Starting phenix.real_space_refine (version: dev) on Mon Dec 12 21:20:00 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v5c_21052/12_2022/6v5c_21052.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v5c_21052/12_2022/6v5c_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_21052/12_2022/6v5c_21052.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v5c_21052/12_2022/6v5c_21052.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v5c_21052/12_2022/6v5c_21052.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v5c_21052/12_2022/6v5c_21052.pdb" } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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-4807/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: 7.44, per 1000 atoms: 0.61 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: 5.69 Conformation dependent library (CDL) restraints added in 1.7 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: 3.50 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: 4.13 Time building geometry restraints manager: 6.09 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: 6461 18.29 - 36.58: 840 36.58 - 54.87: 170 54.87 - 73.16: 56 73.16 - 91.46: 18 Dihedral angle restraints: 7545 sinusoidal: 3642 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 7542 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 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. 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: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.000 Check model and map are aligned: 0.180 Convert atoms to be neutral: 0.100 Process input model: 37.500 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.160 ------------------------------------------------------------------------------- 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= 0.453 Angle : 1.265 18.044 17379 Z= 0.723 Chirality : 0.071 0.642 1943 Planarity : 0.008 0.085 1998 Dihedral : 17.234 91.456 5015 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 18.25 Ramachandran Plot: Outliers : 0.38 % Allowed : 13.72 % Favored : 85.90 % Rotamer Outliers : 1.84 % 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 *********************** 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 : 1.438 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 outliers start: 22 outliers final: 11 residues processed: 151 average time/residue: 0.2395 time to fit residues: 53.5794 Evaluate side-chains 101 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 90 time to evaluate : 1.874 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1352 time to fit residues: 4.1301 ------------------------------------------------------------------------------- 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: 5.9990 chunk 70 optimal weight: 4.9990 chunk 55 optimal weight: 8.9990 chunk 108 optimal weight: 20.0000 chunk 41 optimal weight: 2.9990 chunk 65 optimal weight: 20.0000 chunk 80 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 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 680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 894 GLN ** 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** ** B 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 660 HIS B 678 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.054 12655 Z= 0.308 Angle : 0.801 11.973 17379 Z= 0.413 Chirality : 0.045 0.237 1943 Planarity : 0.006 0.068 1998 Dihedral : 12.610 88.381 2241 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 24.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 14.33 % Favored : 85.59 % Rotamer Outliers : 0.25 % 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: -3.97 (0.21), residues: 1312 helix: -1.19 (0.21), residues: 530 sheet: -2.86 (0.51), residues: 61 loop : -3.97 (0.20), residues: 721 *********************** 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 114 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 111 time to evaluate : 1.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 114 average time/residue: 0.2288 time to fit residues: 39.8232 Evaluate side-chains 92 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 91 time to evaluate : 1.424 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1077 time to fit residues: 2.0783 ------------------------------------------------------------------------------- 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: 20.0000 chunk 38 optimal weight: 1.9990 chunk 104 optimal weight: 7.9990 chunk 85 optimal weight: 6.9990 chunk 34 optimal weight: 9.9990 chunk 125 optimal weight: 2.9990 chunk 135 optimal weight: 10.0000 chunk 111 optimal weight: 30.0000 chunk 124 optimal weight: 6.9990 chunk 42 optimal weight: 0.6980 chunk 100 optimal weight: 10.0000 overall best weight: 3.9388 ------------------------------------------------------------------------------- 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 ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 625 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 12655 Z= 0.287 Angle : 0.754 11.964 17379 Z= 0.386 Chirality : 0.043 0.187 1943 Planarity : 0.006 0.065 1998 Dihedral : 12.472 88.282 2241 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 22.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.63 % Favored : 85.37 % Rotamer Outliers : 0.08 % 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: -3.51 (0.22), residues: 1312 helix: -0.50 (0.23), residues: 513 sheet: -2.73 (0.52), residues: 64 loop : -3.90 (0.20), residues: 735 *********************** 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 114 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 113 time to evaluate : 1.477 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 outliers start: 1 outliers final: 1 residues processed: 114 average time/residue: 0.2216 time to fit residues: 38.5945 Evaluate side-chains 91 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 90 time to evaluate : 1.286 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1072 time to fit residues: 1.9432 ------------------------------------------------------------------------------- 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: 20.0000 chunk 94 optimal weight: 4.9990 chunk 65 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 84 optimal weight: 0.4980 chunk 125 optimal weight: 8.9990 chunk 133 optimal weight: 10.0000 chunk 119 optimal weight: 0.6980 chunk 35 optimal weight: 7.9990 chunk 111 optimal weight: 40.