Starting phenix.real_space_refine on Sat Sep 12 00:34:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6v5c_21052/09_2026/6v5c_21052.cif Found real_map, /net/cci-nas-00/data/ceres_data/6v5c_21052/09_2026/6v5c_21052.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6v5c_21052/09_2026/6v5c_21052.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6v5c_21052/09_2026/6v5c_21052.map" model { file = "/net/cci-nas-00/data/ceres_data/6v5c_21052/09_2026/6v5c_21052.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6v5c_21052/09_2026/6v5c_21052.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6v5c_21052/09_2026/6v5c_21052.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6v5c_21052/09_2026/6v5c_21052.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.007 sd= 0.091 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 66 5.49 5 S 69 5.16 5 C 7523 2.51 5 N 2158 2.21 5 O 2435 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12251 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 903, 7371 Classifications: {'peptide': 903} Link IDs: {'PTRANS': 49, 'TRANS': 853} Chain breaks: 1 Chain: "C" Number of atoms: 1747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1747 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 208} Chain breaks: 4 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 1739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1739 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 8, 'TRANS': 207} Chain breaks: 4 Chain: "D" Number of atoms: 1394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1394 Classifications: {'RNAv2': 66} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 29, 'rna3p_pyr': 35} Link IDs: {'rna2p': 2, 'rna3p': 63} Chain breaks: 1 Time building chain proxies: 2.75, per 1000 atoms: 0.22 Number of scatterers: 12251 At special positions: 0 Unit cell: (97.52, 114.48, 169.6, 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 69 16.00 P 66 15.00 O 2435 8.00 N 2158 7.00 C 7523 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 - 3.00 Amino acid : True - 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: 0.97 Conformation dependent library (CDL) restraints added in 523.5 milliseconds 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2530 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 9 sheets defined 42.9% alpha, 6.1% beta 27 base pairs and 39 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'A' and resid 442 through 447 removed outlier: 3.573A pdb=" N TYR A 445 " --> pdb=" O ARG A 442 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASP A 446 " --> pdb=" O ASP A 443 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS A 447 " --> pdb=" O LEU A 444 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 442 through 447' Processing helix chain 'A' and resid 504 through 512 removed outlier: 3.849A pdb=" N LYS A 512 " --> pdb=" O ILE A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 538 removed outlier: 4.470A pdb=" N GLY A 533 " --> pdb=" O MET A 530 " (cutoff:3.500A) Proline residue: A 534 - end of helix Processing helix chain 'A' and resid 642 through 654 Processing helix chain 'A' and resid 698 through 708 Processing helix chain 'A' and resid 726 through 737 Processing helix chain 'A' and resid 777 through 781 removed outlier: 4.343A pdb=" N ALA A 780 " --> pdb=" O ILE A 777 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLN A 781 " --> pdb=" O ARG A 778 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 777 through 781' Processing helix chain 'A' and resid 782 through 786 Processing helix chain 'A' and resid 787 through 804 Processing helix chain 'A' and resid 812 through 830 removed outlier: 3.932A pdb=" N GLN A 816 " --> pdb=" O GLN A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 875 removed outlier: 4.157A pdb=" N HIS A 868 " --> pdb=" O PRO A 864 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N CYS A 875 " --> pdb=" O ARG A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 882 removed outlier: 3.544A pdb=" N ASP A 880 " --> pdb=" O MET A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 897 Processing helix chain 'A' and resid 909 through 920 Processing helix chain 'A' and resid 965 through 986 removed outlier: 3.984A pdb=" N LEU A 971 " --> pdb=" O ARG A 967 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ALA A 974 " --> pdb=" O PHE A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 1004 Processing helix chain 'A' and resid 1005 through 1017 Processing helix chain 'A' and resid 1033 through 1055 Processing helix chain 'A' and resid 1056 through 1063 removed outlier: 3.998A pdb=" N ALA A1060 " --> pdb=" O SER A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1064 through 1069 Processing helix chain 'A' and resid 1071 through 1080 Processing helix chain 'A' and resid 1084 through 1089 removed outlier: 3.522A pdb=" N GLN A1089 " --> pdb=" O PRO A1085 " (cutoff:3.500A) Processing helix chain 'A' and resid 1103 through 1115 removed outlier: 4.062A pdb=" N LEU A1107 " --> pdb=" O VAL A1103 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1127 removed outlier: 4.368A pdb=" N LEU A1124 " --> pdb=" O HIS A1120 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1165 removed outlier: 4.444A pdb=" N LEU A1149 " --> pdb=" O ARG A1145 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR A1159 " --> pdb=" O GLN A1155 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE A1164 " --> pdb=" O GLU A1160 " (cutoff:3.500A) Processing helix chain 'A' and resid 1170 through 1182 Processing helix chain 'A' and resid 1185 through 1195 Processing helix chain 'A' and resid 1214 through 1226 Processing helix chain 'A' and resid 1234 through 1245 removed outlier: 3.589A pdb=" N HIS A1238 " --> pdb=" O LEU A1234 " (cutoff:3.500A) Processing helix chain 'A' and resid 1248 through 1255 Processing helix chain 'A' and resid 1260 through 1269 removed outlier: 3.737A pdb=" N GLN A1264 " --> pdb=" O ASP