0.82 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 852 HIS 0.004 0.001 HIS A 953 PHE 0.016 0.001 PHE B 331 TYR 0.022 0.002 TYR A 805 ARG 0.003 0.000 ARG B 100 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 132 time to evaluate : 1.228 Fit side-chains revert: symmetry clash REVERT: B 40 LYS cc_start: 0.7774 (mttt) cc_final: 0.7424 (pttm) outliers start: 3 outliers final: 1 residues processed: 134 average time/residue: 0.2661 time to fit residues: 49.6890 Evaluate side-chains 105 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 104 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 487 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 2.9990 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 30.0000 chunk 33 optimal weight: 20.0000 chunk 65 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 0.0040 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 7.9990 chunk 74 optimal weight: 8.9990 chunk 116 optimal weight: 10.0000 overall best weight: 5.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1129 GLN A1169 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.0840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 11596 Z= 0.290 Angle : 0.579 6.854 15947 Z= 0.310 Chirality : 0.041 0.173 1759 Planarity : 0.005 0.055 1835 Dihedral : 19.866 174.402 2002 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.00 % Allowed : 8.31 % Favored : 90.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.24), residues: 1247 helix: 1.22 (0.21), residues: 634 sheet: 0.10 (0.56), residues: 107 loop : -0.81 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 852 HIS 0.004 0.001 HIS B 265 PHE 0.016 0.002 PHE A 546 TYR 0.013 0.002 TYR A 805 ARG 0.002 0.000 ARG A 663 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 111 time to evaluate : 1.184 Fit side-chains revert: symmetry clash REVERT: B 40 LYS cc_start: 0.7890 (mttt) cc_final: 0.7418 (pttm) REVERT: B 310 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.7003 (mp0) outliers start: 11 outliers final: 8 residues processed: 118 average time/residue: 0.2716 time to fit residues: 44.5750 Evaluate side-chains 111 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 102 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 310 GLU Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 878 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 4.9990 chunk 36 optimal weight: 20.0000 chunk 96 optimal weight: 7.9990 chunk 79 optimal weight: 7.9990 chunk 32 optimal weight: 9.9990 chunk 116 optimal weight: 30.0000 chunk 125 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 chunk 115 optimal weight: 20.0000 chunk 39 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 669 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11596 Z= 0.268 Angle : 0.551 6.866 15947 Z= 0.294 Chirality : 0.040 0.183 1759 Planarity : 0.004 0.049 1835 Dihedral : 19.686 176.996 2002 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.82 % Allowed : 12.15 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.25), residues: 1247 helix: 1.32 (0.21), residues: 634 sheet: 0.30 (0.57), residues: 107 loop : -0.82 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 852 HIS 0.004 0.001 HIS B 265 PHE 0.015 0.002 PHE A 546 TYR 0.012 0.001 TYR A 805 ARG 0.002 0.000 ARG B 100 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 105 time to evaluate : 1.305 Fit side-chains revert: symmetry clash REVERT: B 40 LYS cc_start: 0.7958 (mttt) cc_final: 0.7491 (pttm) REVERT: B 112 ILE cc_start: 0.8571 (tt) cc_final: 0.8291 (tt) REVERT: B 168 MET cc_start: 0.8302 (ttp) cc_final: 0.8083 (ttm) outliers start: 9 outliers final: 6 residues processed: 110 average time/residue: 0.2834 time to fit residues: 43.7101 Evaluate side-chains 101 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 95 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1025 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 20.0000 chunk 87 optimal weight: 10.0000 chunk 60 optimal weight: 0.0980 chunk 12 optimal weight: 9.9990 chunk 55 optimal weight: 4.9990 chunk 78 optimal weight: 7.9990 chunk 116 optimal weight: 20.0000 chunk 123 optimal weight: 10.0000 chunk 61 optimal weight: 4.9990 chunk 110 optimal weight: 9.9990 chunk 33 optimal weight: 20.0000 overall best weight: 5.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 11596 Z= 0.302 Angle : 0.570 9.846 15947 Z= 0.302 Chirality : 0.041 0.164 1759 Planarity : 0.004 0.048 1835 Dihedral : 19.652 175.988 2000 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.74 % Allowed : 13.33 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.25), residues: 1247 helix: 1.21 (0.21), residues: 640 sheet: 0.40 (0.57), residues: 107 loop : -0.83 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 852 HIS 0.004 0.001 HIS B 265 PHE 0.014 0.002 PHE A 826 TYR 0.014 0.002 TYR A 805 ARG 0.002 0.000 ARG A 663 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 102 time to evaluate : 1.274 Fit side-chains revert: symmetry clash REVERT: B 40 LYS cc_start: 0.7956 (mttt) cc_final: 