Starting phenix.real_space_refine on Thu Feb 15 12:13:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v5c_21052/02_2024/6v5c_21052.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v5c_21052/02_2024/6v5c_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v5c_21052/02_2024/6v5c_21052.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v5c_21052/02_2024/6v5c_21052.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v5c_21052/02_2024/6v5c_21052.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v5c_21052/02_2024/6v5c_21052.pdb" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 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 Residue "A ARG 440": "NH1" <-> "NH2" Residue "A ARG 544": "NH1" <-> "NH2" Residue "A PHE 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 736": "OE1" <-> "OE2" Residue "A ARG 938": "NH1" <-> "NH2" Residue "A GLU 966": "OE1" <-> "OE2" Residue "A GLU 992": "OE1" <-> "OE2" Residue "A GLU 1017": "OE1" <-> "OE2" Residue "A ARG 1032": "NH1" <-> "NH2" Residue "A ARG 1131": "NH1" <-> "NH2" Residue "A ARG 1213": "NH1" <-> "NH2" Residue "A ARG 1248": "NH1" <-> "NH2" Residue "A GLU 1251": "OE1" <-> "OE2" Residue "A ARG 1273": "NH1" <-> "NH2" Residue "A ARG 1296": "NH1" <-> "NH2" Residue "A ARG 1342": "NH1" <-> "NH2" Residue "A ARG 1349": "NH1" <-> "NH2" Residue "C GLU 502": "OE1" <-> "OE2" Residue "C GLU 534": "OE1" <-> "OE2" Residue "C ARG 570": "NH1" <-> "NH2" Residue "C GLU 574": "OE1" <-> "OE2" Residue "C ASP 579": "OD1" <-> "OD2" Residue "C GLU 594": "OE1" <-> "OE2" Residue "C GLU 626": "OE1" <-> "OE2" Residue "C ARG 670": "NH1" <-> "NH2" Residue "C GLU 737": "OE1" <-> "OE2" Residue "C GLU 748": "OE1" <-> "OE2" Residue "C ARG 750": "NH1" <-> "NH2" Residue "B GLU 502": "OE1" <-> "OE2" Residue "B GLU 512": "OE1" <-> "OE2" Residue "B GLU 536": "OE1" <-> "OE2" Residue "B PHE 641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 745": "OE1" <-> "OE2" Residue "B ARG 746": "NH1" <-> "NH2" Residue "B GLU 747": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 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: {'RNA': 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: 6.59, per 1000 atoms: 0.54 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.15 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 3.66 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: 4.09 Time building geometry restraints manager: 5.52 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: 97.25 - 105.97: 625 105.97 - 114.68: 7591 114.68 - 123.40: 8358 123.40 - 132.11: 772 132.11 - 140.83: 33 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 - 18.29: 6535 18.29 - 36.58: 870 36.58 - 54.87: 222 54.87 - 73.16: 124 73.16 - 91.46: 22 Dihedral angle restraints: 7773 sinusoidal: 3870 harmonic: 3903 Sorted by residual: dihedral pdb=" CA ASN B 668 " pdb=" C ASN B 668 " pdb=" N LYS B 669 " pdb=" CA LYS B 669 " ideal model delta harmonic sigma weight residual -180.00 -143.52 -36.48 0 5.00e+00 4.00e-02 5.32e+01 dihedral pdb=" CA VAL A 773 " pdb=" C VAL A 773 " pdb=" N HIS A 774 " pdb=" CA HIS A 774 " ideal model delta harmonic sigma weight residual 180.00 144.62 35.38 0 5.00e+00 4.00e-02 5.01e+01 dihedral pdb=" CA HIS A 983 " pdb=" C HIS A 983 " pdb=" N LEU A 984 " pdb=" CA LEU A 984 " ideal model delta harmonic sigma weight residual 180.00 146.50 33.50 0 5.00e+00 4.00e-02 4.49e+01 ... (remaining 7770 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 1845 0.128 - 0.257: 84 0.257 - 0.385: 5 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 2.520 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 2.520 ... (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 