A1260 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N CYS A1269 " --> pdb=" O LEU A1265 " (cutoff:3.500A) Processing helix chain 'A' and resid 1303 through 1307 removed outlier: 3.690A pdb=" N GLY A1306 " --> pdb=" O TYR A1303 " (cutoff:3.500A) Processing helix chain 'A' and resid 1317 through 1332 removed outlier: 3.753A pdb=" N GLU A1321 " --> pdb=" O ILE A1317 " (cutoff:3.500A) Processing helix chain 'A' and resid 1340 through 1345 removed outlier: 4.188A pdb=" N ILE A1344 " --> pdb=" O GLN A1340 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU A1345 " --> pdb=" O LYS A1341 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1340 through 1345' Processing helix chain 'C' and resid 511 through 523 Processing helix chain 'C' and resid 561 through 575 removed outlier: 3.881A pdb=" N LYS C 565 " --> pdb=" O LYS C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 616 removed outlier: 4.393A pdb=" N ALA C 615 " --> pdb=" O THR C 612 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY C 616 " --> pdb=" O SER C 613 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 612 through 616' Processing helix chain 'C' and resid 618 through 631 removed outlier: 3.661A pdb=" N LEU C 624 " --> pdb=" O PRO C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 668 through 685 Processing helix chain 'C' and resid 693 through 698 Processing helix chain 'C' and resid 729 through 750 Processing helix chain 'B' and resid 511 through 523 removed outlier: 3.939A pdb=" N ILE B 515 " --> pdb=" O SER B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 576 Processing helix chain 'B' and resid 597 through 601 removed outlier: 4.098A pdb=" N HIS B 600 " --> pdb=" O TYR B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 613 removed outlier: 3.556A pdb=" N THR B 612 " --> pdb=" O TYR B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 627 Processing helix chain 'B' and resid 668 through 685 removed outlier: 3.958A pdb=" N GLY B 672 " --> pdb=" O ASN B 668 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N HIS B 685 " --> pdb=" O LEU B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 698 Processing helix chain 'B' and resid 730 through 748 Processing sheet with id=AA1, first strand: chain 'A' and resid 413 through 415 removed outlier: 6.691A pdb=" N ARG A 414 " --> pdb=" O VAL A 696 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 572 through 573 Processing sheet with id=AA3, first strand: chain 'A' and resid 572 through 573 removed outlier: 4.529A pdb=" N ARG A 684 " --> pdb=" O GLU A 602 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N PHE A 604 " --> pdb=" O MET A 682 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N MET A 682 " --> pdb=" O PHE A 604 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 618 through 621 removed outlier: 3.664A pdb=" N CYS A 618 " --> pdb=" O ILE A 629 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 740 through 741 Processing sheet with id=AA6, first strand: chain 'A' and resid 1289 through 1290 Processing sheet with id=AA7, first strand: chain 'C' and resid 530 through 534 removed outlier: 3.564A pdb=" N ASN C 531 " --> pdb=" O SER C 545 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N SER C 545 " --> pdb=" O ASN C 531 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE C 533 " --> pdb=" O GLY C 543 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N VAL C 546 " --> pdb=" O TYR C 553 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 639 through 641 Processing sheet with id=AA9, first strand: chain 'B' and resid 529 through 533 removed outlier: 4.047A pdb=" N GLY B 554 " --> pdb=" O VAL B 546 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ILE B 548 " --> pdb=" O THR B 552 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N THR B 552 " --> pdb=" O ILE B 548 " (cutoff:3.500A) 386 hydrogen bonds defined for protein. 1098 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 65 hydrogen bonds 122 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 39 stacking parallelities Total time for adding SS restraints: 2.24 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1944 1.32 - 1.45: 3905 1.45 - 1.58: 6565 1.58 - 1.72: 133 1.72 - 1.85: 108 Bond restraints: 12655 Sorted by residual: bond pdb=" CA ASN A 963 " pdb=" C ASN A 963 " ideal model delta sigma weight residual 1.525 1.430 0.095 1.27e-02 6.20e+03 5.63e+01 bond pdb=" CA TYR C 609 " pdb=" C TYR C 609 " ideal model delta sigma weight residual 1.523 1.600 -0.076 1.34e-02 5.57e+03 3.24e+01 bond pdb=" CA VAL C 608 " pdb=" C VAL C 608 " ideal model delta sigma weight residual 1.520 1.587 -0.067 1.20e-02 6.94e+03 3.14e+01 bond pdb=" N TYR C 621 " pdb=" CA TYR C 621 " ideal model delta sigma weight residual 1.459 1.392 0.067 1.20e-02 6.94e+03 3.13e+01 bond pdb=" CA TRP A1258 " pdb=" C TRP A1258 " ideal model delta sigma weight residual 1.530 1.471 0.059 1.17e-02 7.31e+03 2.57e+01 ... (remaining 12650 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.61: 17014 3.61 - 7.22: 298 7.22 - 10.83: 47 10.83 - 14.44: 12 14.44 - 18.04: 8 Bond angle restraints: 17379 Sorted by residual: angle pdb=" N VAL C 608 " pdb=" CA VAL C 608 " pdb=" C VAL C 608 " ideal model delta sigma weight residual 113.47 130.83 -17.36 1.01e+00 9.80e-01 2.95e+02 angle pdb=" CA GLU A 736 " pdb=" C GLU A 736 " pdb=" N CYS A 737 " ideal model delta sigma weight residual 117.72 103.02 14.70 1.31e+00 5.83e-01 1.26e+02 angle pdb=" C THR A 958 " pdb=" N PRO A 959 " pdb=" CA PRO A 959 " ideal model delta sigma weight residual 119.84 106.39 13.45 1.25e+00 6.40e-01 1.16e+02 angle pdb=" N TRP A1258 " pdb=" CA TRP A1258 " pdb=" C TRP A1258 " ideal model delta sigma weight residual 111.28 97.25 14.03 1.35e+00 5.49e-01 1.08e+02 angle pdb=" N GLU C 604 " pdb=" CA GLU C 604 " pdb=" C GLU C 604 " ideal model delta sigma weight residual 113.01 125.43 -12.42 1.20e+00 6.94e-01 1.07e+02 ... (remaining 17374 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 