Starting phenix.real_space_refine on Thu Mar 14 23:55:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iv6_9742/03_2024/6iv6_9742_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iv6_9742/03_2024/6iv6_9742.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iv6_9742/03_2024/6iv6_9742.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iv6_9742/03_2024/6iv6_9742.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iv6_9742/03_2024/6iv6_9742_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iv6_9742/03_2024/6iv6_9742_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.013 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: 5 Type Number sf(0) Gaussians P 26 5.49 5 S 21 5.16 5 C 6406 2.51 5 N 1722 2.21 5 O 1983 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 106": "OE1" <-> "OE2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A ARG 198": "NH1" <-> "NH2" Residue "A GLU 223": "OE1" <-> "OE2" Residue "A GLU 273": "OE1" <-> "OE2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "A ARG 328": "NH1" <-> "NH2" Residue "A GLU 361": "OE1" <-> "OE2" Residue "A ARG 375": "NH1" <-> "NH2" Residue "A GLU 423": "OE1" <-> "OE2" Residue "A GLU 473": "OE1" <-> "OE2" Residue "A ARG 495": "NH1" <-> "NH2" Residue "A GLU 530": "OE1" <-> "OE2" Residue "A GLU 537": "OE1" <-> "OE2" Residue "A GLU 560": "OE1" <-> "OE2" Residue "A TYR 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 734": "OE1" <-> "OE2" Residue "A GLU 807": "OE1" <-> "OE2" Residue "A ARG 817": "NH1" <-> "NH2" Residue "A ARG 878": "NH1" <-> "NH2" Residue "A ARG 896": "NH1" <-> "NH2" Residue "A ARG 926": "NH1" <-> "NH2" Residue "A GLU 1009": "OE1" <-> "OE2" Residue "A ARG 1060": "NH1" <-> "NH2" Residue "A ARG 1261": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10158 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1209, 9611 Classifications: {'peptide': 1209} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'CIS': 4, 'PTRANS': 35, 'TRANS': 1169} Chain breaks: 4 Unresolved non-hydrogen bonds: 267 Unresolved non-hydrogen angles: 338 Unresolved non-hydrogen dihedrals: 229 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 7, 'ARG:plan': 3, 'ALY:plan-2': 4, 'TYR:plan': 5, 'ASN:plan1': 4, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 9, 'HIS:plan': 7} Unresolved non-hydrogen planarities: 178 Chain: "G" Number of atoms: 547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 547 Classifications: {'RNA': 26} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 4, 'rna3p_pur': 7, 'rna3p_pyr': 11} Link IDs: {'rna2p': 8, 'rna3p': 17} Time building chain proxies: 5.91, per 1000 atoms: 0.58 Number of scatterers: 10158 At special positions: 0 Unit cell: (110.39, 101.26, 113.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 21 16.00 P 26 15.00 O 1983 8.00 N 1722 7.00 C 6406 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.94 Conformation dependent library (CDL) restraints added in 1.7 seconds 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2278 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 47 helices and 7 sheets defined 35.2% alpha, 6.2% beta 6 base pairs and 10 stacking pairs defined. Time for finding SS restraints: 4.95 Creating SS restraints... Processing helix chain 'A' and resid 27 through 33 Processing helix chain 'A' and resid 35 through 64 removed outlier: 4.460A pdb=" N GLN A 47 " --> pdb=" O ALA A 43 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LYS A 48 " --> pdb=" O ASP A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 80 Processing helix chain 'A' and resid 93 through 109 removed outlier: 4.212A pdb=" N GLU A 106 " --> pdb=" O VAL A 102 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE A 107 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL A 108 " --> pdb=" O ARG A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 145 Processing helix chain 'A' and resid 164 through 167 removed outlier: 3.656A pdb=" N PHE A 167 " --> pdb=" O SER A 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 164 through 167' Processing helix chain 'A' and resid 170 through 176 removed outlier: 4.068A pdb=" N ASN A 176 " --> pdb=" O ASP A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 192 Processing helix chain 'A' and resid 195 through 206 removed outlier: 3.635A pdb=" N LEU A 206 " --> pdb=" O ASN A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 226 removed outlier: 3.529A pdb=" N ASN A 222 " --> pdb=" O ASP A 218 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 224 " --> pdb=" O ILE A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 233 No H-bonds generated for 'chain 'A' and resid 231 through 233' Processing helix chain 'A' and resid 241 through 243 No H-bonds generated for 'chain 'A' and resid 241 through 243' Processing helix chain 'A' and resid 246 through 257 removed outlier: 3.654A pdb=" N ALA A 251 " --> pdb=" O GLU A 247 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A 255 " --> pdb=" O ALA A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 278 removed outlier: 3.503A pdb=" N ASN A 276 " --> pdb=" O ASN A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 325 removed outlier: 3.529A pdb=" N CYS A 320 " --> pdb=" O ASP A 316 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN A 324 " --> pdb=" O CYS A 320 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU A 325 " --> pdb=" O GLN A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 342 Processing helix chain 'A' and resid 356 through 365 removed outlier: 4.766A pdb=" N ASN A 360 " --> pdb=" O LYS A 357 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLU A 361 " --> pdb=" O ASN A 358 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS A 364 " --> pdb=" O GLU A 361 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN A 365 " --> pdb=" O LEU A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 379 Processing helix chain 'A' and resid 382 through 384 No H-bonds generated for 'chain 'A' and resid 382 through 384' Processing helix