0.7553 (pttm) REVERT: B 60 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7609 (tt0) REVERT: B 100 ARG cc_start: 0.7371 (mtt90) cc_final: 0.7114 (mtp180) REVERT: B 112 ILE cc_start: 0.8549 (tt) cc_final: 0.8339 (tt) REVERT: B 168 MET cc_start: 0.8329 (ttp) cc_final: 0.8114 (ttm) outliers start: 19 outliers final: 15 residues processed: 117 average time/residue: 0.2708 time to fit residues: 44.6272 Evaluate side-chains 111 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 95 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 60 GLN Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1018 MET Chi-restraints excluded: chain A residue 1025 THR Chi-restraints excluded: chain A residue 1087 ILE Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1233 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 4.9990 chunk 70 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 92 optimal weight: 0.3980 chunk 51 optimal weight: 0.7980 chunk 105 optimal weight: 0.9990 chunk 85 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 63 optimal weight: 9.9990 chunk 111 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11596 Z= 0.165 Angle : 0.496 10.423 15947 Z= 0.264 Chirality : 0.037 0.155 1759 Planarity : 0.004 0.046 1835 Dihedral : 19.519 178.556 2000 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.28 % Allowed : 14.34 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.25), residues: 1247 helix: 1.60 (0.22), residues: 631 sheet: 0.72 (0.60), residues: 101 loop : -0.75 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 852 HIS 0.003 0.001 HIS A 433 PHE 0.013 0.001 PHE A 826 TYR 0.013 0.001 TYR B 161 ARG 0.001 0.000 ARG B 100 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 106 time to evaluate : 1.146 Fit side-chains revert: symmetry clash REVERT: B 40 LYS cc_start: 0.7882 (mttt) cc_final: 0.7505 (pttm) REVERT: B 60 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7593 (tt0) REVERT: B 168 MET cc_start: 0.8293 (ttp) cc_final: 0.8090 (ttm) REVERT: A 926 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.7179 (mm-30) REVERT: A 1064 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.6838 (tm-30) REVERT: A 1201 MET cc_start: 0.7361 (ttp) cc_final: 0.6980 (ttt) outliers start: 14 outliers final: 7 residues processed: 117 average time/residue: 0.2701 time to fit residues: 44.1925 Evaluate side-chains 107 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 97 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 GLN Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 926 GLU Chi-restraints excluded: chain A residue 1018 MET Chi-restraints excluded: chain A residue 1025 THR Chi-restraints excluded: chain A residue 1064 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 40.0000 chunk 111 optimal weight: 8.9990 chunk 24 optimal weight: 4.9990 chunk 72 optimal weight: 9.9990 chunk 30 optimal weight: 0.3980 chunk 123 optimal weight: 0.0050 chunk 102 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 overall best weight: 2.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11596 Z= 0.192 Angle : 0.504 9.454 15947 Z= 0.267 Chirality : 0.038 0.153 1759 Planarity : 0.004 0.044 1835 Dihedral : 19.465 176.409 2000 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.64 % Allowed : 14.43 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.25), residues: 1247 helix: 1.68 (0.22), residues: 632 sheet: 0.64 (0.58), residues: 106 loop : -0.74 (0.28), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 852 HIS 0.003 0.001 HIS A 433 PHE 0.012 0.001 PHE A 826 TYR 0.011 0.001 TYR B 161 ARG 0.001 0.000 ARG B 100 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 105 time to evaluate : 1.225 Fit side-chains revert: symmetry clash REVERT: B 40 LYS cc_start: 0.7919 (mttt) cc_final: 0.7508 (pttm) REVERT: B 60 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.7581 (tt0) REVERT: B 168 MET cc_start: 0.8320 (ttp) cc_final: 0.8088 (ttm) REVERT: A 926 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.7176 (mm-30) REVERT: A 1212 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8087 (tp) outliers start: 18 outliers final: 14 residues processed: 118 average time/residue: 0.2795 time to fit residues: 46.4563 Evaluate side-chains 112 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 95 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 60 GLN Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 926 GLU Chi-restraints excluded: chain A residue 1018 MET Chi-restraints excluded: chain A residue 1020 ASN Chi-restraints excluded: chain A residue 1025 THR Chi-restraints excluded: chain A residue 1087 ILE Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1212 LEU Chi-restraints excluded: chain A residue 1233 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 chunk 90 optimal weight: 20.0000 chunk 104 optimal weight: 6.9990 chunk 69 optimal weight: 5.9990 chunk 123 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 chunk 76 optimal weight: 0.