6365 17.88 - 35.76: 850 35.76 - 53.64: 236 53.64 - 71.52: 72 71.52 - 89.40: 22 Dihedral angle restraints: 7545 sinusoidal: 3642 harmonic: 3903 Sorted by residual: dihedral pdb=" C4' A D 63 " pdb=" C3' A D 63 " pdb=" C2' A D 63 " pdb=" C1' A D 63 " ideal model delta sinusoidal sigma weight residual 36.34 -35.29 71.63 1 3.10e+00 1.04e-01 6.84e+02 dihedral pdb=" C4' C D 41 " pdb=" C3' C D 41 " pdb=" C2' C D 41 " pdb=" C1' C D 41 " ideal model delta sinusoidal sigma weight residual 36.34 -34.42 70.77 1 3.10e+00 1.04e-01 6.70e+02 dihedral pdb=" O4' A D 63 " pdb=" C4' A D 63 " pdb=" C3' A D 63 " pdb=" C2' A D 63 " ideal model delta sinusoidal sigma weight residual -35.15 23.78 -58.93 1 4.00e+00 6.25e-02 2.90e+02 ... (remaining 7542 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 1775 0.128 - 0.257: 147 0.257 - 0.385: 12 0.385 - 0.514: 5 0.514 - 0.642: 4 Chirality restraints: 1943 Sorted by residual: chirality pdb=" CA VAL C 608 " pdb=" N VAL C 608 " pdb=" C VAL C 608 " pdb=" CB VAL C 608 " both_signs ideal model delta sigma weight residual False 2.44 1.80 0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" CA TYR C 621 " pdb=" N TYR C 621 " pdb=" C TYR C 621 " pdb=" CB TYR C 621 " both_signs ideal model delta sigma weight residual False 2.51 1.87 0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" CA GLU C 604 " pdb=" N GLU C 604 " pdb=" C GLU C 604 " pdb=" CB GLU C 604 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.59 2.00e-01 2.50e+01 8.61e+00 ... (remaining 1940 not shown) Planarity restraints: 1998 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 736 " -0.017 2.00e-02 2.50e+03 4.11e-02 1.69e+01 pdb=" C GLU A 736 " 0.071 2.00e-02 2.50e+03 pdb=" O GLU A 736 " -0.029 2.00e-02 2.50e+03 pdb=" N CYS A 737 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1258 " -0.043 2.00e-02 2.50e+03 2.23e-02 1.24e+01 pdb=" CG TRP A1258 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP A1258 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP A1258 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A1258 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP A1258 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A1258 " 0.043 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1258 " -0.013 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1258 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP A1258 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 514 " -0.056 5.00e-02 4.00e+02 8.53e-02 1.17e+01 pdb=" N PRO A 515 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO A 515 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 515 " -0.046 5.00e-02 4.00e+02 ... (remaining 1995 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 238 2.60 - 3.17: 10110 3.17 - 3.75: 21409 3.75 - 4.32: 26159 4.32 - 4.90: 38977 Nonbonded interactions: 96893 Sorted by model distance: nonbonded pdb=" O MET A 740 " pdb=" CZ PHE A 847 " model vdw 2.023 3.340 nonbonded pdb=" O PHE A1252 " pdb=" ND2 ASN A1255 " model vdw 2.038 3.120 nonbonded pdb=" CE MET A 740 " pdb=" CB CYS A 920 " model vdw 2.105 3.860 nonbonded pdb=" OG SER C 613 " pdb=" CB SER C 619 " model vdw 2.185 3.440 nonbonded pdb=" OE2 GLU C 594 " pdb=" NH2 ARG C 696 " model vdw 2.239 3.120 ... (remaining 96888 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 493 through 495 or (resid 496 and (name N or name CA or na \ me C or name O or name CB )) or resid 500 through 749)) selection = (chain 'C' and resid 493 through 749) } 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: 1.200 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: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.130 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 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 : 0.007 0.095 12655 Z= 0.400 Angle : 1.291 18.044 17379 Z= 0.724 Chirality : 0.082 0.642 1943 Planarity : 0.008 0.085 1998 Dihedral : 18.013 89.398 5015 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 18.17 Ramachandran Plot: Outliers : 0.38 % Allowed : 13.72 % Favored : 85.90 % Rotamer: Outliers : 1.84 % Allowed : 11.82 % Favored : 86.34 % Cbeta Deviations : 0.55 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.64 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.86 (0.19), residues: 1312 helix: -2.35 (0.19), residues: 502 sheet: -3.03 (0.50), residues: 61 loop : -4.08 (0.19), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 548 TYR 0.050 0.003 TYR C 621 PHE 0.024 0.003 PHE A 631 TRP 0.043 0.003 TRP A1258 HIS 0.011 0.002 HIS A 573 Details of bonding type rmsd/Z covalent geometry : bond 0.00698 / 0.40 (12655) covalent geometry : angle 1.29127 / 0.72 (17379) hydrogen bonds : bond 0.16366 / 10.83 ( 449) hydrogen bonds : angle 7.95975 / 5.42 ( 1220) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 699 MET cc_start: 0.8229 (tpp) cc_final: 0.7596 (tpt) REVERT: A 784 TYR cc_start: 0.7424 (m-10) cc_final: 0.7058 (m-80) REVERT: A 861 MET cc_start: 0.9215 (mpp) cc_final: 0.8689 (mpp) REVERT: A 897 MET cc_start: 0.8434 (ttp) cc_final: 0.8215 (ttp) REVERT: A 1011 MET cc_start: 0.8934 (mmm) cc_final: 0.8657 (tpp) REVERT: A 1014 LYS cc_start: 0.9689 (tptm) cc_final: 0.9434 (tppt) REVERT: A 1022 MET cc_start: 0.8525 (ptm) cc_final: 0.8177 (ptp) REVERT: A 1026 HIS cc_start: 0.8599 (OUTLIER) cc_final: 0.7809 (t70) REVERT: A 1043 CYS cc_start: 0.8906 (p) cc_final: 0.8673 (p) REVERT: A 1151 ASP cc_start: 0.8645 (p0) cc_final: 0.8376 (p0) REVERT: A 1235 GLU cc_start: 0.9489 (mt-10) cc_final: 0.9083 (tp30) REVERT: A 1241 MET cc_start: 0.9166 (mmm) cc_final: 0.8901 (mmt) REVERT: C 501 LYS cc_start: 0.6871 (ptmm) cc_final: 0.5667 (mttt) REVERT: C 520 MET cc_start: 0.8558 (mtp) cc_final: 0.8009 (ttt) REVERT: C 609 TYR cc_start: 0.1694 (OUTLIER) cc_final: 0.0350 (m-80) REVERT: B 682 GLN cc_start: 0.8821 (mm110) cc_final: 0.8351 (mt0) REVERT: B 697 MET cc_start: 0.9302 (mtp) cc_final: 0.9032 (mmm) outliers start: 22 outliers final: 11 residues processed: 151 average time/residue: 0.1037 time to fit residues: 23.5324 Evaluate side-chains 108 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 7.9990 chunk 55 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 964 HIS ** A1120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1136 ASN ** A1187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 521 GLN B 625 HIS B 660 HIS ** B 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.055697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.042582 restraints weight = 95306.