Starting phenix.real_space_refine on Sat Dec 9 04:52:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iv6_9742/12_2023/6iv6_9742_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iv6_9742/12_2023/6iv6_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_9742/12_2023/6iv6_9742.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iv6_9742/12_2023/6iv6_9742.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iv6_9742/12_2023/6iv6_9742_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iv6_9742/12_2023/6iv6_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-1.21rc1-5172/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: 6.18, per 1000 atoms: 0.61 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: 4.27 Conformation dependent library (CDL) restraints added in 1.9 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: 5.13 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: 3.55 Time building geometry restraints manager: 4.54 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: 6029 35.87 - 71.73: 167 71.73 - 107.60: 17 107.60 - 143.47: 1 143.47 - 179.33: 3 Dihedral angle restraints: 6217 sinusoidal: 2677 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 6214 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: 1.030 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: 3.990 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 33.740 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.270 ------------------------------------------------------------------------------- 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 : 17.331 179.332 3939 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 : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 171 average time/residue: 0.2596 time to fit residues: 60.4236 Evaluate side-chains 112 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 110 time to evaluate : 1.065 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0984 time to fit residues: 1.8605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 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: 1.4800 ------------------------------------------------------------------------------- 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 522 ASN A 526 ASN A 565 ASN A 612 ASN A 684 ASN ** A 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 718 GLN A 742 GLN A 780 ASN A 843 ASN A 859 ASN A 869 ASN A 910 GLN A 962 ASN A1089 HIS A1251 ASN ** A1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.2363 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= 0.239 Angle : 0.645 11.126 14204 Z= 0.326 Chirality : 0.042 0.193 1564 Planarity : 0.004 0.042 1754 Dihedral : 14.070 175.459 1663 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.42 % Favored : 91.49 % Rotamer: Outliers : 2.72 % Allowed : 16.25 % Favored : 81.03 % 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: -3.90 (0.20), residues: 1187 helix: -2.54 (0.19), residues: 414 sheet: -2.65 (0.45), residues: 121 loop : -2.65 (0.20), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1106 HIS 0.012 0.001 HIS A 509 PHE 0.018 0.002 PHE A 18 TYR 0.025 0.002 TYR A 121 ARG 0.009 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 147 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 120 time to evaluate : 1.126 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 16 residues processed: 144 average time/residue: 0.2157 time to fit residues: 44.5957 Evaluate side-chains 114 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 98 time to evaluate : 1.127 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.0955 time to fit residues: 4.3540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 92 optimal weight: 5.9990 chunk 75 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 110 optimal weight: 0.0980 chunk 119 optimal weight: 0.3980 chunk 98 optimal weight: 0.9990 chunk 37 optimal weight: 9.9990 chunk 89 optimal weight: 0.8980 chunk 109 optimal weight: 7.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 GLN A 276 ASN A 324 ASN A 358 ASN A 506 ASN A 526 ASN ** A 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1198 ASN A1259 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10427 Z= 0.151 Angle : 0.562 10.013 14204 Z= 0.282 Chirality : 0.040 0.206 1564 Planarity : 0.003 0.035 1754 Dihedral : 13.837 178.221 1663 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 2.12 % Allowed : 19.17 % Favored : 78.71 % 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: -3.15 (0.21), residues: 1187 helix: -1.51 (0.22), residues: 426 sheet: -2.48 (0.46), residues: 121 loop : -2.46 (0.21), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 575 HIS 0.004 0.001 HIS A 156 PHE 0.014 0.001 PHE A 18 TYR 0.026 0.001 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 128 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 107 time to evaluate : 1.211 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 6 residues processed: 123 average time/residue: 0.2503 time to fit residues: 43.9944 Evaluate side-chains 99 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 93 time to evaluate : 1.109 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1000 time to fit residues: 2.6355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 chunk 111 optimal weight: 9.9990 chunk 117 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 105 optimal weight: 0.6980 chunk 31 optimal weight: 0.0970 chunk 98 optimal weight: 2.