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 11596 Z= 0.291 Angle : 0.556 10.569 15947 Z= 0.294 Chirality : 0.040 0.170 1759 Planarity : 0.004 0.043 1835 Dihedral : 19.538 175.336 2000 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.56 % Allowed : 14.16 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.25), residues: 1247 helix: 1.41 (0.21), residues: 640 sheet: 0.62 (0.59), residues: 102 loop : -0.80 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 235 HIS 0.004 0.001 HIS B 265 PHE 0.015 0.002 PHE A 886 TYR 0.013 0.002 TYR A 805 ARG 0.001 0.000 ARG B 100 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 100 time to evaluate : 1.214 Fit side-chains revert: symmetry clash REVERT: B 40 LYS cc_start: 0.7999 (mttt) cc_final: 0.7575 (pttm) REVERT: B 60 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.7573 (tt0) REVERT: B 100 ARG cc_start: 0.7411 (mtt90) cc_final: 0.7121 (mtp180) REVERT: B 112 ILE cc_start: 0.8578 (tt) cc_final: 0.8359 (tt) REVERT: B 168 MET cc_start: 0.8368 (ttp) cc_final: 0.8149 (ttm) REVERT: A 926 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.7195 (mp0) REVERT: A 1212 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8175 (tp) outliers start: 28 outliers final: 22 residues processed: 121 average time/residue: 0.2499 time to fit residues: 43.1214 Evaluate side-chains 122 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 97 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 60 GLN Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 926 GLU Chi-restraints excluded: chain A residue 1018 MET Chi-restraints excluded: chain A residue 1020 ASN Chi-restraints excluded: chain A residue 1025 THR Chi-restraints excluded: chain A residue 1027 VAL Chi-restraints excluded: chain A residue 1087 ILE Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1212 LEU Chi-restraints excluded: chain A residue 1233 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 10.0000 chunk 73 optimal weight: 0.9990 chunk 37 optimal weight: 9.9990 chunk 24 optimal weight: 20.0000 chunk 23 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 84 optimal weight: 8.9990 chunk 60 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 chunk 112 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11596 Z= 0.203 Angle : 0.516 10.108 15947 Z= 0.275 Chirality : 0.038 0.155 1759 Planarity : 0.004 0.043 1835 Dihedral : 19.445 176.011 2000 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.01 % Allowed : 14.70 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.25), residues: 1247 helix: 1.59 (0.22), residues: 631 sheet: 0.71 (0.59), residues: 101 loop : -0.80 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 864 HIS 0.003 0.001 HIS A 433 PHE 0.013 0.001 PHE A 826 TYR 0.011 0.001 TYR B 161 ARG 0.001 0.000 ARG B 100 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 102 time to evaluate : 1.253 Fit side-chains revert: symmetry clash REVERT: B 40 LYS cc_start: 0.7992 (mttt) cc_final: 0.7569 (pttm) REVERT: B 60 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7568 (tt0) REVERT: B 100 ARG cc_start: 0.7401 (mtt90) cc_final: 0.7120 (mtp180) REVERT: B 112 ILE cc_start: 0.8584 (tt) cc_final: 0.8337 (tt) REVERT: B 168 MET cc_start: 0.8338 (ttp) cc_final: 0.8121 (ttm) REVERT: A 591 LEU cc_start: 0.6772 (OUTLIER) cc_final: 0.6412 (pp) REVERT: A 926 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.7242 (mm-30) REVERT: A 1212 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8096 (tp) outliers start: 22 outliers final: 18 residues processed: 119 average time/residue: 0.2818 time to fit residues: 46.6056 Evaluate side-chains 120 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 98 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 60 GLN Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 926 GLU Chi-restraints excluded: chain A residue 1018 MET Chi-restraints excluded: chain A residue 1020 ASN Chi-restraints excluded: chain A residue 1025 THR Chi-restraints excluded: chain A residue 1027 VAL Chi-restraints excluded: chain A residue 1087 ILE Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1212 LEU Chi-restraints excluded: chain A residue 1233 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 6.9990 chunk 107 optimal weight: 8.9990 chunk 114 optimal weight: 10.0000 chunk 69 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 35 optimal weight: 20.0000 chunk 103 optimal weight: 9.9990 chunk 108 optimal weight: 2.9990 chunk 75 optimal weight: 7.9990 chunk 121 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11596 Z= 0.234 Angle : 0.530 9.841 15947 Z= 0.281 Chirality : 0.039 0.173 1759 Planarity : 0.004 0.043 1835 Dihedral : 19.461 175.398 2000 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.37 % Allowed : 14.79 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.25), residues: 1247 helix: 1.48 (0.21), residues: 637 sheet: 0.73 (0.59), residues: 101 loop : -0.77 (0.28), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 235 HIS 0.003 0.001 HIS B 265 PHE 0.013 0.001 PHE A 826 TYR 0.011 0.001 TYR B 161 ARG 0.001 0.000 ARG A 663 