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.043974 restraints weight = 58909.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.044903 restraints weight = 42049.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.045531 restraints weight = 33257.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.045972 restraints weight = 28187.016| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 12655 Z= 0.253 Angle : 0.918 11.764 17379 Z= 0.443 Chirality : 0.055 0.554 1943 Planarity : 0.006 0.070 1998 Dihedral : 13.655 80.291 2241 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 18.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 14.10 % Favored : 85.82 % Rotamer: Outliers : 0.25 % Allowed : 8.13 % Favored : 91.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.93 (0.21), residues: 1312 helix: -1.15 (0.21), residues: 523 sheet: -2.72 (0.58), residues: 51 loop : -3.93 (0.19), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1000 TYR 0.028 0.002 TYR A 872 PHE 0.018 0.002 PHE B 641 TRP 0.018 0.002 TRP A1258 HIS 0.010 0.002 HIS A1026 Details of bonding type rmsd/Z covalent geometry : bond 0.00529 / 0.25 (12655) covalent geometry : angle 0.91842 / 0.44 (17379) hydrogen bonds : bond 0.05651 / 3.56 ( 449) hydrogen bonds : angle 6.18915 / 4.28 ( 1220) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 115 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 562 ARG cc_start: 0.7475 (tpp-160) cc_final: 0.7100 (tpp80) REVERT: A 722 MET cc_start: 0.8912 (tmm) cc_final: 0.8628 (tmm) REVERT: A 740 MET cc_start: 0.8514 (mtp) cc_final: 0.7827 (tpt) REVERT: A 773 VAL cc_start: 0.8811 (t) cc_final: 0.8508 (t) REVERT: A 897 MET cc_start: 0.8485 (ttp) cc_final: 0.8019 (ttp) REVERT: A 1011 MET cc_start: 0.9070 (mmm) cc_final: 0.8647 (tpp) REVERT: A 1235 GLU cc_start: 0.9516 (mt-10) cc_final: 0.9135 (mm-30) REVERT: A 1241 MET cc_start: 0.9312 (mmm) cc_final: 0.8992 (mmt) REVERT: A 1322 MET cc_start: 0.9090 (ttt) cc_final: 0.8800 (ttt) REVERT: C 494 VAL cc_start: 0.6766 (m) cc_final: 0.6191 (t) REVERT: C 501 LYS cc_start: 0.6649 (ptmm) cc_final: 0.5467 (mmtm) REVERT: C 520 MET cc_start: 0.8404 (mtp) cc_final: 0.7877 (mmm) REVERT: C 697 MET cc_start: 0.7822 (ptt) cc_final: 0.7405 (ptt) REVERT: B 682 GLN cc_start: 0.8918 (mm110) cc_final: 0.8535 (mt0) outliers start: 3 outliers final: 0 residues processed: 118 average time/residue: 0.1036 time to fit residues: 18.4249 Evaluate side-chains 94 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 21 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 48 optimal weight: 0.4980 chunk 93 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 81 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 12 optimal weight: 8.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 924 GLN ** A1026 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1294 HIS ** C 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 678 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.058183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.045270 restraints weight = 94220.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.046767 restraints weight = 56185.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.047758 restraints weight = 39298.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.048418 restraints weight = 30609.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.048891 restraints weight = 25693.802| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 12655 Z= 0.149 Angle : 0.783 12.272 17379 Z= 0.373 Chirality : 0.051 0.244 1943 Planarity : 0.005 0.069 1998 Dihedral : 13.081 75.015 2241 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.42 % Favored : 87.58 % Rotamer: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.30 (0.22), residues: 1312 helix: -0.41 (0.23), residues: 510 sheet: -2.05 (0.61), residues: 56 loop : -3.74 (0.20), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1000 TYR 0.036 0.002 TYR A 872 PHE 0.017 0.002 PHE A1343 TRP 0.018 0.001 TRP C 665 HIS 0.012 0.001 HIS A 774 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 (12655) covalent geometry : angle 0.78331 / 0.37 (17379) hydrogen bonds : bond 0.04692 / 2.93 ( 449) hydrogen bonds : angle 5.56001 / 3.82 ( 1220) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 562 ARG cc_start: 0.7323 (tpp-160) cc_final: 0.7005 (tpp80) REVERT: A 722 MET cc_start: 0.8898 (tmm) cc_final: 0.8629 (tmm) REVERT: A 897 MET cc_start: 0.7947 (ttp) cc_final: 0.7738 (ttp) REVERT: A 1011 MET cc_start: 0.9053 (mmm) cc_final: 0.8785 (tpp) REVERT: A 1146 MET cc_start: 0.8710 (mpp) cc_final: 0.8390 (mpp) REVERT: A 1235 GLU cc_start: 0.9469 (mt-10) cc_final: 0.9078 (mm-30) REVERT: A 1241 MET cc_start: 0.9418 (mmm) cc_final: 0.9034 (mmt) REVERT: A 1308 ARG cc_start: 0.8199 (ptt180) cc_final: 0.7820 (ptm160) REVERT: A 1322 MET cc_start: 0.9029 (ttt) cc_final: 0.8707 (ttt) REVERT: C 501 LYS cc_start: 0.6527 (ptmm) cc_final: 0.5621 (mmtm) REVERT: C 520 MET cc_start: 0.8386 (mtp) cc_final: 0.7974 (ttm) REVERT: C 697 MET cc_start: 0.7883 (ptt) cc_final: 0.7476 (ptt) REVERT: B 520 MET cc_start: 0.8913 (ttp) cc_final: 0.8473 (ppp) REVERT: B 521 GLN cc_start: 0.9428 (mm110) cc_final: 0.8706 (tm-30) REVERT: B 697 MET cc_start: 0.8683 (mmm) cc_final: 0.8444 (mmt) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.0980 time to fit residues: 19.2354 Evaluate side-chains 96 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 4 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 9 optimal weight: 7.9990 chunk 88 optimal weight: 0.4980 chunk 107 optimal weight: 4.9990 chunk 70 optimal weight: 6.9990 chunk 54 optimal weight: 9.9990 chunk 92 optimal weight: 10.0000 chunk 75 optimal weight: 2.9990 chunk 110 optimal weight: 20.0000 chunk 50 optimal weight: 0.8980 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 934 HIS ** A1026 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.057324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.044562 restraints weight = 95150.