chain 'A' and resid 426 through 431 removed outlier: 3.857A pdb=" N THR A 430 " --> pdb=" O ILE A 426 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 426 through 431' Processing helix chain 'A' and resid 456 through 459 No H-bonds generated for 'chain 'A' and resid 456 through 459' Processing helix chain 'A' and resid 465 through 468 No H-bonds generated for 'chain 'A' and resid 465 through 468' Processing helix chain 'A' and resid 495 through 500 Processing helix chain 'A' and resid 502 through 510 removed outlier: 3.535A pdb=" N ASN A 506 " --> pdb=" O ASP A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 552 removed outlier: 4.002A pdb=" N GLU A 530 " --> pdb=" O ASN A 526 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ALA A 533 " --> pdb=" O GLY A 529 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASP A 536 " --> pdb=" O GLY A 532 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU A 537 " --> pdb=" O ALA A 533 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N LYS A 540 " --> pdb=" O ASP A 536 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N ILE A 541 " --> pdb=" O GLU A 537 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N ALA A 542 " --> pdb=" O LEU A 538 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N THR A 543 " --> pdb=" O ALA A 539 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A 544 " --> pdb=" O LYS A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 580 No H-bonds generated for 'chain 'A' and resid 578 through 580' Processing helix chain 'A' and resid 629 through 632 No H-bonds generated for 'chain 'A' and resid 629 through 632' Processing helix chain 'A' and resid 649 through 656 Processing helix chain 'A' and resid 660 through 662 No H-bonds generated for 'chain 'A' and resid 660 through 662' Processing helix chain 'A' and resid 670 through 685 removed outlier: 3.848A pdb=" N ILE A 676 " --> pdb=" O CYS A 672 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP A 677 " --> pdb=" O HIS A 673 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE A 678 " --> pdb=" O ALA A 674 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN A 684 " --> pdb=" O LYS A 680 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS A 685 " --> pdb=" O ALA A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 715 removed outlier: 3.554A pdb=" N VAL A 712 " --> pdb=" O PHE A 708 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU A 713 " --> pdb=" O TYR A 709 " (cutoff:3.500A) Proline residue: A 714 - end of helix Processing helix chain 'A' and resid 726 through 733 removed outlier: 3.664A pdb=" N LEU A 732 " --> pdb=" O TYR A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 748 No H-bonds generated for 'chain 'A' and resid 746 through 748' Processing helix chain 'A' and resid 758 through 763 removed outlier: 3.519A pdb=" N TYR A 762 " --> pdb=" O LEU A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 771 No H-bonds generated for 'chain 'A' and resid 769 through 771' Processing helix chain 'A' and resid 827 through 830 No H-bonds generated for 'chain 'A' and resid 827 through 830' Processing helix chain 'A' and resid 851 through 853 No H-bonds generated for 'chain 'A' and resid 851 through 853' Processing helix chain 'A' and resid 856 through 864 Processing helix chain 'A' and resid 915 through 925 removed outlier: 3.538A pdb=" N ILE A 924 " --> pdb=" O ASP A 920 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 961 removed outlier: 3.833A pdb=" N ILE A 939 " --> pdb=" O GLU A 935 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS A 940 " --> pdb=" O ILE A 936 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N SER A 948 " --> pdb=" O SER A 944 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N HIS A 949 " --> pdb=" O GLY A 945 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N HIS A 952 " --> pdb=" O SER A 948 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU A 959 " --> pdb=" O SER A 955 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS A 960 " --> pdb=" O GLN A 956 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR A 961 " --> pdb=" O LEU A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 998 removed outlier: 4.006A pdb=" N ASN A 988 " --> pdb=" O GLN A 984 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 1064 through 1073 removed outlier: 3.778A pdb=" N GLN A1068 " --> pdb=" O ILE A1064 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ALA A1069 " --> pdb=" O ALA A1065 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS A1073 " --> pdb=" O ALA A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1134 through 1139 Processing helix chain 'A' and resid 1155 through 1159 removed outlier: 4.086A pdb=" N CYS A1159 " --> pdb=" O VAL A1155 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1155 through 1159' Processing helix chain 'A' and resid 1166 through 1178 removed outlier: 3.667A pdb=" N LEU A1177 " --> pdb=" O LEU A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1237 removed outlier: 3.579A pdb=" N GLY A1221 " --> pdb=" O ALA A1217 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA A1222 " --> pdb=" O ASP A1218 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE A1225 " --> pdb=" O GLY A1221 " (cutoff:3.500A) Processing helix chain 'A' and resid 1251 through 1259 removed outlier: 3.552A pdb=" N LEU A1255 " --> pdb=" O ASN A1251 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN A1259 " --> pdb=" O LEU A1255 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 12 through 18 Processing sheet with id= B, first strand: chain 'A' and resid 19 through 22 removed outlier: 4.836A pdb=" N TYR A 594 " --> pdb=" O ILE A 743 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 561 through 564 removed outlier: 4.624A pdb=" N ILE A 785 " --> pdb=" O LEU A 564 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 618 through 621 Processing sheet with id= E, first strand: chain 'A' and resid 895 through 897 removed outlier: 3.536A pdb=" N ARG A 896 " --> pdb=" O LEU A 883 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A 883 " --> pdb=" O ARG A 896 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLU A 968 " --> pdb=" O ILE A 873 " (cutoff:3.500A) removed outlier: 9.244A pdb=" N ARG A 875 " --> pdb=" O GLU A 968 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N PHE A1037 " --> pdb=" O LEU A 967 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1077 through 1079 removed outlier: 3.818A pdb=" N ILE A1090 " --> pdb=" O TRP A1106 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TRP A1106 " --> pdb=" O ILE A1090 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 1181 through 1183 229 hydrogen bonds defined for protein. 