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 101 time to evaluate : 1.256 Fit side-chains revert: symmetry clash REVERT: B 40 LYS cc_start: 0.7945 (mttt) cc_final: 0.7535 (pttm) REVERT: B 60 GLN cc_start: 0.8031 (OUTLIER) cc_final: 0.7565 (tt0) REVERT: B 100 ARG cc_start: 0.7448 (mtt90) cc_final: 0.7140 (mtp180) REVERT: B 112 ILE cc_start: 0.8562 (tt) cc_final: 0.8318 (tt) REVERT: B 168 MET cc_start: 0.8362 (ttp) cc_final: 0.8153 (ttm) REVERT: A 591 LEU cc_start: 0.6822 (OUTLIER) cc_final: 0.6452 (pp) REVERT: A 926 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.7215 (mp0) REVERT: A 1212 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8145 (tp) outliers start: 26 outliers final: 20 residues processed: 122 average time/residue: 0.2900 time to fit residues: 49.1407 Evaluate side-chains 122 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 98 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 60 GLN Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 926 GLU Chi-restraints excluded: chain A residue 1018 MET Chi-restraints excluded: chain A residue 1020 ASN Chi-restraints excluded: chain A residue 1025 THR Chi-restraints excluded: chain A residue 1027 VAL Chi-restraints excluded: chain A residue 1087 ILE Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1212 LEU Chi-restraints excluded: chain A residue 1233 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 6.9990 chunk 57 optimal weight: 20.0000 chunk 84 optimal weight: 0.9980 chunk 127 optimal weight: 10.0000 chunk 117 optimal weight: 30.0000 chunk 101 optimal weight: 7.9990 chunk 10 optimal weight: 0.6980 chunk 78 optimal weight: 9.9990 chunk 62 optimal weight: 20.0000 chunk 80 optimal weight: 7.9990 chunk 108 optimal weight: 4.9990 overall best weight: 4.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11596 Z= 0.247 Angle : 0.538 9.826 15947 Z= 0.285 Chirality : 0.039 0.159 1759 Planarity : 0.004 0.043 1835 Dihedral : 19.468 175.243 2000 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.37 % Allowed : 14.70 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.25), residues: 1247 helix: 1.43 (0.21), residues: 640 sheet: 0.69 (0.59), residues: 101 loop : -0.77 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 852 HIS 0.003 0.001 HIS B 265 PHE 0.013 0.001 PHE A 826 TYR 0.011 0.001 TYR B 161 ARG 0.001 0.000 ARG A 663 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 99 time to evaluate : 1.188 Fit side-chains revert: symmetry clash REVERT: B 40 LYS cc_start: 0.7925 (mttt) cc_final: 0.7528 (pttm) REVERT: B 60 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7567 (tt0) REVERT: B 100 ARG cc_start: 0.7451 (mtt90) cc_final: 0.7134 (mtp180) REVERT: B 112 ILE cc_start: 0.8559 (tt) cc_final: 0.8308 (tt) REVERT: B 168 MET cc_start: 0.8363 (ttp) cc_final: 0.8130 (ttm) REVERT: A 591 LEU cc_start: 0.6849 (OUTLIER) cc_final: 0.6487 (pp) REVERT: A 926 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.7206 (mp0) REVERT: A 1212 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8155 (tp) outliers start: 26 outliers final: 21 residues processed: 120 average time/residue: 0.2918 time to fit residues: 49.0090 Evaluate side-chains 123 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 98 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 60 GLN Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 926 GLU Chi-restraints excluded: chain A residue 1018 MET Chi-restraints excluded: chain A residue 1020 ASN Chi-restraints excluded: chain A residue 1025 THR Chi-restraints excluded: chain A residue 1027 VAL Chi-restraints excluded: chain A residue 1087 ILE Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1212 LEU Chi-restraints excluded: chain A residue 1233 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 10.0000 chunk 93 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 chunk 101 optimal weight: 7.9990 chunk 42 optimal weight: 0.0170 chunk 104 optimal weight: 7.9990 chunk 12 optimal weight: 20.0000 chunk 18 optimal weight: 9.9990 chunk 89 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 overall best weight: 4.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.161038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.137217 restraints weight = 13753.101| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.18 r_work: 0.3170 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11596 Z= 0.250 Angle : 0.538 9.817 15947 Z= 0.285 Chirality : 0.039 0.160 1759 Planarity : 0.004 0.042 1835 Dihedral : 19.469 174.993 2000 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.28 % Allowed : 15.07 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.25), residues: 1247 helix: 1.41 (0.21), residues: 640 sheet: 0.62 (0.58), residues: 102 loop : -0.78 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 852 HIS 0.004 0.001 HIS B 265 PHE 0.013 0.001 PHE A 826 TYR 0.011 0.001 TYR A 805 ARG 0.001 0.000 ARG A 663 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2124.49 seconds wall clock time: 39 minutes 29.94 seconds (2369.94 seconds total)