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: 0.750 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: 4.240 Check model and map are aligned: 0.170 Set scattering table: 0.120 Process input model: 35.970 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 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= 0.453 Angle : 1.265 18.044 17379 Z= 0.723 Chirality : 0.071 0.642 1943 Planarity : 0.008 0.085 1998 Dihedral : 19.090 91.456 5243 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.86 (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 TRP 0.043 0.003 TRP A1258 HIS 0.011 0.002 HIS A 573 PHE 0.024 0.003 PHE A 631 TYR 0.050 0.003 TYR C 621 ARG 0.010 0.001 ARG A 548 *********************** 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 fitting. rotamer outliers: 22 poor density : 129 time to evaluate : 1.396 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: 0.8214 (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: 0.2327 time to fit residues: 51.9470 Evaluate side-chains 108 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 95 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 10.0000 chunk 104 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 chunk 35 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 55 optimal weight: 8.9990 chunk 108 optimal weight: 20.0000 chunk 41 optimal weight: 0.9990 chunk 65 optimal weight: 20.0000 chunk 80 optimal weight: 6.9990 chunk 125 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN A 964 HIS ** A1026 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** C 736 GLN ** B 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 625 HIS B 660 HIS B 678 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12655 Z= 0.224 Angle : 0.734 11.972 17379 Z= 0.376 Chirality : 0.043 0.220 1943 Planarity : 0.006 0.067 1998 Dihedral : 17.544 86.298 2469 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 18.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.80 % Favored : 87.12 % Rotamer: Outliers : 0.25 % Allowed : 6.12 % Favored : 93.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.82 (0.21), residues: 1312 helix: -1.01 (0.22), residues: 523 sheet: -2.51 (0.59), residues: 50 loop : -3.92 (0.19), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 665 HIS 0.008 0.001 HIS A1026 PHE 0.019 0.002 PHE A1343 TYR 0.027 0.001 TYR A 872 ARG 0.007 0.000 ARG A 548 *********************** 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 127 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 124 time to evaluate : 1.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 722 MET cc_start: 0.8828 (tmm) cc_final: 0.8552 (tmm) REVERT: A 848 TRP cc_start: 0.8004 (m-90) cc_final: 0.7633 (m-90) REVERT: A 897 MET cc_start: 0.8307 (ttp) cc_final: 0.7880 (ttp) REVERT: A 920 CYS cc_start: 0.8287 (p) cc_final: 0.8023 (p) REVERT: A 1011 MET cc_start: 0.9007 (mmm) cc_final: 0.8760 (tpp) REVERT: A 1146 MET cc_start: 0.8689 (mpp) cc_final: 0.8369 (mpp) REVERT: A 1235 GLU cc_start: 0.9451 (mt-10) cc_final: 0.9088 (mm-30) REVERT: A 1241 MET cc_start: 0.9337 (mmm) cc_final: 0.8988 (mmt) REVERT: A 1322 MET cc_start: 0.9024 (ttt) cc_final: 0.8735 (ttt) REVERT: C 494 VAL cc_start: 0.6538 (m) cc_final: 0.6124 (t) REVERT: C 520 MET cc_start: 0.8410 (mtp) cc_final: 0.8012 (ttm) REVERT: C 697 MET cc_start: 0.7835 (ptt) cc_final: 0.7468 (ptt) outliers start: 3 outliers final: 0 residues processed: 127 average time/residue: 0.2262 time to fit residues: 42.8191 Evaluate side-chains 98 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 69 optimal weight: 9.9990 chunk 38 optimal weight: 20.0000 chunk 104 optimal weight: 9.9990 chunk 85 optimal weight: 5.9990 chunk 34 optimal weight: 10.0000 chunk 125 optimal weight: 9.9990 chunk 135 optimal weight: 10.0000 chunk 111 optimal weight: 20.0000 chunk 124 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 100 optimal weight: 0.1980 overall best weight: 4.