657 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 14 hydrogen bonds 24 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 10 stacking parallelities Total time for adding SS restraints: 3.28 Time building geometry restraints manager: 4.30 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: 2749 1.33 - 1.45: 2062 1.45 - 1.57: 5529 1.57 - 1.69: 52 1.69 - 1.81: 35 Bond restraints: 10427 Sorted by residual: bond pdb=" C ALY A 153 " pdb=" O ALY A 153 " ideal model delta sigma weight residual 1.231 1.363 -0.132 2.00e-02 2.50e+03 4.35e+01 bond pdb=" C ALY A 635 " pdb=" O ALY A 635 " ideal model delta sigma weight residual 1.231 1.360 -0.129 2.00e-02 2.50e+03 4.16e+01 bond pdb=" C ALY A 816 " pdb=" O ALY A 816 " ideal model delta sigma weight residual 1.231 1.359 -0.128 2.00e-02 2.50e+03 4.09e+01 bond pdb=" N GLN A 281 " pdb=" CA GLN A 281 " ideal model delta sigma weight residual 1.459 1.505 -0.046 1.20e-02 6.94e+03 1.44e+01 bond pdb=" N ASN A 280 " pdb=" CA ASN A 280 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.20e-02 6.94e+03 9.44e+00 ... (remaining 10422 not shown) Histogram of bond angle deviations from ideal: 96.38 - 104.50: 203 104.50 - 112.62: 5247 112.62 - 120.74: 5248 120.74 - 128.86: 3414 128.86 - 136.98: 92 Bond angle restraints: 14204 Sorted by residual: angle pdb=" C THR A 518 " pdb=" N THR A 519 " pdb=" CA THR A 519 " ideal model delta sigma weight residual 121.70 136.98 -15.28 1.80e+00 3.09e-01 7.21e+01 angle pdb=" O ALY A 635 " pdb=" C ALY A 635 " pdb=" N VAL A 636 " ideal model delta sigma weight residual 123.00 111.47 11.53 1.60e+00 3.91e-01 5.19e+01 angle pdb=" CA ALY A 153 " pdb=" C ALY A 153 " pdb=" O ALY A 153 " ideal model delta sigma weight residual 120.80 109.97 10.83 1.70e+00 3.46e-01 4.06e+01 angle pdb=" C GLY A 120 " pdb=" N TYR A 121 " pdb=" CA TYR A 121 " ideal model delta sigma weight residual 121.54 132.60 -11.06 1.91e+00 2.74e-01 3.35e+01 angle pdb=" C GLN A 281 " pdb=" N HIS A 282 " pdb=" CA HIS A 282 " ideal model delta sigma weight residual 121.70 131.91 -10.21 1.80e+00 3.09e-01 3.22e+01 ... (remaining 14199 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.87: 6061 35.87 - 71.73: 183 71.73 - 107.60: 17 107.60 - 143.47: 1 143.47 - 179.33: 3 Dihedral angle restraints: 6265 sinusoidal: 2725 harmonic: 3540 Sorted by residual: dihedral pdb=" O4' C G 23 " pdb=" C1' C G 23 " pdb=" N1 C G 23 " pdb=" C2 C G 23 " ideal model delta sinusoidal sigma weight residual 200.00 51.91 148.09 1 1.50e+01 4.44e-03 7.89e+01 dihedral pdb=" O4' U G 16 " pdb=" C1' U G 16 " pdb=" N1 U G 16 " pdb=" C2 U G 16 " ideal model delta sinusoidal sigma weight residual 232.00 52.67 179.33 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U G 15 " pdb=" C1' U G 15 " pdb=" N1 U G 15 " pdb=" C2 U G 15 " ideal model delta sinusoidal sigma weight residual -128.00 48.81 -176.81 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 6262 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1338 0.074 - 0.148: 199 0.148 - 0.223: 21 0.223 - 0.297: 5 0.297 - 0.371: 1 Chirality restraints: 1564 Sorted by residual: chirality pdb=" CB ILE A1029 " pdb=" CA ILE A1029 " pdb=" CG1 ILE A1029 " pdb=" CG2 ILE A1029 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.44e+00 chirality pdb=" CA ASP A 665 " pdb=" N ASP A 665 " pdb=" C ASP A 665 " pdb=" CB ASP A 665 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CB THR A 516 " pdb=" CA THR A 516 " pdb=" OG1 THR A 516 " pdb=" CG2 THR A 516 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 1561 not shown) Planarity restraints: 1754 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALY A 153 " 0.080 2.00e-02 2.50e+03 1.55e-01 2.41e+02 pdb=" C ALY A 153 " -0.269 2.00e-02 2.50e+03 pdb=" O ALY A 153 " 0.090 2.00e-02 2.50e+03 pdb=" N LEU A 154 " 0.099 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALY A 635 " 0.083 2.00e-02 2.50e+03 1.53e-01 2.35e+02 pdb=" C ALY A 635 " -0.265 2.00e-02 2.50e+03 pdb=" O ALY A 635 " 0.089 2.00e-02 2.50e+03 pdb=" N VAL A 636 " 0.094 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 112 " -0.023 2.00e-02 2.50e+03 4.75e-02 2.25e+01 pdb=" C GLY A 112 " 0.082 2.00e-02 2.50e+03 pdb=" O GLY A 112 " -0.031 2.00e-02 2.50e+03 pdb=" N ASN A 113 " -0.028 2.00e-02 2.50e+03 ... (remaining 1751 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2523 2.79 - 3.32: 8671 3.32 - 3.84: 16020 3.84 - 4.37: 18970 4.37 - 4.90: 31994 Nonbonded interactions: 78178 Sorted by model distance: nonbonded pdb=" OH TYR A 623 " pdb=" O LEU A 779 " model vdw 2.261 2.440 nonbonded pdb=" OH TYR A 10 " pdb=" OD1 ASN A 998 " model vdw 2.318 2.440 nonbonded pdb=" O THR A 208 " pdb=" OG SER A 214 " model vdw 2.321 2.440 nonbonded pdb=" O LYS A 512 " pdb=" OG1 THR A 515 " model vdw 2.338 2.440 nonbonded pdb=" OH TYR A 353 " pdb=" OD1 ASN A 522 " model vdw 2.342 2.440 ... (remaining 78173 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.240 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: 4.020 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 31.690 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 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 0.132 10427 Z= 0.354 Angle : 1.041 15.413 14204 Z= 0.578 Chirality : 0.053 0.371 1564 Planarity : 0.008 0.155 1754 Dihedral : 17.648 179.332 3987 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.66 % Favored : 93.26 % Rotamer: Outliers : 0.61 % Allowed : 8.38 % Favored : 91.