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 GLN A 276 ASN A 526 ASN A 612 ASN ** A 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 759 HIS ** A1101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10427 Z= 0.142 Angle : 0.544 10.858 14204 Z= 0.269 Chirality : 0.040 0.244 1564 Planarity : 0.003 0.032 1754 Dihedral : 13.725 178.898 1663 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 2.32 % Allowed : 20.79 % Favored : 76.89 % 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: -2.63 (0.22), residues: 1187 helix: -0.87 (0.24), residues: 435 sheet: -2.33 (0.46), residues: 123 loop : -2.30 (0.22), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 575 HIS 0.004 0.001 HIS A 156 PHE 0.023 0.001 PHE A 344 TYR 0.028 0.001 TYR A 356 ARG 0.005 0.000 ARG A 104 *********************** 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 124 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 101 time to evaluate : 1.100 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 9 residues processed: 117 average time/residue: 0.2132 time to fit residues: 37.3009 Evaluate side-chains 99 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 90 time to evaluate : 1.113 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0981 time to fit residues: 3.0911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 87 optimal weight: 8.9990 chunk 48 optimal weight: 8.9990 chunk 100 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 chunk 105 optimal weight: 0.6980 chunk 29 optimal weight: 8.9990 chunk 39 optimal weight: 0.7980 overall best weight: 2.4986 ------------------------------------------------------------------------------- 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 526 ASN A 642 ASN ** A 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1018 GLN ** A1101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10427 Z= 0.336 Angle : 0.704 12.030 14204 Z= 0.352 Chirality : 0.047 0.434 1564 Planarity : 0.004 0.043 1754 Dihedral : 14.165 172.927 1663 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.36 % Favored : 89.64 % Rotamer: Outliers : 3.03 % Allowed : 21.49 % Favored : 75.48 % 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: -2.93 (0.22), residues: 1187 helix: -1.26 (0.23), residues: 439 sheet: -2.47 (0.48), residues: 117 loop : -2.37 (0.22), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 575 HIS 0.006 0.001 HIS A 916 PHE 0.021 0.002 PHE A 344 TYR 0.021 0.002 TYR A 327 ARG 0.005 0.001 ARG A 549 *********************** 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 128 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 98 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 17 residues processed: 121 average time/residue: 0.2233 time to fit residues: 39.6650 Evaluate side-chains 105 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 88 time to evaluate : 1.105 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1047 time to fit residues: 4.7921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 69 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 118 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 9 optimal weight: 7.9990 chunk 39 optimal weight: 7.9990 chunk 61 optimal weight: 10.0000 chunk 113 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 526 ASN A 612 ASN ** A 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 855 ASN ** A 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.4316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 10427 Z= 0.419 Angle : 0.775 15.489 14204 Z= 0.387 Chirality : 0.050 0.472 1564 Planarity : 0.005 0.102 1754 Dihedral : 14.425 172.859 1663 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.37 % Favored : 88.63 % Rotamer: Outliers : 2.52 % Allowed : 22.81 % Favored : 74.67 % 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: -3.28 (0.22), residues: 1187 helix: -1.64 (0.22), residues: 443 sheet: -2.58 (0.47), residues: 122 loop : -2.51 (0.22), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 575 HIS 0.006 0.002 HIS A 241 PHE 0.023 0.002 PHE A 471 TYR 0.033 0.002 TYR A 121 ARG 0.008 0.001 ARG A 17 *********************** 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 120 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 95 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 16 residues processed: 117 average time/residue: 0.2259 time to fit residues: 39.1221 Evaluate side-chains 105 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 89 time to evaluate : 1.166 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1211 time to fit residues: 4.9411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 86 optimal weight: 0.0770 chunk 66 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 117 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 72 optimal weight: 0.6980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 526 ASN ** A 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.4287 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= 0.155 Angle : 0.591 13.046 14204 Z= 0.289 Chirality : 0.041 0.416 1564 Planarity : 0.003 0.040 1754 Dihedral : 13.874 177.875 1663 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 1.41 % Allowed : 23.51 % Favored : 75.08 % 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: -2.66 (0.23), residues: 1187 helix: -0.87 (0.24), residues: 432 sheet: -2.40 (0.47), residues: 122 loop : -2.32 (0.22), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 575 HIS 0.005 0.001 HIS A 156 PHE 0.020 0.001 PHE A 370 TYR 0.032 0.001 TYR A 121 ARG 0.003 0.000 ARG A 104 *********************** 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 113 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 99 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 110 average time/residue: 0.2119 time to fit residues: 34.4381 Evaluate side-chains 94 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 87 time to evaluate : 1.118 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1037 time to fit residues: 