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 12655 Z= 0.314 Angle : 0.766 11.689 17379 Z= 0.393 Chirality : 0.043 0.181 1943 Planarity : 0.006 0.065 1998 Dihedral : 17.627 87.639 2469 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 24.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.41 % Favored : 85.59 % Rotamer: Outliers : 0.08 % Allowed : 7.63 % Favored : 92.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.47 (0.22), residues: 1312 helix: -0.55 (0.22), residues: 526 sheet: -2.20 (0.52), residues: 74 loop : -3.93 (0.20), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 665 HIS 0.014 0.002 HIS A 774 PHE 0.018 0.002 PHE B 598 TYR 0.041 0.002 TYR A 872 ARG 0.008 0.001 ARG A1000 *********************** 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 117 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 116 time to evaluate : 1.418 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 722 MET cc_start: 0.8807 (tmm) cc_final: 0.8492 (tmm) REVERT: A 848 TRP cc_start: 0.8053 (m-90) cc_final: 0.7801 (m-90) REVERT: A 862 MET cc_start: 0.9148 (tpt) cc_final: 0.8909 (mmm) REVERT: A 897 MET cc_start: 0.8262 (ttp) cc_final: 0.7993 (ttp) REVERT: A 937 MET cc_start: 0.4031 (mpp) cc_final: 0.3543 (mpp) REVERT: A 1011 MET cc_start: 0.8994 (mmm) cc_final: 0.8718 (tpp) REVERT: A 1146 MET cc_start: 0.8767 (mpp) cc_final: 0.8389 (mpp) REVERT: A 1235 GLU cc_start: 0.9528 (mt-10) cc_final: 0.9148 (mm-30) REVERT: A 1241 MET cc_start: 0.9378 (mmm) cc_final: 0.9053 (mmt) REVERT: A 1322 MET cc_start: 0.9045 (ttt) cc_final: 0.8742 (ttt) REVERT: C 520 MET cc_start: 0.8404 (mtp) cc_final: 0.7844 (mmm) REVERT: C 697 MET cc_start: 0.7818 (ptt) cc_final: 0.7485 (ptt) REVERT: B 682 GLN cc_start: 0.8798 (mm110) cc_final: 0.8436 (mt0) REVERT: B 697 MET cc_start: 0.8734 (mmm) cc_final: 0.8410 (tpt) outliers start: 1 outliers final: 0 residues processed: 117 average time/residue: 0.2105 time to fit residues: 38.0774 Evaluate side-chains 90 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 124 optimal weight: 8.9990 chunk 94 optimal weight: 0.9980 chunk 65 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 chunk 125 optimal weight: 0.3980 chunk 133 optimal weight: 10.0000 chunk 119 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 111 optimal weight: 40.0000 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 934 HIS A1080 ASN ** 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 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12655 Z= 0.172 Angle : 0.666 11.345 17379 Z= 0.333 Chirality : 0.041 0.190 1943 Planarity : 0.005 0.065 1998 Dihedral : 17.161 84.927 2469 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.12 % Favored : 87.88 % Rotamer: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.22), residues: 1312 helix: -0.21 (0.23), residues: 532 sheet: -1.61 (0.61), residues: 52 loop : -3.72 (0.20), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1258 HIS 0.008 0.001 HIS A 774 PHE 0.018 0.002 PHE A1343 TYR 0.037 0.001 TYR A 872 ARG 0.003 0.000 ARG A 548 *********************** 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 136 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 1.381 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 682 MET cc_start: 0.7127 (tmm) cc_final: 0.6924 (tmm) REVERT: A 697 LEU cc_start: 0.8365 (tp) cc_final: 0.8011 (mt) REVERT: A 722 MET cc_start: 0.8812 (tmm) cc_final: 0.8546 (tmm) REVERT: A 848 TRP cc_start: 