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % 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: -5.17 (0.17), residues: 1187 helix: -4.23 (0.11), residues: 426 sheet: -2.75 (0.43), residues: 124 loop : -3.01 (0.19), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A1042 HIS 0.006 0.001 HIS A 193 PHE 0.020 0.002 PHE A 18 TYR 0.034 0.002 TYR A 327 ARG 0.007 0.001 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 166 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ASP cc_start: 0.7129 (t0) cc_final: 0.6854 (t0) REVERT: A 162 LYS cc_start: 0.6627 (mttt) cc_final: 0.5393 (mmtt) REVERT: A 293 ARG cc_start: 0.7049 (mtp180) cc_final: 0.6771 (mtm180) REVERT: A 380 TYR cc_start: 0.4658 (m-80) cc_final: 0.2956 (t80) REVERT: A 498 LYS cc_start: 0.7230 (pptt) cc_final: 0.5649 (mmmm) REVERT: A 560 GLU cc_start: 0.6791 (mt-10) cc_final: 0.6464 (mt-10) REVERT: A 894 GLU cc_start: 0.8383 (pt0) cc_final: 0.8165 (tt0) REVERT: A 921 LYS cc_start: 0.5492 (ttpt) cc_final: 0.5243 (mtmt) REVERT: A 1061 TYR cc_start: 0.7244 (t80) cc_final: 0.6786 (t80) REVERT: A 1104 GLN cc_start: 0.7497 (mt0) cc_final: 0.7268 (mt0) REVERT: A 1113 ASP cc_start: 0.7285 (t70) cc_final: 0.6663 (t70) REVERT: A 1115 ARG cc_start: 0.7624 (mmt-90) cc_final: 0.7252 (mmt90) REVERT: A 1243 ASN cc_start: 0.5276 (t0) cc_final: 0.5013 (t0) outliers start: 6 outliers final: 2 residues processed: 171 average time/residue: 0.2512 time to fit residues: 58.5531 Evaluate side-chains 117 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 115 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 1216 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 62 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 37 optimal weight: 0.0050 chunk 58 optimal weight: 6.9990 chunk 71 optimal weight: 0.3980 chunk 110 optimal weight: 1.9990 overall best weight: 1.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 HIS A 204 GLN A 219 GLN A 236 HIS A 269 GLN A 276 ASN A 279 HIS A 296 HIS A 324 ASN A 506 ASN A 522 ASN A 526 ASN A 565 ASN A 612 ASN A 642 ASN A 684 ASN ** A 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 718 GLN A 742 GLN A 843 ASN A 859 ASN A 869 ASN A 910 GLN A 962 ASN A1089 HIS ** A1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10427 Z= 0.263 Angle : 0.667 11.813 14204 Z= 0.337 Chirality : 0.043 0.195 1564 Planarity : 0.004 0.039 1754 Dihedral : 15.040 175.126 1714 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.42 % Favored : 91.49 % Rotamer: Outliers : 2.93 % Allowed : 16.45 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % 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: -4.00 (0.19), residues: 1187 helix: -2.66 (0.18), residues: 426 sheet: -2.67 (0.45), residues: 121 loop : -2.67 (0.20), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 575 HIS 0.013 0.002 HIS A 279 PHE 0.019 0.002 PHE A 18 TYR 0.025 0.002 TYR A 121 ARG 0.007 0.001 ARG A 104 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 116 time to evaluate : 1.107 Fit side-chains revert: symmetry clash REVERT: A 42 MET cc_start: 0.7923 (ttm) cc_final: 0.7540 (ttt) REVERT: A 162 LYS cc_start: 0.6641 (mttt) cc_final: 0.5382 (mmtt) REVERT: A 243 LEU cc_start: 0.6757 (OUTLIER) cc_final: 0.6513 (pp) REVERT: A 328 ARG cc_start: 0.5487 (mmm160) cc_final: 0.4982 (mtp-110) REVERT: A 342 ASP cc_start: 0.6452 (m-30) cc_final: 0.6208 (m-30) REVERT: A 380 TYR cc_start: 0.4594 (m-80) cc_final: 0.2692 (t80) REVERT: A 460 LYS cc_start: 0.4118 (mmtp) cc_final: 0.3302 (mmtp) REVERT: A 509 HIS cc_start: 0.7744 (m-70) cc_final: 0.7461 (m170) REVERT: A 560 GLU cc_start: 0.7102 (mt-10) cc_final: 0.6786 (mt-10) REVERT: A 794 MET cc_start: 0.8113 (mmm) cc_final: 0.7880 (mmm) REVERT: A 921 LYS cc_start: 0.5736 (ttpt) cc_final: 0.5158 (mttt) REVERT: A 935 GLU cc_start: 0.6092 (mm-30) cc_final: 0.5725 (mp0) REVERT: A 1061 TYR cc_start: 0.7541 (t80) cc_final: 0.7300 (t80) REVERT: A 1068 GLN cc_start: 0.7176 (mm110) cc_final: 0.6938 (mp10) REVERT: A 1115 ARG cc_start: 0.7864 (mmt-90) cc_final: 0.7534 (mmt90) REVERT: A 1208 LEU cc_start: 0.6946 (tt) cc_final: 0.6559 (tp) outliers start: 29 outliers final: 18 residues processed: 142 average time/residue: 0.2248 time to fit residues: 45.2468 Evaluate side-chains 119 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 100 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 522 ASN Chi-restraints excluded: chain A residue 582 ASP Chi-restraints excluded: chain A residue 603 HIS Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 901 ILE Chi-restraints excluded: chain A residue 902 THR Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 1033 THR Chi-restraints excluded: chain A residue 1055 ASP Chi-restraints excluded: chain A residue 1082 ASP Chi-restraints excluded: chain A residue 1147 ILE Chi-restraints excluded: chain A residue 1154 LEU Chi-restraints excluded: chain A residue 1216 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 75 optimal weight: 0.0980 chunk 30 optimal weight: 5.9990 chunk 110 optimal weight: 7.9990 chunk 119 optimal weight: 4.9990 chunk 98 optimal weight: 0.7980 chunk 37 optimal weight: 0.0570 chunk 89 optimal weight: 3.9990 chunk 109 optimal weight: 8.9990 overall best weight: 1.5902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 ASN ** A 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 526 ASN A 612 ASN ** A 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 780 ASN A1198 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10427 Z= 0.235 Angle : 0.630 10.169 14204 Z= 0.317 Chirality : 0.043 0.195 1564 Planarity : 0.004 0.034 1754 Dihedral : 14.896 175.403 1714 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 4.54 % Allowed : 18.16 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % 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: -3.44 (0.21), residues: 1187 helix: -1.82 (0.22), residues: 427 sheet: -2.64 (0.46), residues: 121 loop : -2.56 (0.21), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 575 HIS 0.007 0.001 HIS A 509 PHE 0.017 0.001 PHE A 18 TYR 0.026 0.002 TYR A 121 ARG 0.005 0.000 ARG A 104 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 110 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 MET cc_start: 0.7965 (ttm) cc_final: 0.7585 (ttt) REVERT: A 162 LYS cc_start: 0.6641 (mttt) cc_final: 0.5456 (mmtt) REVERT: A 328 ARG cc_start: 0.5442 (mmm160) cc_final: 0.4919 (mtp180) REVERT: A 460 LYS cc_start: 0.4225 (mmtp) cc_final: 0.3480 (mmtp) REVERT: A 498 LYS cc_start: 0.7583 (pptt) cc_final: 0.5938 (mmmm) REVERT: A 499 GLU cc_start: 0.7172 (mm-30) cc_final: 0.6824 (mm-30) REVERT: A 921 LYS cc_start: 0.5461 (ttpt) cc_final: 0.5011 (mtmt) REVERT: A 935 GLU cc_start: 0.6384 (mm-30) cc_final: 0.5814 (mp0) REVERT: A 1115 ARG cc_start: 0.7980 (mmt-90) cc_final: 0.7573 (mmt90) REVERT: A 1208 LEU cc_start: 0.6959 (tt) cc_final: 0.6574 (tp) outliers start: 45 outliers final: 24 residues processed: 147 average time/residue: 0.2283 time to fit residues: 47.0219 Evaluate side-chains 126 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 102 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 522 ASN Chi-restraints excluded: chain A residue 582 ASP Chi-restraints excluded: chain A residue 603 HIS Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 901 ILE Chi-restraints excluded: chain A residue 902 THR Chi-restraints excluded: chain A residue 911 MET Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 1055 ASP Chi-restraints excluded: chain A residue 1147 ILE Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1216 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 52 optimal weight: 0.7980 chunk 74 optimal weight: 10.0000 chunk 111 optimal weight: 7.9990 chunk 117 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 522 ASN A 526 ASN ** A 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1251 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10427 Z= 0.204 Angle : 0.601 11.114 14204 Z= 0.300 Chirality : 0.042 0.193 1564 Planarity : 0.004 0.055 1754 Dihedral : 14.808 175.981 1714 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.18 % Favored : 90.82 % Rotamer: Outliers : 4.64 % Allowed : 19.78 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % 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: -3.02 (0.22), residues: 1187 helix: -1.28 (0.24), residues: 434 sheet: -2.62 (0.45), residues: 123 loop : -2.44 (0.21), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 575 HIS 0.006 0.001 HIS A 156 PHE 0.013 0.001 PHE A 18 TYR 0.029 0.002 TYR A 121 ARG 0.007 0.001 ARG A 495 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 105 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 MET cc_start: 0.7936 (ttm) cc_final: 0.7542 (ttt) REVERT: A 72 LYS cc_start: 0.5647 (mmtt) cc_final: 0.5239 (mmmt) REVERT: A 162 LYS cc_start: 0.6628 (mttt) cc_final: 0.6289 (mtmm) REVERT: A 328 ARG cc_start: 0.5370 (mmm160) cc_final: 0.4827 (mtp180) REVERT: A 498 LYS cc_start: 0.7568 (pptt) cc_final: 0.5858 (mmmm) REVERT: A 784 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7523 (mt-10) REVERT: A 794 MET cc_start: 0.8158 (mmm) cc_final: 0.7827 (mmm) REVERT: A 921 LYS cc_start: 0.5436 (ttpt) cc_final: 0.5016 (mtmt) REVERT: A 950 VAL cc_start: 0.8621 (OUTLIER) cc_final: 0.8383 (p) REVERT: A 1115 ARG cc_start: 0.7958 (mmt-90) cc_final: 0.7567 (mmt90) outliers start: 46 outliers final: 33 residues processed: 144 average time/residue: 0.2212 time to fit residues: 45.5680 Evaluate side-chains 136 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 101 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 522 ASN Chi-restraints excluded: chain A residue 582 ASP Chi-restraints excluded: chain A residue 603 HIS Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 723 ASP Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 784 GLU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 901 ILE Chi-restraints excluded: chain A residue 902 THR Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 1033 THR Chi-restraints excluded: chain A residue 1082 ASP Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1147 ILE Chi-restraints excluded: chain A residue 1154 LEU Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1216 ASN Chi-restraints excluded: chain A residue 1227 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 87 optimal weight: 9.9990 chunk 48 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 60 optimal weight: 8.9990 chunk 105 optimal weight: 6.9990 chunk 29 optimal weight: 8.9990 chunk 39 optimal weight: 4.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 269 GLN A 522 ASN A 526 ASN ** A 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1018 GLN ** A1101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 10427 Z= 0.371 Angle : 0.732 13.854 14204 Z= 0.364 Chirality : 0.047 0.215 1564 Planarity : 0.005 0.079 1754 Dihedral : 15.111 172.914 1714 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.36 % Favored : 89.64 % Rotamer: Outliers : 5.85 % Allowed : 20.18 % Favored : 73.