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.045921 restraints weight = 59414.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.046853 restraints weight = 42757.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.047480 restraints weight = 33854.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.047913 restraints weight = 28714.232| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12655 Z= 0.173 Angle : 0.791 11.776 17379 Z= 0.376 Chirality : 0.050 0.237 1943 Planarity : 0.005 0.069 1998 Dihedral : 12.859 75.775 2241 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.87 % Favored : 86.13 % Rotamer: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.13 (0.22), residues: 1312 helix: -0.28 (0.23), residues: 516 sheet: -1.45 (0.73), residues: 45 loop : -3.69 (0.20), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1000 TYR 0.038 0.002 TYR A 872 PHE 0.018 0.002 PHE A 604 TRP 0.031 0.002 TRP A 725 HIS 0.007 0.001 HIS A1294 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 (12655) covalent geometry : angle 0.79115 / 0.38 (17379) hydrogen bonds : bond 0.04652 / 2.90 ( 449) hydrogen bonds : angle 5.44517 / 3.73 ( 1220) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 636 MET cc_start: 0.8750 (tpt) cc_final: 0.8492 (tpp) REVERT: A 682 MET cc_start: 0.7735 (tmm) cc_final: 0.7143 (tmm) REVERT: A 722 MET cc_start: 0.8990 (tmm) cc_final: 0.8696 (tmm) REVERT: A 740 MET cc_start: 0.7901 (tpp) cc_final: 0.7424 (tpp) REVERT: A 862 MET cc_start: 0.8984 (mmm) cc_final: 0.8752 (mmm) REVERT: A 897 MET cc_start: 0.8265 (ttp) cc_final: 0.7813 (ttp) REVERT: A 1011 MET cc_start: 0.9014 (mmm) cc_final: 0.8759 (tpp) REVERT: A 1022 MET cc_start: 0.8628 (ptp) cc_final: 0.8217 (ptp) REVERT: A 1040 MET cc_start: 0.9083 (mmt) cc_final: 0.8742 (mmt) REVERT: A 1241 MET cc_start: 0.9398 (mmm) cc_final: 0.9009 (mmt) REVERT: A 1308 ARG cc_start: 0.8171 (ptt180) cc_final: 0.7797 (ptm160) REVERT: A 1322 MET cc_start: 0.9029 (ttt) cc_final: 0.8779 (ttt) REVERT: C 501 LYS cc_start: 0.6409 (ptmm) cc_final: 0.5854 (mmtm) REVERT: C 520 MET cc_start: 0.8257 (mtp) cc_final: 0.7883 (ttm) REVERT: C 697 MET cc_start: 0.7866 (ptt) cc_final: 0.7532 (ptt) REVERT: B 521 GLN cc_start: 0.9432 (mm110) cc_final: 0.7978 (tm-30) REVERT: B 682 GLN cc_start: 0.8916 (mm110) cc_final: 0.8596 (mt0) REVERT: B 697 MET cc_start: 0.8607 (mmm) cc_final: 0.8250 (tpt) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.0942 time to fit residues: 16.9236 Evaluate side-chains 89 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 102 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 93 optimal weight: 20.0000 chunk 121 optimal weight: 8.9990 chunk 125 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 chunk 99 optimal weight: 0.5980 chunk 116 optimal weight: 10.0000 chunk 97 optimal weight: 6.9990 chunk 2 optimal weight: 20.0000 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1026 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.055852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.043153 restraints weight = 96710.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.044468 restraints weight = 60493.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.045354 restraints weight = 43728.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.045960 restraints weight = 34833.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.046379 restraints weight = 29691.846| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 12655 Z= 0.231 Angle : 0.851 11.404 17379 Z= 0.408 Chirality : 0.052 0.254 1943 Planarity : 0.006 0.068 1998 Dihedral : 12.831 77.096 2241 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 19.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.17 % Favored : 84.83 % Rotamer: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.14 (0.22), residues: 1312 helix: -0.29 (0.23), residues: 514 sheet: -1.45 (0.75), residues: 45 loop : -3.68 (0.20), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1000 TYR 0.052 0.002 TYR A 872 PHE 0.017 0.002 PHE A1343 TRP 0.025 0.002 TRP A 725 HIS 0.010 0.001 HIS A 859 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.23 (12655) covalent geometry : angle 0.85056 / 0.41 (17379) hydrogen bonds : bond 0.05166 / 3.24 ( 449) hydrogen bonds : angle 5.59424 / 3.84 ( 1220) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 682 MET cc_start: 0.7912 (tmm) cc_final: 0.7616 (tmm) REVERT: A 722 MET cc_start: 0.8893 (tmm) cc_final: 0.8581 (tmm) REVERT: A 740 MET cc_start: 0.8034 (tpp) cc_final: 0.7468 (tpp) REVERT: A 897 MET cc_start: 0.8292 (ttp) cc_final: 0.7905 (ttp) REVERT: A 1011 MET cc_start: 0.8995 (mmm) cc_final: 0.8746 (tpp) REVERT: A 1022 MET cc_start: 0.8687 (ptp) cc_final: 0.8403 (ptp) REVERT: A 1040 MET cc_start: 0.8958 (mmt) cc_final: 0.8121 (mmt) REVERT: A 1241 MET cc_start: 0.9349 (mmm) cc_final: 0.9008 (mmt) REVERT: A 1308 ARG cc_start: 0.8100 (ptt180) cc_final: 0.7763 (ptm160) REVERT: A 1322 MET cc_start: 0.9084 (ttt) cc_final: 0.8814 (ttt) REVERT: C 501 LYS cc_start: 0.6560 (ptmm) cc_final: 0.5851 (mmtm) REVERT: C 514 CYS cc_start: 0.9644 (m) cc_final: 0.9438 (m) REVERT: C 520 MET cc_start: 0.8376 (mtp) cc_final: 0.8027 (ttp) REVERT: C 697 MET cc_start: 0.7815 (ptt) cc_final: 0.7484 (ptt) REVERT: B 520 MET cc_start: 0.9006 (ttp) cc_final: 0.8164 (ttp) REVERT: B 682 GLN cc_start: 0.8920 (mm110) cc_final: 0.8656 (mt0) REVERT: B 697 MET cc_start: 0.8705 (mmm) cc_final: 0.8364 (tpt) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.0821 time to fit residues: 14.2363 Evaluate side-chains 83 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 132 optimal weight: 9.9990 chunk 10 optimal weight: 0.9990 chunk 62 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 135 optimal weight: 10.0000 chunk 122 optimal weight: 10.0000 chunk 101 optimal weight: 9.9990 chunk 128 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1026 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 632 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.056064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.043293 restraints weight = 95798.