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 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** ** A1294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 736 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 12655 Z= 0.191 Angle : 0.691 11.801 17379 Z= 0.346 Chirality : 0.042 0.191 1943 Planarity : 0.005 0.064 1998 Dihedral : 11.990 85.215 2241 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 17.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.11 % Favored : 86.89 % Rotamer Outliers : 0.08 % 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: -3.13 (0.22), residues: 1312 helix: -0.21 (0.23), residues: 525 sheet: -1.68 (0.57), residues: 62 loop : -3.80 (0.20), residues: 725 *********************** 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 fitting. rotamer outliers: 1 poor density : 115 time to evaluate : 1.377 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 outliers start: 1 outliers final: 1 residues processed: 116 average time/residue: 0.2274 time to fit residues: 40.4548 Evaluate side-chains 92 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 91 time to evaluate : 1.386 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0930 time to fit residues: 2.0846 ------------------------------------------------------------------------------- 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: 2.9990 chunk 1 optimal weight: 1.9990 chunk 99 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 113 optimal weight: 9.9990 chunk 92 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 68 optimal weight: 7.9990 chunk 119 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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** A 894 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 ** 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: 0.8067 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.063 12655 Z= 0.337 Angle : 0.782 11.487 17379 Z= 0.401 Chirality : 0.045 0.199 1943 Planarity : 0.006 0.060 1998 Dihedral : 12.299 87.354 2241 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 26.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.78 % Favored : 84.22 % Rotamer Outliers : 0.08 % 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: -3.13 (0.22), residues: 1312 helix: -0.14 (0.23), residues: 517 sheet: -2.10 (0.52), residues: 67 loop : -3.78 (0.20), residues: 728 *********************** 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 : 1.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 102 average time/residue: 0.2197 time to fit residues: 35.6226 Evaluate side-chains 83 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 82 time to evaluate : 1.407 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1134 time to fit residues: 2.0602 ------------------------------------------------------------------------------- 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: 20.0000 chunk 26 optimal weight: 9.9990 chunk 78 optimal weight: 0.2980 chunk 32 optimal weight: 7.9990 chunk 133 optimal weight: 10.0000 chunk 110 optimal weight: 8.9990 chunk 61 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 128 optimal weight: 10.0000 overall best weight: 4.2588 ------------------------------------------------------------------------------- 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** ** A1120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1255 ASN ** A1294 HIS ** 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: 0.8055 moved from start: 0.3397 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= 0.292 Angle : 0.749 11.832 17379 Z= 0.382 Chirality : 0.044 0.226 1943 Planarity : 0.006 0.061 1998 Dihedral : 12.278 86.155 2241 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 24.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.78 % Favored : 84.22 % Rotamer Outliers : 0.08 % 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: -3.09 (0.22), residues: 1312 helix: -0.18 (0.23), residues: 526 sheet: -1.66 (0.56), residues: 67 loop : -3.79 (0.20), residues: 719 *********************** 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 100 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 99 time to evaluate : 1.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 100 average time/residue: 0.2232 time to fit residues: 34.9503 Evaluate side-chains 86 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 85 time to evaluate : 1.426 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1498 time to fit residues: 2.1420 ------------------------------------------------------------------------------- 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: 7.9990 chunk 97 optimal weight: 9.9990 chunk 75 optimal weight: 0.3980 chunk 112 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 133 optimal weight: 10.0000 chunk 83 optimal weight: 0.0770 chunk 81 optimal weight: 9.9990 chunk 61 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 overall best weight: 1.0942 ------------------------------------------------------------------------------- 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** A1080 ASN ** A1187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1256 GLN ** A1294 HIS ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 12655 Z= 0.187 Angle : 0.697 13.822 17379 Z= 0.345 Chirality : 0.042 0.219 1943 Planarity : 0.005 0.063 1998 Dihedral : 11.806 83.384 2241 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 18.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.03 % Favored : 86.97 % Rotamer Outliers : 0.08 % 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: -2.83 (0.23), residues: 1312 helix: 0.11 (0.24), residues: 523 sheet: -1.43 (0.59), residues: 62 loop : -3.69 (0.20), residues: 727 *********************** 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 113 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 112 time to evaluate : 1.