0.7704 (m-90) cc_final: 0.7211 (m-90) REVERT: A 897 MET cc_start: 0.8116 (ttp) cc_final: 0.7738 (ttp) REVERT: A 937 MET cc_start: 0.4274 (mpp) cc_final: 0.3899 (mpp) REVERT: A 969 GLU cc_start: 0.9360 (pp20) cc_final: 0.9066 (pp20) REVERT: A 973 ASP cc_start: 0.9219 (p0) cc_final: 0.8775 (p0) REVERT: A 1011 MET cc_start: 0.9003 (mmm) cc_final: 0.8754 (tpp) REVERT: A 1022 MET cc_start: 0.8525 (ptp) cc_final: 0.8303 (ptp) REVERT: A 1040 MET cc_start: 0.8983 (mmt) cc_final: 0.8646 (mmt) REVERT: A 1235 GLU cc_start: 0.9431 (mt-10) cc_final: 0.9028 (mm-30) REVERT: A 1241 MET cc_start: 0.9465 (mmm) cc_final: 0.9016 (mmt) REVERT: A 1308 ARG cc_start: 0.8038 (ptt180) cc_final: 0.7671 (ptm160) REVERT: A 1322 MET cc_start: 0.9048 (ttt) cc_final: 0.8722 (ttt) REVERT: A 1330 GLU cc_start: 0.8878 (pt0) cc_final: 0.8521 (pt0) REVERT: C 501 LYS cc_start: 0.6642 (ptmm) cc_final: 0.5600 (mmtm) REVERT: C 520 MET cc_start: 0.8297 (mtp) cc_final: 0.7999 (ttm) REVERT: C 697 MET cc_start: 0.7815 (ptt) cc_final: 0.7529 (ptt) REVERT: B 520 MET cc_start: 0.8762 (ttp) cc_final: 0.7788 (ppp) REVERT: B 697 MET cc_start: 0.8599 (mmm) cc_final: 0.8326 (tpp) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.2382 time to fit residues: 47.6110 Evaluate side-chains 97 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 75 optimal weight: 9.9990 chunk 1 optimal weight: 0.2980 chunk 99 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 113 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 68 optimal weight: 20.0000 chunk 119 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 chunk 44 optimal weight: 5.9990 overall best weight: 4.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1080 ASN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 12655 Z= 0.314 Angle : 0.757 11.775 17379 Z= 0.389 Chirality : 0.044 0.222 1943 Planarity : 0.005 0.059 1998 Dihedral : 17.352 83.921 2469 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 24.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.62 % Favored : 84.38 % Rotamer: Outliers : 0.08 % Allowed : 3.77 % Favored : 96.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.12 (0.22), residues: 1312 helix: -0.24 (0.23), residues: 529 sheet: -1.92 (0.54), residues: 68 loop : -3.75 (0.20), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 725 HIS 0.009 0.001 HIS A 983 PHE 0.017 0.002 PHE A 653 TYR 0.050 0.002 TYR A 872 ARG 0.007 0.001 ARG A1000 *********************** 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 102 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 101 time to evaluate : 1.302 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 848 TRP cc_start: 0.7915 (m-90) cc_final: 0.7612 (m-90) REVERT: A 897 MET cc_start: 0.8231 (ttp) cc_final: 0.7945 (ttp) REVERT: A 937 MET cc_start: 0.4251 (mpp) cc_final: 0.3845 (mpp) REVERT: A 1011 MET cc_start: 0.8985 (mmm) cc_final: 0.8724 (tpp) REVERT: A 1022 MET cc_start: 0.8778 (ptp) cc_final: 0.8275 (ptp) REVERT: A 1040 MET cc_start: 0.9342 (mmm) cc_final: 0.8863 (mmt) REVERT: A 1146 MET cc_start: 0.8821 (mpp) cc_final: 0.8351 (mpp) REVERT: A 1241 MET cc_start: 0.9444 (mmm) cc_final: 0.9076 (mmt) REVERT: A 1308 ARG cc_start: 0.8195 (ptt180) cc_final: 0.7839 (ptt180) REVERT: A 1322 MET cc_start: 0.9058 (ttt) cc_final: 0.8805 (ttt) REVERT: A 1330 GLU cc_start: 0.8977 (pt0) cc_final: 0.8647 (pt0) REVERT: C 501 LYS cc_start: 0.6667 (ptmm) cc_final: 0.6397 (mmtm) REVERT: C 514 CYS cc_start: 0.9446 (m) cc_final: 0.9227 (m) REVERT: C 520 MET cc_start: 0.8338 (mtp) cc_final: 0.7804 (mmm) REVERT: C 697 MET cc_start: 0.7889 (ptt) cc_final: 0.7608 (ptt) REVERT: B 697 MET cc_start: 0.8707 (mmm) cc_final: 0.8262 (tpt) outliers