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.044623 restraints weight = 59832.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.045525 restraints weight = 43051.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.046140 restraints weight = 34200.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.046567 restraints weight = 29097.377| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 12655 Z= 0.204 Angle : 0.814 11.732 17379 Z= 0.390 Chirality : 0.051 0.266 1943 Planarity : 0.005 0.068 1998 Dihedral : 12.667 77.655 2241 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 17.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 14.94 % Favored : 84.98 % Rotamer: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.05 (0.22), residues: 1312 helix: -0.27 (0.23), residues: 523 sheet: -1.50 (0.68), residues: 57 loop : -3.63 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 548 TYR 0.054 0.002 TYR A 872 PHE 0.022 0.002 PHE B 598 TRP 0.020 0.002 TRP A 725 HIS 0.008 0.001 HIS A 983 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.20 (12655) covalent geometry : angle 0.81436 / 0.39 (17379) hydrogen bonds : bond 0.04856 / 3.02 ( 449) hydrogen bonds : angle 5.45961 / 3.75 ( 1220) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 682 MET cc_start: 0.7901 (tmm) cc_final: 0.7656 (tmm) REVERT: A 722 MET cc_start: 0.8638 (tmm) cc_final: 0.8404 (tmm) REVERT: A 740 MET cc_start: 0.8134 (tpp) cc_final: 0.7707 (tpp) REVERT: A 848 TRP cc_start: 0.7871 (m-90) cc_final: 0.7626 (m-90) REVERT: A 862 MET cc_start: 0.9054 (mmm) cc_final: 0.8741 (mmm) REVERT: A 937 MET cc_start: 0.4338 (mpp) cc_final: 0.3887 (mpp) REVERT: A 1011 MET cc_start: 0.9045 (mmm) cc_final: 0.8813 (tpp) REVERT: A 1022 MET cc_start: 0.8746 (ptp) cc_final: 0.8503 (ptp) REVERT: A 1040 MET cc_start: 0.8997 (mmt) cc_final: 0.8211 (mmt) REVERT: A 1146 MET cc_start: 0.8888 (mpp) cc_final: 0.8423 (mpp) REVERT: A 1241 MET cc_start: 0.9387 (mmm) cc_final: 0.9022 (mmt) REVERT: A 1308 ARG cc_start: 0.8117 (ptt180) cc_final: 0.7747 (ptm160) REVERT: A 1322 MET cc_start: 0.9074 (ttt) cc_final: 0.8793 (ttt) REVERT: C 501 LYS cc_start: 0.7211 (pptt) cc_final: 0.6596 (mmtm) REVERT: C 520 MET cc_start: 0.8412 (mtp) cc_final: 0.7919 (mmm) REVERT: C 530 TYR cc_start: 0.8541 (m-80) cc_final: 0.7683 (m-80) REVERT: C 697 MET cc_start: 0.7800 (ptt) cc_final: 0.7496 (ptt) REVERT: B 520 MET cc_start: 0.8989 (ttp) cc_final: 0.8186 (ttp) REVERT: B 682 GLN cc_start: 0.8921 (mm110) cc_final: 0.8668 (mt0) REVERT: B 697 MET cc_start: 0.8588 (mmm) cc_final: 0.8196 (tpt) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.0928 time to fit residues: 15.9301 Evaluate side-chains 86 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 88 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 86 optimal weight: 6.9990 chunk 127 optimal weight: 9.9990 chunk 117 optimal weight: 20.0000 chunk 98 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 chunk 95 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 chunk 18 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 812 GLN ** A1026 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 632 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.055131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.042489 restraints weight = 97320.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.043778 restraints weight = 60937.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.044650 restraints weight = 44117.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.045220 restraints weight = 35244.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.045623 restraints weight = 30215.214| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 12655 Z= 0.245 Angle : 0.863 12.495 17379 Z= 0.414 Chirality : 0.052 0.293 1943 Planarity : 0.006 0.067 1998 Dihedral : 12.610 78.670 2241 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 20.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.32 % Favored : 84.68 % Rotamer: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.07 (0.22), residues: 1312 helix: -0.21 (0.23), residues: 514 sheet: -1.62 (0.71), residues: 52 loop : -3.65 (0.21), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 548 TYR 0.064 0.002 TYR A 872 PHE 0.024 0.002 PHE A1343 TRP 0.017 0.002 TRP A 725 HIS 0.009 0.001 HIS A 983 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.25 (12655) covalent geometry : angle 0.86267 / 0.41 (17379) hydrogen bonds : bond 0.05256 / 3.28 ( 449) hydrogen bonds : angle 5.59300 / 3.84 ( 1220) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 636 MET cc_start: 0.8625 (tpt) cc_final: 0.8225 (tpp) REVERT: A 722 MET cc_start: 0.8665 (tmm) cc_final: 0.8398 (tmm) REVERT: A 740 MET cc_start: 0.7923 (tpp) cc_final: 0.7515 (tpp) REVERT: A 897 MET cc_start: 0.8349 (ttp) cc_final: 0.8146 (ttp) REVERT: A 937 MET cc_start: 0.4255 (mpp) cc_final: 0.3826 (mpp) REVERT: A 1011 MET cc_start: 0.8997 (mmm) cc_final: 0.8794 (tpp) REVERT: A 1022 MET cc_start: 0.8742 (ptp) cc_final: 0.8513 (ptp) REVERT: A 1040 MET cc_start: 0.8994 (mmt) cc_final: 0.8355 (mmt) REVERT: A 1235 GLU cc_start: 0.9457 (mt-10) cc_final: 0.9255 (mm-30) REVERT: A 