2.9443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 chunk 22 optimal weight: 0.2980 chunk 74 optimal weight: 9.9990 chunk 80 optimal weight: 3.9990 chunk 58 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 526 ASN ** A 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.4527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 10427 Z= 0.402 Angle : 0.757 13.529 14204 Z= 0.374 Chirality : 0.049 0.501 1564 Planarity : 0.005 0.088 1754 Dihedral : 14.313 172.181 1663 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.63 % Favored : 88.37 % Rotamer: Outliers : 1.82 % Allowed : 24.22 % 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: -2.94 (0.23), residues: 1187 helix: -1.32 (0.23), residues: 441 sheet: -2.44 (0.49), residues: 116 loop : -2.35 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A1254 HIS 0.012 0.002 HIS A 509 PHE 0.021 0.002 PHE A 471 TYR 0.024 0.002 TYR A 121 ARG 0.003 0.001 ARG A 17 *********************** 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 107 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 89 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 11 residues processed: 103 average time/residue: 0.2261 time to fit residues: 34.0512 Evaluate side-chains 98 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 87 time to evaluate : 1.079 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0937 time to fit residues: 3.5279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 109 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 33 optimal weight: 0.3980 chunk 99 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 115 optimal weight: 7.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 526 ASN ** A 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.4519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 10427 Z= 0.176 Angle : 0.618 15.224 14204 Z= 0.302 Chirality : 0.042 0.375 1564 Planarity : 0.003 0.054 1754 Dihedral : 13.944 175.785 1663 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 0.81 % Allowed : 24.92 % Favored : 74.27 % 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: -2.53 (0.23), residues: 1187 helix: -0.75 (0.25), residues: 419 sheet: -2.37 (0.47), residues: 122 loop : -2.22 (0.22), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP A1042 HIS 0.009 0.001 HIS A 509 PHE 0.017 0.001 PHE A 344 TYR 0.034 0.001 TYR A 121 ARG 0.003 0.000 ARG A 104 *********************** 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 101 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 93 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 97 average time/residue: 0.2149 time to fit residues: 31.3538 Evaluate side-chains 91 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 85 time to evaluate : 1.208 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1003 time to fit residues: 2.7838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 96 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 59 optimal weight: 8.9990 chunk 76 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 526 ASN ** A 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.4630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 10427 Z= 0.316 Angle : 0.701 15.514 14204 Z= 0.344 Chirality : 0.046 0.465 1564 Planarity : 0.004 0.075 1754 Dihedral : 14.155 172.615 1663 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.70 % Favored : 89.30 % Rotamer: Outliers : 0.40 % Allowed : 24.82 % 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: -1.03 (0.24), residues: 438 sheet: -2.35 (0.50), residues: 116 loop : -2.27 (0.23), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A1042 HIS 0.013 0.002 HIS A 509 PHE 0.018 0.002 PHE A 344 TYR 0.026 0.002 TYR A 121 ARG 0.006 0.000 ARG A 474 ********************** 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 87 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 83 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 86 average time/residue: 0.2266 time to fit residues: 28.5867 Evaluate side-chains 85 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 82 time to evaluate : 1.237 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0975 time to fit residues: 2.1969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 6.9990 chunk 89 optimal weight: 0.7980 chunk 14 optimal weight: 0.0050 chunk 26 optimal weight: 8.9990 chunk 96 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 overall best weight: 1.1198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN A 526 ASN ** A 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.185804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.181785 restraints weight = 12373.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.180741 restraints weight = 19135.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.179926 restraints weight = 22212.155| |-----------------------------------------------------------------------------| r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.4645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10427 Z= 0.195 Angle : 0.623 14.789 14204 Z= 0.304 Chirality : 0.042 0.395 1564 Planarity : 0.004 0.058 1754 Dihedral : 13.947 175.181 1663 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 0.20 % Allowed : 25.83 % 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: -2.49 (0.23), residues: 1187 helix: -0.67 (0.25), residues: 420 sheet: -2.34 (0.48), residues: 122 loop : -2.23 (0.22), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A1042 HIS 0.012 0.001 HIS A 509 PHE 0.017 0.001 PHE A 344 TYR 0.032 0.001 TYR A 121 ARG 0.014 0.000 ARG A 104 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1972.21 seconds wall clock time: 36 minutes 47.45 seconds (2207.45 seconds total)