start: 1 outliers final: 0 residues processed: 102 average time/residue: 0.2566 time to fit residues: 39.2645 Evaluate side-chains 86 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 120 optimal weight: 7.9990 chunk 26 optimal weight: 10.0000 chunk 78 optimal weight: 4.9990 chunk 32 optimal weight: 10.0000 chunk 133 optimal weight: 10.0000 chunk 110 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 128 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 567 ASN ** A 680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 826 GLN ** 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 566 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 12655 Z= 0.297 Angle : 0.750 11.655 17379 Z= 0.382 Chirality : 0.044 0.214 1943 Planarity : 0.005 0.060 1998 Dihedral : 17.383 85.301 2469 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 23.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.32 % Favored : 84.68 % Rotamer: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.22), residues: 1312 helix: -0.27 (0.22), residues: 534 sheet: -1.22 (0.67), residues: 50 loop : -3.71 (0.20), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 725 HIS 0.009 0.001 HIS A 983 PHE 0.036 0.002 PHE A 970 TYR 0.057 0.002 TYR A 872 ARG 0.007 0.001 ARG A 548 *********************** 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 97 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 1.375 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 848 TRP cc_start: 0.7912 (m-90) cc_final: 0.7553 (m-90) REVERT: A 897 MET cc_start: 0.8283 (ttp) cc_final: 0.8062 (ttp) REVERT: A 937 MET cc_start: 0.4331 (mpp) cc_final: 0.3458 (mtt) REVERT: A 1011 MET cc_start: 0.9005 (mmm) cc_final: 0.8771 (tpp) REVERT: A 1022 MET cc_start: 0.8739 (ptp) cc_final: 0.8433 (ptp) REVERT: A 1040 MET cc_start: 0.9351 (mmm) cc_final: 0.9104 (mmt) REVERT: A 1146 MET cc_start: 0.8891 (mpp) cc_final: 0.8367 (mpp) REVERT: A 1241 MET cc_start: 0.9464 (mmm) cc_final: 0.9056 (mmt) REVERT: A 1308 ARG cc_start: 0.8125 (ptt180) cc_final: 0.7728 (ptm160) REVERT: A 1322 MET cc_start: 0.9084 (ttt) cc_final: 0.8797 (ttt) REVERT: A 1330 GLU cc_start: 0.9011 (pt0) cc_final: 0.8659 (pt0) REVERT: C 501 LYS cc_start: 0.6656 (ptmm) cc_final: 0.6421 (mmtm) REVERT: C 520 MET cc_start: 0.8377 (mtp) cc_final: 0.7958 (ttm) REVERT: C 697 MET cc_start: 0.7841 (ptt) cc_final: 0.7591 (ptt) REVERT: B 682 GLN cc_start: 0.8785 (mm110) cc_final: 0.8571 (mt0) REVERT: B 697 MET cc_start: 0.8739 (mmm) cc_final: 0.8342 (tpt) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.2497 time to fit residues: 37.1911 Evaluate side-chains 87 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 15 optimal weight: 4.9990 chunk 76 optimal weight: 30.0000 chunk 97 optimal weight: 0.0980 chunk 75 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 chunk 133 optimal weight: 10.0000 chunk 83 optimal weight: 4.9990 chunk 81 optimal weight: 9.9990 chunk 61 optimal weight: 8.9990 chunk 82 optimal weight: 10.0000 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 826 GLN ** 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 B 685 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3528 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= 0.218 Angle : 0.702 12.289 17379 Z= 0.352 Chirality : 0.043 0.220 1943 Planarity : 0.005 0.074 1998 Dihedral : 17.186 83.505 2469 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 20.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.79 % Favored : 85.