1241 MET cc_start: 0.9362 (mmm) cc_final: 0.9009 (mmt) REVERT: A 1308 ARG cc_start: 0.8022 (ptt180) cc_final: 0.7668 (ptt180) REVERT: A 1322 MET cc_start: 0.9104 (ttt) cc_final: 0.8843 (ttt) REVERT: C 501 LYS cc_start: 0.7255 (pptt) cc_final: 0.6007 (ptpt) REVERT: C 520 MET cc_start: 0.8457 (mtp) cc_final: 0.7973 (mmm) REVERT: C 697 MET cc_start: 0.7869 (ptt) cc_final: 0.7566 (ptt) REVERT: B 682 GLN cc_start: 0.9004 (mm110) cc_final: 0.8801 (mt0) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.0845 time to fit residues: 13.6424 Evaluate side-chains 84 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 15 optimal weight: 4.9990 chunk 128 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 14 optimal weight: 0.1980 chunk 119 optimal weight: 0.0980 chunk 35 optimal weight: 5.9990 chunk 116 optimal weight: 4.9990 chunk 133 optimal weight: 9.9990 chunk 50 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 63 optimal weight: 9.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 680 HIS A 812 GLN ** A1026 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1080 ASN ** A1120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 495 GLN ** C 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.056943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.044247 restraints weight = 94369.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.045610 restraints weight = 58874.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.046541 restraints weight = 42330.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.047169 restraints weight = 33564.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.047602 restraints weight = 28477.273| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 12655 Z= 0.150 Angle : 0.795 12.855 17379 Z= 0.375 Chirality : 0.050 0.292 1943 Planarity : 0.005 0.068 1998 Dihedral : 12.348 78.413 2241 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.87 % Favored : 86.13 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.85 (0.23), residues: 1312 helix: 0.02 (0.23), residues: 513 sheet: -1.40 (0.69), residues: 57 loop : -3.59 (0.21), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 548 TYR 0.052 0.002 TYR A 872 PHE 0.029 0.002 PHE A 970 TRP 0.016 0.001 TRP B 665 HIS 0.006 0.001 HIS A 859 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (12655) covalent geometry : angle 0.79502 / 0.37 (17379) hydrogen bonds : bond 0.04555 / 2.79 ( 449) hydrogen bonds : angle 5.26566 / 3.62 ( 1220) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 740 MET cc_start: 0.8086 (tpp) cc_final: 0.7825 (tpp) REVERT: A 862 MET cc_start: 0.8949 (mmm) cc_final: 0.8613 (mmm) REVERT: A 897 MET cc_start: 0.8247 (ttp) cc_final: 0.7902 (tmm) REVERT: A 937 MET cc_start: 0.4268 (mpp) cc_final: 0.3288 (mtt) REVERT: A 1011 MET cc_start: 0.8978 (mmm) cc_final: 0.8761 (tpp) REVERT: A 1022 MET cc_start: 0.8763 (ptp) cc_final: 0.8353 (ptp) REVERT: A 1040 MET cc_start: 0.9052 (mmt) cc_final: 0.8435 (mmt) REVERT: A 1146 MET cc_start: 0.8894 (mpp) cc_final: 0.8507 (mpp) REVERT: A 1235 GLU cc_start: 0.9439 (mt-10) cc_final: 0.9218 (mm-30) REVERT: A 1241 MET cc_start: 0.9420 (mmm) cc_final: 0.9011 (mmt) REVERT: A 1258 TRP cc_start: 0.8099 (t60) cc_final: 0.7516 (t-100) REVERT: A 1308 ARG cc_start: 0.8154 (ptt180) cc_final: 0.7795 (ptm160) REVERT: A 1322 MET cc_start: 0.9015 (ttt) cc_final: 0.8717 (ttt) REVERT: C 501 LYS cc_start: 0.7707 (pptt) cc_final: 0.6886 (ptpt) REVERT: C 520 MET cc_start: 0.8433 (mtp) cc_final: 0.7959 (mmm) REVERT: C 697 MET cc_start: 0.7791 (ptt) cc_final: 0.7498 (ptt) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.0902 time to fit residues: 16.1077 Evaluate side-chains 89 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 17 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 111 optimal weight: 30.0000 chunk 118 optimal weight: 4.9990 chunk 136 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 95 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 812 GLN ** A1026 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1173 HIS ** A1187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 521 GLN B 685 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.055757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.042995 restraints weight = 95759.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.044361 restraints weight = 59395.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.045267 restraints weight = 42622.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.045894 restraints weight = 33774.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.046320 restraints weight = 28687.941| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 12655 Z= 0.212 Angle : 0.839 12.688 17379 Z= 0.400 Chirality : 0.051 0.306 1943 Planarity : 0.005 0.069 1998 Dihedral : 12.333 79.428 2241 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 18.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.32 % Favored : 84.68 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.89 (0.22), residues: 1312 helix: -0.02 (0.23), residues: 512 sheet: -1.22 (0.85), residues: 42 loop : -3.57 (0.20), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1000 TYR 0.067 0.002 TYR A 872 PHE 0.031 0.002 PHE A 970 TRP 0.015 0.001 TRP A 725 HIS 0.007 0.001 HIS A 983 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.21 (12655) covalent geometry : angle 0.83937 / 0.40 (17379) hydrogen bonds : bond 0.04990 / 3.08 ( 449) hydrogen bonds : angle 5.39439 / 3.71 ( 1220) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 740 MET cc_start: 0.7791 (tpp) cc_final: 0.7573 (tpp) REVERT: A 862 MET cc_start: 0.8921 (mmm) cc_final: 0.8655 (mmm) REVERT: A 897 MET cc_start: 0.8307 (ttp) cc_final: 0.8047 (ttp) REVERT: A 935 MET cc_start: 0.3352 (tpp) cc_final: 0.2899 (tpp) REVERT: A 937 MET cc_start: 0.4299 (mpp) cc_final: 0.3571 (mtt) REVERT: A 1011 MET cc_start: 0.8939 (mmm) cc_final: 0.8714 (tpp) REVERT: A 1040 MET cc_start: 