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 113 average time/residue: 0.2111 time to fit residues: 37.0908 Evaluate side-chains 87 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 86 time to evaluate : 1.384 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1479 time to fit residues: 2.0558 ------------------------------------------------------------------------------- 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: 8.9990 chunk 26 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 90 optimal weight: 20.0000 chunk 65 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 104 optimal weight: 0.9990 chunk 120 optimal weight: 0.0870 overall best weight: 0.7760 ------------------------------------------------------------------------------- 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 ** 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 ** C 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 632 HIS B 685 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 12655 Z= 0.170 Angle : 0.677 12.137 17379 Z= 0.337 Chirality : 0.042 0.211 1943 Planarity : 0.005 0.063 1998 Dihedral : 11.383 80.278 2241 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.65 % Favored : 87.35 % Rotamer Outliers : 0.17 % 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: -2.70 (0.23), residues: 1312 helix: 0.08 (0.23), residues: 532 sheet: -1.06 (0.65), residues: 57 loop : -3.55 (0.21), residues: 723 *********************** 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 116 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 114 time to evaluate : 1.475 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 outliers start: 2 outliers final: 1 residues processed: 116 average time/residue: 0.2134 time to fit residues: 38.5685 Evaluate side-chains 84 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 83 time to evaluate : 1.405 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1516 time to fit residues: 2.0650 ------------------------------------------------------------------------------- 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: 0.1980 chunk 116 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 97 optimal weight: 20.0000 chunk 38 optimal weight: 0.9980 chunk 112 optimal weight: 3.9990 chunk 117 optimal weight: 20.0000 chunk 81 optimal weight: 10.0000 chunk 131 optimal weight: 3.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- 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** ** 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 685 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 12655 Z= 0.204 Angle : 0.689 12.036 17379 Z= 0.346 Chirality : 0.042 0.197 1943 Planarity : 0.005 0.062 1998 Dihedral : 11.317 79.204 2241 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 19.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.48 % Favored : 85.52 % Rotamer Outliers : 0.00 % 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: 0.15 (0.23), residues: 531 sheet: -0.85 (0.72), residues: 52 loop : -3.53 (0.20), residues: 729 *********************** 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 110 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.2074 time to fit residues: 36.4977 Evaluate side-chains 85 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 1.508 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8766 ------------------------------------------------------------------------------- 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: 2.9990 chunk 62 optimal weight: 0.6980 chunk 91 optimal weight: 9.9990 chunk 137 optimal weight: 10.0000 chunk 126 optimal weight: 20.0000 chunk 109 optimal weight: 30.0000 chunk 11 optimal weight: 0.0570 chunk 84 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 116 optimal weight: 9.9990 overall best weight: 2.7504 ------------------------------------------------------------------------------- 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** ** 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 599 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 12655 Z= 0.226 Angle : 0.725 15.688 17379 Z= 0.361 Chirality : 0.043 0.195 1943 Planarity : 0.005 0.061 1998 Dihedral : 11.296 78.897 2241 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 19.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.48 % Favored : 85.52 % Rotamer Outliers : 0.00 % 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: 0.14 (0.23), residues: 533 sheet: -0.90 (0.72), residues: 52 loop : -3.54 (0.21), residues: 727 ********************** 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 103 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 1.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.2155 time to fit residues: 35.1344 Evaluate side-chains 80 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 1.479 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8956 ------------------------------------------------------------------------------- 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: 0.0020 chunk 100 optimal weight: 4.9990 chunk 16 optimal weight: 8.9990 chunk 30 optimal weight: 0.5980 chunk 109 optimal weight: 30.0000 chunk 45 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 chunk 13 optimal weight: 0.0010 chunk 20 optimal weight: 4.9990 chunk 96 optimal weight: 6.9990 chunk 6 optimal weight: 0.5980 overall best weight: 1.2396 ------------------------------------------------------------------------------- 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** A1042 ASN ** 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 = 0.3486 r_free = 0.3486 target = 0.059132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.046638 restraints weight = 94363.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.048032 restraints weight = 58583.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.048970 restraints weight = 41983.509| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.4298 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= 0.181 Angle : 0.690 12.105 17379 Z= 0.342 Chirality : 0.042 0.198 1943 Planarity : 0.005 0.062 1998 Dihedral : 10.943 77.237 2241 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.80 % Favored : 87.20 % Rotamer Outliers : 0.00 % 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: 0.19 (0.23), residues: 534 sheet: -0.63 (0.74), residues: 52 loop : -3.52 (0.20), residues: 726 =============================================================================== Job complete usr+sys time: 1964.27 seconds wall clock time: 37 minutes 38.10 seconds (2258.10 seconds total)