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.22), residues: 1312 helix: -0.03 (0.23), residues: 531 sheet: -1.35 (0.64), residues: 57 loop : -3.67 (0.21), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 725 HIS 0.009 0.001 HIS B 632 PHE 0.022 0.002 PHE A1343 TYR 0.052 0.002 TYR A 872 ARG 0.006 0.000 ARG A 548 *********************** 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 109 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 697 LEU cc_start: 0.8452 (tp) cc_final: 0.8110 (mt) REVERT: A 848 TRP cc_start: 0.7902 (m-90) cc_final: 0.7532 (m-90) REVERT: A 862 MET cc_start: 0.8825 (mmm) cc_final: 0.8573 (mmm) REVERT: A 937 MET cc_start: 0.4210 (mpp) cc_final: 0.3358 (mtt) REVERT: A 1011 MET cc_start: 0.9008 (mmm) cc_final: 0.8792 (tpp) REVERT: A 1022 MET cc_start: 0.8912 (ptp) cc_final: 0.8433 (ptp) REVERT: A 1040 MET cc_start: 0.9385 (mmm) cc_final: 0.9100 (tpp) REVERT: A 1146 MET cc_start: 0.8849 (mpp) cc_final: 0.8346 (mpp) REVERT: A 1308 ARG cc_start: 0.8175 (ptt180) cc_final: 0.7787 (ptm160) REVERT: A 1322 MET cc_start: 0.9067 (ttt) cc_final: 0.8809 (ttt) REVERT: A 1330 GLU cc_start: 0.8960 (pt0) cc_final: 0.8575 (pt0) REVERT: C 514 CYS cc_start: 0.9425 (m) cc_final: 0.9224 (m) REVERT: C 520 MET cc_start: 0.8405 (mtp) cc_final: 0.7971 (ttm) REVERT: C 697 MET cc_start: 0.7795 (ptt) cc_final: 0.7543 (ptt) REVERT: B 682 GLN cc_start: 0.8775 (mm110) cc_final: 0.8562 (mt0) REVERT: B 697 MET cc_start: 0.8741 (mmm) cc_final: 0.8341 (tpt) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.2114 time to fit residues: 35.6813 Evaluate side-chains 93 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 53 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 chunk 40 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 84 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 65 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 120 optimal weight: 0.0060 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1026 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1080 ASN ** A1187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 632 HIS B 685 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3755 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= 0.187 Angle : 0.691 12.407 17379 Z= 0.342 Chirality : 0.042 0.219 1943 Planarity : 0.005 0.062 1998 Dihedral : 16.878 80.267 2469 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 18.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.96 % Favored : 87.04 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.23), residues: 1312 helix: 0.23 (0.24), residues: 525 sheet: -1.20 (0.65), residues: 57 loop : -3.57 (0.21), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 665 HIS 0.009 0.001 HIS A 859 PHE 0.018 0.002 PHE A1343 TYR 0.048 0.001 TYR A 872 ARG 0.005 0.000 ARG B 696 *********************** 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 115 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 1.479 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 618 CYS cc_start: 0.8476 (t) cc_final: 0.8259 (t) REVERT: A 636 MET cc_start: 0.8406 (mmt) cc_final: 0.7795 (tpp) REVERT: A 697 LEU cc_start: 0.8444 (tp) cc_final: 0.8151 (mt) REVERT: A 848 TRP cc_start: 0.7846 (m-90) cc_final: 0.7461 (m-90) REVERT: A 862 MET cc_start: 0.8771 (mmm) cc_final: 0.8448 (mmm) REVERT: A 937 MET cc_start: 0.4316 (mpp) cc_final: 0.3489 (mtt) REVERT: A 1011 MET cc_start: 0.8962 (mmm) cc_final: 0.8761 (tpp) REVERT: A 1022 MET cc_start: 0.8866 (ptp) cc_final: 0.8262 (ptp) REVERT: A 1040 MET cc_start: 0.9408 (mmm) cc_final: 0.8871 (tpp) REVERT: A 1146 MET cc_start: 0.8854 (mpp) cc_final: 0.8383 (mpp) REVERT: A 1235 GLU cc_start: 0.9452 (mt-10) cc_final: 0.9216 (mm-30) REVERT: A 1241 MET cc_start: 0.9639 (mmt) cc_final: 0.9050 (mmt) REVERT: A 1322 MET cc_start: 0.9031 (ttt) cc_final: 0.8754 (ttt) REVERT: A 1330 GLU cc_start: 0.8891 (pt0) cc_final: 0.8619 (pt0) REVERT: C 514 CYS cc_start: 0.9357 (m) cc_final: 0.9147 (m) REVERT: C 520 MET cc_start: 0.8362 (mtp) cc_final: 0.7829 (mmm) REVERT: C 621 TYR cc_start: 0.9552 (t80) cc_final: 0.9335 (t80) REVERT: B 682 GLN cc_start: 0.8722 (mm110) cc_final: 0.8466 (mt0) REVERT: B 697 MET cc_start: 0.8691 (mmm) cc_final: 0.8278 (tpt) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.2108 time to fit residues: 37.4492 Evaluate side-chains 94 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 127 optimal weight: 10.0000 chunk 116 optimal weight: 9.9990 chunk 123 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 97 optimal weight: 0.0170 chunk 38 optimal weight: 7.9990 chunk 112 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 overall best weight: 2.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1026 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1173 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 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 685 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12655 Z= 0.209 Angle : 0.690 12.031 17379 Z= 0.344 Chirality : 0.042 0.188 1943 Planarity : 0.005 0.061 1998 Dihedral : 16.771 78.201 2469 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 19.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.18 % Favored : 85.82 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.23), residues: 1312 helix: 0.26 (0.24), residues: 526 sheet: -0.99 (0.69), residues: 52 loop : -3.53 (0.21), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 725 HIS 0.008 0.001 HIS A 859 PHE 0.021 0.002 PHE A 970 TYR 0.050 0.002 TYR A 872 ARG 0.006 0.000 ARG A 548 *********************** 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 109 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 1.496 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: 0.8497 (t) cc_final: 0.8283 (t) REVERT: A 697 LEU cc_start: 0.8437 (tp) cc_final: 0.8086 (mt) REVERT: A 848 TRP cc_start: 0.7876 (m-90) cc_final: 0.7475 (m-90) REVERT: A 862 MET cc_start: 0.8793 (mmm) cc_final: 0.8471 (mmm) REVERT: A 937 MET cc_start: 0.4469 (mpp) cc_final: 0.3664 (mtt) REVERT: A 1040 MET cc_start: 0.9365 (mmm) cc_final: 0.8848 (tpp) REVERT: A 1146 MET cc_start: 0.8859 (mpp) cc_final: 0.8406 (mpp) REVERT: A 1235 GLU cc_start: 0.9466 (mt-10) cc_final: 0.9221 (mm-30) REVERT: A 1241 MET cc_start: 0.9664 (mmt) cc_final: 0.9174 (mmt) REVERT: A 1322 MET cc_start: 0.9041 (ttt) cc_final: 0.8778 (ttt) REVERT: A 1330 GLU cc_start: 0.8887 (pt0) cc_final: 0.8593 (pt0) REVERT: C 514 CYS cc_start: 0.9346 (m) cc_final: 0.9137 (m) REVERT: C 520 MET cc_start: 0.8361 (mtp) cc_final: 0.7972 (ttm) REVERT: C 621 TYR cc_start: 0.9569 (t80) cc_final: 0.9368 (t80) REVERT: B 682 GLN cc_start: 0.8761 (mm110) cc_final: 0.8505 (mt0) REVERT: B 697 MET cc_start: 0.8712 (mmm) cc_final: 0.8291 (tpt) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.2175 time to fit residues: 36.9108 Evaluate side-chains 91 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 79 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 91 optimal weight: 0.5980 chunk 137 optimal weight: 10.0000 chunk 126 optimal weight: 7.9990 chunk 109 optimal weight: 30.0000 chunk 11 optimal weight: 0.6980 chunk 84 optimal weight: 10.0000 chunk 67 optimal weight: 9.9990 chunk 86 optimal weight: 1.9990 chunk 116 optimal weight: 9.