0.9043 (mmt) cc_final: 0.8516 (mmt) REVERT: A 1146 MET cc_start: 0.8856 (mpp) cc_final: 0.8446 (mpp) REVERT: A 1235 GLU cc_start: 0.9419 (mt-10) cc_final: 0.9206 (mm-30) REVERT: A 1241 MET cc_start: 0.9472 (mmm) cc_final: 0.9059 (tpp) REVERT: A 1308 ARG cc_start: 0.8030 (ptt180) cc_final: 0.7758 (ptm160) REVERT: A 1322 MET cc_start: 0.9087 (ttt) cc_final: 0.8826 (ttt) REVERT: C 501 LYS cc_start: 0.7322 (pptt) cc_final: 0.6515 (ptpt) REVERT: C 514 CYS cc_start: 0.9540 (m) cc_final: 0.9329 (m) REVERT: C 520 MET cc_start: 0.8451 (mtp) cc_final: 0.7964 (mmm) REVERT: C 697 MET cc_start: 0.7833 (ptt) cc_final: 0.7472 (ptt) REVERT: B 520 MET cc_start: 0.8938 (ppp) cc_final: 0.8488 (ppp) REVERT: B 521 GLN cc_start: 0.9633 (mm-40) cc_final: 0.8481 (tm-30) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.0862 time to fit residues: 14.3467 Evaluate side-chains 89 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 47 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 38 optimal weight: 9.9990 chunk 24 optimal weight: 0.0870 chunk 45 optimal weight: 0.7980 chunk 49 optimal weight: 9.9990 chunk 43 optimal weight: 0.0010 chunk 26 optimal weight: 0.1980 chunk 70 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 overall best weight: 0.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 HIS A 663 ASN A 701 GLN ** A 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 812 GLN ** A1026 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1042 ASN A1105 GLN ** A1187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 632 HIS C 736 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.059245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.046693 restraints weight = 94745.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.048078 restraints weight = 60026.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.049009 restraints weight = 43301.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.049651 restraints weight = 34351.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.050088 restraints weight = 29112.494| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 12655 Z= 0.128 Angle : 0.782 12.262 17379 Z= 0.365 Chirality : 0.050 0.297 1943 Planarity : 0.005 0.070 1998 Dihedral : 11.954 78.281 2241 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.20 % Favored : 87.80 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.76 (0.22), residues: 1312 helix: 0.01 (0.23), residues: 524 sheet: -0.74 (0.85), residues: 41 loop : -3.51 (0.20), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 548 TYR 0.039 0.001 TYR A 872 PHE 0.021 0.002 PHE A 970 TRP 0.016 0.001 TRP B 665 HIS 0.007 0.001 HIS A 774 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (12655) covalent geometry : angle 0.78246 / 0.37 (17379) hydrogen bonds : bond 0.04292 / 2.61 ( 449) hydrogen bonds : angle 4.99980 / 3.39 ( 1220) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 618 CYS cc_start: 0.8537 (t) cc_final: 0.8322 (t) REVERT: A 636 MET cc_start: 0.8096 (mmt) cc_final: 0.7691 (tpp) REVERT: A 699 MET cc_start: 0.8842 (mmp) cc_final: 0.8555 (mmp) REVERT: A 862 MET cc_start: 0.8960 (mmm) cc_final: 0.8645 (mmm) REVERT: A 937 MET cc_start: 0.4269 (mpp) cc_final: 0.3411 (mtt) REVERT: A 1011 MET cc_start: 0.8907 (mmm) cc_final: 0.8678 (tpp) REVERT: A 1022 MET cc_start: 0.8549 (ptp) cc_final: 0.8282 (ptp) REVERT: A 1146 MET cc_start: 0.8840 (mpp) cc_final: 0.8427 (mpp) REVERT: A 1235 GLU cc_start: 0.9411 (mt-10) cc_final: 0.9133 (mm-30) REVERT: A 1241 MET cc_start: 0.9656 (mmm) cc_final: 0.9279 (tpp) REVERT: A 1322 MET cc_start: 0.8966 (ttt) cc_final: 0.8737 (ttt) REVERT: C 514 CYS cc_start: 0.9486 (m) cc_final: 0.9282 (m) REVERT: C 520 MET cc_start: 0.8513 (mtp) cc_final: 0.8188 (ttm) REVERT: C 697 MET cc_start: 0.8022 (ptt) cc_final: 0.7686 (ptt) REVERT: B 520 MET cc_start: 0.8836 (ppp) cc_final: 0.8434 (ppp) REVERT: B 521 GLN cc_start: 0.9655 (mm-40) cc_final: 0.8746 (tm-30) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.0938 time to fit residues: 17.3316 Evaluate side-chains 88 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 131 optimal weight: 4.9990 chunk 106 optimal weight: 9.9990 chunk 68 optimal weight: 20.0000 chunk 21 optimal weight: 0.0570 chunk 87 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 110 optimal weight: 8.9990 chunk 17 optimal weight: 6.9990 overall best weight: 3.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 830 GLN ** A1026 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.057357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.044753 restraints weight = 95614.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.046067 restraints weight = 61048.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.046951 restraints weight = 44344.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.047569 restraints weight = 35362.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.047987 restraints weight = 30140.193| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.4339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12655 Z= 0.179 Angle : 0.803 12.885 17379 Z= 0.381 Chirality : 0.050 0.311 1943 Planarity : 0.005 0.069 1998 Dihedral : 11.928 79.691 2241 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.03 % Favored : 86.97 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.76 (0.22), residues: 1312 helix: 0.12 (0.23), residues: 518 sheet: -1.06 (0.75), residues: 52 loop : -3.58 (0.20), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1000 TYR 0.057 0.002 TYR A 872 PHE 0.020 0.002 PHE A 970 TRP 0.012 0.001 TRP B 665 HIS 0.007 0.001 HIS A 774 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.18 (12655) covalent geometry : angle 0.80266 / 0.38 (17379) hydrogen bonds : bond 0.04640 / 2.85 ( 449) hydrogen bonds : angle 5.10867 / 3.50 ( 1220) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1851.41 seconds wall clock time: 33 minutes 6.73 seconds (1986.73 seconds total)