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % 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: -3.19 (0.22), residues: 1187 helix: -1.51 (0.23), residues: 445 sheet: -2.74 (0.45), residues: 123 loop : -2.46 (0.22), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 575 HIS 0.006 0.001 HIS A 241 PHE 0.031 0.002 PHE A 344 TYR 0.024 0.002 TYR A 121 ARG 0.007 0.001 ARG A 474 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 104 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 MET cc_start: 0.8013 (ttm) cc_final: 0.7659 (ttt) REVERT: A 162 LYS cc_start: 0.6672 (mttt) cc_final: 0.6342 (mtmm) REVERT: A 328 ARG cc_start: 0.5618 (mmm160) cc_final: 0.5103 (mtp180) REVERT: A 498 LYS cc_start: 0.7575 (pptt) cc_final: 0.6000 (mmtp) REVERT: A 921 LYS cc_start: 0.5469 (ttpt) cc_final: 0.5159 (mtmt) REVERT: A 950 VAL cc_start: 0.8643 (OUTLIER) cc_final: 0.8438 (p) REVERT: A 1115 ARG cc_start: 0.8092 (mmt-90) cc_final: 0.7743 (mmt90) REVERT: A 1208 LEU cc_start: 0.7207 (tt) cc_final: 0.6857 (tp) outliers start: 58 outliers final: 43 residues processed: 152 average time/residue: 0.2031 time to fit residues: 45.0354 Evaluate side-chains 143 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 99 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 269 GLN Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 522 ASN Chi-restraints excluded: chain A residue 582 ASP Chi-restraints excluded: chain A residue 603 HIS Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 723 ASP Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 784 GLU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 901 ILE Chi-restraints excluded: chain A residue 902 THR Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 911 MET Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 1033 THR Chi-restraints excluded: chain A residue 1055 ASP Chi-restraints excluded: chain A residue 1082 ASP Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1147 ILE Chi-restraints excluded: chain A residue 1154 LEU Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1177 LEU Chi-restraints excluded: chain A residue 1216 ASN Chi-restraints excluded: chain A residue 1227 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 0.9990 chunk 23 optimal weight: 8.9990 chunk 69 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 chunk 118 optimal weight: 0.1980 chunk 97 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 9 optimal weight: 9.9990 chunk 39 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 113 optimal weight: 0.5980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 522 ASN A 526 ASN ** A 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 855 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 10427 Z= 0.156 Angle : 0.585 11.080 14204 Z= 0.288 Chirality : 0.041 0.190 1564 Planarity : 0.003 0.044 1754 Dihedral : 14.774 176.863 1714 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 4.34 % Allowed : 20.89 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % 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: -2.70 (0.23), residues: 1187 helix: -0.89 (0.24), residues: 430 sheet: -2.57 (0.45), residues: 123 loop : -2.31 (0.22), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 575 HIS 0.007 0.001 HIS A 521 PHE 0.023 0.001 PHE A 344 TYR 0.029 0.001 TYR A 121 ARG 0.006 0.000 ARG A 474 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 101 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6386 (OUTLIER) cc_final: 0.5961 (tmm) REVERT: A 42 MET cc_start: 0.7869 (ttm) cc_final: 0.7561 (ttt) REVERT: A 72 LYS cc_start: 0.5673 (mmtt) cc_final: 0.5319 (mmmt) REVERT: A 162 LYS cc_start: 0.6676 (mttt) cc_final: 0.6344 (mtmm) REVERT: A 498 LYS cc_start: 0.7398 (pptt) cc_final: 0.5727 (mmmm) REVERT: A 784 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7420 (mt-10) REVERT: A 921 LYS cc_start: 0.5237 (ttpt) cc_final: 0.4948 (mtmt) REVERT: A 950 VAL cc_start: 0.8583 (OUTLIER) cc_final: 0.8349 (p) REVERT: A 1115 ARG cc_start: 0.8059 (mmt-90) cc_final: 0.7681 (mmt90) REVERT: A 1208 LEU cc_start: 0.6943 (tt) cc_final: 0.6582 (tp) outliers start: 43 outliers final: 29 residues processed: 138 average time/residue: 0.1992 time to fit residues: 39.6108 Evaluate side-chains 127 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 95 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 522 ASN Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 582 ASP Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 605 LYS Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 723 ASP Chi-restraints excluded: chain A residue 770 ASP Chi-restraints excluded: chain A residue 784 GLU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 902 THR Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1015 ASN Chi-restraints excluded: chain A residue 1033 THR Chi-restraints excluded: chain A residue 1055 ASP Chi-restraints excluded: chain A residue 1082 ASP Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1154 LEU Chi-restraints excluded: chain A residue 1155 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 9.9990 chunk 67 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 66 optimal weight: 0.0000 chunk 99 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 522 ASN A 526 ASN ** A 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10427 Z= 0.157 Angle : 0.569 10.882 14204 Z= 0.280 Chirality : 0.040 0.188 1564 Planarity : 0.003 0.038 1754 Dihedral : 14.667 177.315 1712 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 4.64 % Allowed : 21.80 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % 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: -2.47 (0.23), residues: 1187 helix: -0.63 (0.25), residues: 427 sheet: -2.40 (0.45), residues: 123 loop : -2.24 (0.22), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 575 HIS 0.009 0.001 HIS A 509 PHE 0.021 0.001 PHE A 344 TYR 0.028 0.001 TYR A 121 ARG 0.006 0.000 ARG A 474 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 100 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6306 (OUTLIER) cc_final: 0.5901 (tmm) REVERT: A 42 MET cc_start: 0.7892 (ttm) cc_final: 0.7511 (ttt) REVERT: A 72 LYS cc_start: 0.5678 (mmtt) cc_final: 0.5309 (mmmt) REVERT: A 86 ASN cc_start: 0.3923 (t0) cc_final: 0.3556 (t0) REVERT: A 162 LYS cc_start: 0.6668 (mttt) cc_final: 0.6340 (mtmm) REVERT: A 328 ARG cc_start: 0.4781 (tpp-160) cc_final: 0.4268 (mtp180) REVERT: A 498 LYS cc_start: 0.7384 (pptt) cc_final: 0.5670 (mmmm) REVERT: A 784 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7422 (mt-10) REVERT: A 921 LYS cc_start: 0.5188 (ttpt) cc_final: 0.4971 (mtmt) REVERT: A 950 VAL cc_start: 0.8604 (OUTLIER) cc_final: 0.8355 (p) REVERT: A 1061 TYR cc_start: 0.7112 (t80) cc_final: 0.6885 (t80) REVERT: A 1115 ARG cc_start: 0.7974 (mmt-90) cc_final: 0.7554 (mmt90) REVERT: A 1208 LEU cc_start: 0.7071 (tt) cc_final: 0.6704 (tp) outliers start: 46 outliers final: 38 residues processed: 140 average time/residue: 0.2273 time to fit residues: 46.8870 Evaluate side-chains 136 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 95 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 3 PHE Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 522 ASN Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 582 ASP Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 605 LYS Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 723 ASP Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 770 ASP Chi-restraints excluded: chain A residue 784 GLU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 901 ILE Chi-restraints excluded: chain A residue 902 THR Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1015 ASN Chi-restraints excluded: chain A residue 1033 THR Chi-restraints excluded: chain A residue 1055 ASP Chi-restraints excluded: chain A residue 1082 ASP Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1147 ILE Chi-restraints excluded: chain A residue 1154 LEU Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1227 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 0.0770 chunk 70 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 22 optimal weight: 0.8980 chunk 74 optimal weight: 9.9990 chunk 80 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 overall best weight: 1.9942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 522 ASN A 526 ASN ** A 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.4197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10427 Z= 0.280 Angle : 0.650 11.550 14204 Z= 0.322 Chirality : 0.044 0.190 1564 Planarity : 0.004 0.058 1754 Dihedral : 14.861 172.772 1712 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.69 % Favored : 90.31 % Rotamer: Outliers : 5.15 % Allowed : 21.09 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % 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: -2.62 (0.23), residues: 1187 helix: -0.82 (0.25), residues: 423 sheet: -2.46 (0.46), residues: 122 loop : -2.28 (0.22), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 689 HIS 0.007 0.001 HIS A 509 PHE 0.022 0.002 PHE A 344 TYR 0.025 0.002 TYR A 121 ARG 0.009 0.001 ARG A 474 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 95 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 MET cc_start: 0.7983 (ttm) cc_final: 0.7617 (ttt) REVERT: A 86 ASN cc_start: 0.3960 (t0) cc_final: 0.3638 (t0) REVERT: A 162 LYS cc_start: 0.6680 (mttt) cc_final: 0.6369 (mtmm) REVERT: A 328 ARG cc_start: 0.4994 (tpp-160) cc_final: 0.4478 (tpp-160) REVERT: A 498 LYS cc_start: 0.7475 (pptt) cc_final: 0.5714 (mmmm) REVERT: A 784 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7426 (mt-10) REVERT: A 921 LYS cc_start: 0.5336 (ttpt) cc_final: 0.5066 (mtmt) REVERT: A 950 VAL cc_start: 0.8614 (OUTLIER) cc_final: 0.8392 (p) REVERT: A 1115 ARG cc_start: 0.8019 (mmt-90) cc_final: 0.7704 (mmt90) REVERT: A 1208 LEU cc_start: 0.7166 (tt) cc_final: 0.6799 (tp) outliers start: 51 outliers final: 45 residues processed: 136 average time/residue: 0.2072 time to fit residues: 41.5374 Evaluate side-chains 138 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 91 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 3 PHE Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 390 ASN Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 522 ASN Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain A residue 582 ASP Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 603 HIS Chi-restraints excluded: chain A residue 605 LYS Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 723 ASP Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 770 ASP Chi-restraints excluded: chain A residue 784 GLU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 901 ILE Chi-restraints excluded: chain A residue 902 THR Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 911 MET Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1015 ASN Chi-restraints excluded: chain A residue 1033 THR Chi-restraints excluded: chain A residue 1055 ASP Chi-restraints excluded: chain A residue 1082 ASP Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1147 ILE Chi-restraints excluded: chain A residue 1154 LEU Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1227 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 0.8980 chunk 102 optimal weight: 7.9990 chunk 109 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 chunk 86 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 99 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 115 optimal weight: 0.2980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 522 ASN A 526 ASN ** A 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10427 Z= 0.155 Angle : 0.580 11.029 14204 Z= 0.284 Chirality : 0.040 0.188 1564 Planarity : 0.003 0.039 1754 Dihedral : 14.683 176.754 1712 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 4.84 % Allowed : 21.70 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % 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: -2.29 (0.24), residues: 1187 helix: -0.47 (0.26), residues: 420 sheet: -2.39 (0.46), residues: 122 loop : -2.11 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 575 HIS 0.006 0.001 HIS A 509 PHE 0.020 0.001 PHE A 344 TYR 0.030 0.001 TYR A 121 ARG 0.009 0.000 ARG A 474 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 98 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6298 (OUTLIER) cc_final: 0.5878 (tmm) REVERT: A 42 MET cc_start: 0.7881 (ttm) cc_final: 0.7547 (ttt) REVERT: A 72 LYS cc_start: 0.5659 (mmtt) cc_final: 0.5364 (mmmt) REVERT: A 162 LYS cc_start: 0.6680 (mttt) cc_final: 0.6353 (mtmm) REVERT: A 328 ARG cc_start: 0.4846 (tpp-160) cc_final: 0.4133 (mtp-110) REVERT: A 498 LYS cc_start: 0.7380 (pptt) cc_final: 0.5664 (mmmm) REVERT: A 784 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7385 (mt-10) REVERT: A 921 LYS cc_start: 0.5157 (ttpt) cc_final: 0.4938 (mtmt) REVERT: A 950 VAL cc_start: 0.8590 (OUTLIER) cc_final: 0.8334 (p) REVERT: A 1115 ARG cc_start: 0.8006 (mmt-90) cc_final: 0.7639 (mmt90) REVERT: A 1193 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8459 (tt) outliers start: 48 outliers final: 41 residues processed: 139 average time/residue: 0.1981 time to fit residues: 40.3790 Evaluate side-chains 136 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 91 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 3 PHE Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 390 ASN Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 522 ASN Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 582 ASP Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 605 LYS Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 723 ASP Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 770 ASP Chi-restraints excluded: chain A residue 784 GLU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 901 ILE Chi-restraints excluded: chain A residue 902 THR Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1015 ASN Chi-restraints excluded: chain A residue 1033 THR Chi-restraints excluded: chain A residue 1055 ASP Chi-restraints excluded: chain A residue 1082 ASP Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1147 ILE Chi-restraints excluded: chain A residue 1154 LEU Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1193 LEU Chi-restraints excluded: chain A residue 1227 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 chunk 111 optimal weight: 9.9990 chunk 96 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 522 ASN A 526 ASN A 583 ASN ** A 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 869 ASN ** A1101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.4492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.056 10427 Z= 0.497 Angle : 0.822 11.266 14204 Z= 0.409 Chirality : 0.051 0.235 1564 Planarity : 0.005 0.077 1754 Dihedral : 15.274 171.239 1712 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.96 % Favored : 87.95 % Rotamer: Outliers : 5.35 % Allowed : 21.49 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % 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: -3.06 (0.22), residues: 1187 helix: -1.39 (0.23), residues: 439 sheet: -2.60 (0.47), residues: 122 loop : -2.41 (0.23), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A1254 HIS 0.007 0.002 HIS A 241 PHE 0.026 0.002 PHE A 471 TYR 0.027 0.003 TYR A1116 ARG 0.010 0.001 ARG A 896 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 96 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 MET cc_start: 0.7994 (ttm) cc_final: 0.7631 (ttt) REVERT: A 162 LYS cc_start: 0.6742 (mttt) cc_final: 0.6413 (mtmm) REVERT: A 370 PHE cc_start: 0.4941 (t80) cc_final: 0.4233 (p90) REVERT: A 498 LYS cc_start: 0.7593 (pptt) cc_final: 0.6026 (mmtp) REVERT: A 921 LYS cc_start: 0.5387 (ttpt) cc_final: 0.5071 (mtmt) REVERT: A 950 VAL cc_start: 0.8641 (OUTLIER) cc_final: 0.8429 (p) REVERT: A 1068 GLN cc_start: 0.8008 (mp10) cc_final: 0.7756 (mp10) REVERT: A 1115 ARG cc_start: 0.8097 (mmt-90) cc_final: 0.7804 (mmt90) REVERT: A 1208 LEU cc_start: 0.7518 (tt) cc_final: 0.7201 (tp) outliers start: 53 outliers final: 46 residues processed: 140 average time/residue: 0.2049 time to fit residues: 41.3632 Evaluate side-chains 142 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 95 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 3 PHE Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 390 ASN Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 522 ASN Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain A residue 582 ASP Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 605 LYS Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 723 ASP Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 770 ASP Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 784 GLU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 901 ILE Chi-restraints excluded: chain A residue 902 THR Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 911 MET Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 1015 ASN Chi-restraints excluded: chain A residue 1033 THR Chi-restraints excluded: chain A residue 1055 ASP Chi-restraints excluded: chain A residue 1082 ASP Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1147 ILE Chi-restraints excluded: chain A residue 1154 LEU Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1227 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 5.9990 chunk 89 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 26 optimal weight: 7.9990 chunk 96 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 522 ASN A 526 ASN A 583 ASN ** A 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 869 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.185424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.180745 restraints weight = 12285.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.179756 restraints weight = 23275.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.168168 restraints weight = 26306.799| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.4478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10427 Z= 0.186 Angle : 0.623 11.281 14204 Z= 0.307 Chirality : 0.041 0.190 1564 Planarity : 0.004 0.048 1754 Dihedral : 14.895 174.383 1712 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 4.34 % Allowed : 22.30 % Favored : 73.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % 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: -2.56 (0.23), residues: 1187 helix: -0.81 (0.25), residues: 428 sheet: -2.49 (0.47), residues: 122 loop : -2.19 (0.23), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 575 HIS 0.006 0.001 HIS A 509 PHE 0.021 0.001 PHE A 344 TYR 0.030 0.001 TYR A 121 ARG 0.012 0.001 ARG A 104 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1999.21 seconds wall clock time: 36 minutes 57.81 seconds (2217.81 seconds total)