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1026 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1042 ASN ** A1173 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 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 599 ASN B 685 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.4126 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= 0.170 Angle : 0.673 11.651 17379 Z= 0.330 Chirality : 0.041 0.202 1943 Planarity : 0.005 0.061 1998 Dihedral : 16.418 75.005 2469 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.12 % Favored : 87.88 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.23), residues: 1312 helix: 0.25 (0.24), residues: 536 sheet: -1.15 (0.67), residues: 62 loop : -3.57 (0.21), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 665 HIS 0.007 0.001 HIS A 859 PHE 0.018 0.002 PHE A 970 TYR 0.036 0.001 TYR A 872 ARG 0.004 0.000 ARG B 696 ********************** 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 113 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 636 MET cc_start: 0.8220 (mmt) cc_final: 0.7709 (tpp) REVERT: A 697 LEU cc_start: 0.8238 (tp) cc_final: 0.7890 (mt) REVERT: A 699 MET cc_start: 0.8861 (mmp) cc_final: 0.8626 (mmm) REVERT: A 848 TRP cc_start: 0.7657 (m-90) cc_final: 0.7048 (m-90) REVERT: A 862 MET cc_start: 0.8765 (mmm) cc_final: 0.8469 (mmm) REVERT: A 937 MET cc_start: 0.4418 (mpp) cc_final: 0.3597 (mtt) REVERT: A 1022 MET cc_start: 0.8673 (ptp) cc_final: 0.8376 (ptp) REVERT: A 1040 MET cc_start: 0.9481 (mmm) cc_final: 0.8950 (mmt) REVERT: A 1146 MET cc_start: 0.8845 (mpp) cc_final: 0.8443 (mpp) REVERT: A 1235 GLU cc_start: 0.9428 (mt-10) cc_final: 0.9177 (mm-30) REVERT: A 1241 MET cc_start: 0.9651 (mmt) cc_final: 0.9096 (mmt) REVERT: A 1322 MET cc_start: 0.9000 (ttt) cc_final: 0.8708 (ttt) REVERT: A 1326 MET cc_start: 0.8847 (mmp) cc_final: 0.8599 (mmp) REVERT: A 1330 GLU cc_start: 0.8866 (pt0) cc_final: 0.8529 (pt0) REVERT: C 520 MET cc_start: 0.8328 (mtp) cc_final: 0.7964 (ttm) REVERT: B 682 GLN cc_start: 0.8704 (mm110) cc_final: 0.8403 (mt0) REVERT: B 697 MET cc_start: 0.8650 (mmm) cc_final: 0.8237 (tpt) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.2058 time to fit residues: 36.4046 Evaluate side-chains 87 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 33 optimal weight: 30.0000 chunk 100 optimal weight: 0.8980 chunk 16 optimal weight: 0.4980 chunk 30 optimal weight: 0.5980 chunk 109 optimal weight: 30.0000 chunk 45 optimal weight: 8.9990 chunk 112 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 96 optimal weight: 20.0000 chunk 6 optimal weight: 10.0000 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1026 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1173 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 521 GLN ** 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 = 0.3506 r_free = 0.3506 target = 0.060164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.047979 restraints weight = 100315.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.049383 restraints weight = 62074.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.050334 restraints weight = 44214.595| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.4224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12655 Z= 0.187 Angle : 0.671 12.174 17379 Z= 0.331 Chirality : 0.041 0.208 1943 Planarity : 0.005 0.061 1998 Dihedral : 16.354 73.660 2469 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 17.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.88 % Favored : 87.12 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.23), residues: 1312 helix: 0.29 (0.24), residues: 536 sheet: -1.13 (0.67), residues: 62 loop : -3.54 (0.21), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 725 HIS 0.008 0.001 HIS A 859 PHE 0.023 0.002 PHE A 681 TYR 0.043 0.001 TYR A 872 ARG 0.004 0.000 ARG A 548 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2063.64 seconds wall clock time: 39 minutes 11.44 seconds (2351.44 seconds total)