Starting phenix.real_space_refine on Sun Mar 24 17:21:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y8r_33684/03_2024/7y8r_33684_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y8r_33684/03_2024/7y8r_33684.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/7y8r_33684/03_2024/7y8r_33684.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y8r_33684/03_2024/7y8r_33684.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y8r_33684/03_2024/7y8r_33684_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y8r_33684/03_2024/7y8r_33684_neut_updated.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= -0.002 sd= 0.053 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: 8 Type Number sf(0) Gaussians P 332 5.49 5 Mg 1 5.21 5 S 174 5.16 5 Be 1 3.05 5 C 26136 2.51 5 N 7753 2.21 5 O 8709 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 23": "NH1" <-> "NH2" Residue "D ARG 92": "NH1" <-> "NH2" Residue "F ARG 19": "NH1" <-> "NH2" Residue "I ARG 377": "NH1" <-> "NH2" Residue "I ARG 426": "NH1" <-> "NH2" Residue "I GLU 518": "OE1" <-> "OE2" Residue "I ARG 528": "NH1" <-> "NH2" Residue "I ARG 841": "NH1" <-> "NH2" Residue "I ARG 885": "NH1" <-> "NH2" Residue "I ARG 906": "NH1" <-> "NH2" Residue "I GLU 920": "OE1" <-> "OE2" Residue "I ARG 967": "NH1" <-> "NH2" Residue "I ARG 1087": "NH1" <-> "NH2" Residue "I ARG 1093": "NH1" <-> "NH2" Residue "I ARG 1157": "NH1" <-> "NH2" Residue "I ARG 1189": "NH1" <-> "NH2" Residue "I ARG 1243": "NH1" <-> "NH2" Residue "I ARG 1244": "NH1" <-> "NH2" Residue "I GLU 1310": "OE1" <-> "OE2" Residue "I ARG 1318": "NH1" <-> "NH2" Residue "I ARG 1336": "NH1" <-> "NH2" Residue "J ARG 39": "NH1" <-> "NH2" Residue "J ARG 62": "NH1" <-> "NH2" Residue "J ARG 95": "NH1" <-> "NH2" Residue "K GLU 46": "OE1" <-> "OE2" Residue "K ARG 248": "NH1" <-> "NH2" Residue "L PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 80": "NH1" <-> "NH2" Residue "L GLU 112": "OE1" <-> "OE2" Residue "L GLU 223": "OE1" <-> "OE2" Residue "L ARG 373": "NH1" <-> "NH2" Residue "L GLU 385": "OE1" <-> "OE2" Residue "L GLU 1806": "OE1" <-> "OE2" Residue "M GLU 24": "OE1" <-> "OE2" Residue "M GLU 58": "OE1" <-> "OE2" Residue "M ARG 121": "NH1" <-> "NH2" Residue "M GLU 122": "OE1" <-> "OE2" Residue "M ARG 155": "NH1" <-> "NH2" Residue "M ARG 190": "NH1" <-> "NH2" Residue "M ARG 201": "NH1" <-> "NH2" Residue "M ARG 261": "NH1" <-> "NH2" Residue "M GLU 330": "OE1" <-> "OE2" Residue "M ARG 366": "NH1" <-> "NH2" Residue "M ARG 370": "NH1" <-> "NH2" Residue "M ARG 376": "NH1" <-> "NH2" Residue "N ARG 443": "NH1" <-> "NH2" Residue "N GLU 479": "OE1" <-> "OE2" Residue "N ARG 487": "NH1" <-> "NH2" Residue "N GLU 645": "OE1" <-> "OE2" Residue "N ARG 917": "NH1" <-> "NH2" Residue "O ARG 466": "NH1" <-> "NH2" Residue "O GLU 603": "OE1" <-> "OE2" Residue "O GLU 625": "OE1" <-> "OE2" Residue "O ARG 882": "NH1" <-> "NH2" Residue "P GLU 198": "OE1" <-> "OE2" Residue "P GLU 257": "OE1" <-> "OE2" Residue "P ARG 334": "NH1" <-> "NH2" Residue "P ARG 351": "NH1" <-> "NH2" Residue "P ARG 446": "NH1" <-> "NH2" Residue "Q ARG 201": "NH1" <-> "NH2" Residue "Q ARG 223": "NH1" <-> "NH2" Residue "Q ARG 239": "NH1" <-> "NH2" Residue "R GLU 217": "OE1" <-> "OE2" Residue "S GLU 132": "OE1" <-> "OE2" Residue "S GLU 138": "OE1" <-> "OE2" Residue "S GLU 195": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 43109 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "B" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 741 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain: "C" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 799 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "D" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 755 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "E" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 806 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "F" Number of atoms: 702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 702 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "G" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 833 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "Z" Number of atoms: 141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 141 Classifications: {'peptide': 29} Incomplete info: {'backbone_only': 4, 'truncation_to_alanine': 25} Link IDs: {'TRANS': 28} Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'UNK:plan-1': 29} Unresolved non-hydrogen planarities: 29 Chain: "I" Number of atoms: 6051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 732, 6051 Classifications: {'peptide': 732} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 20, 'TRANS': 711} Chain breaks: 6 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "J" Number of atoms: 2821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2821 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 19, 'TRANS': 340} Chain breaks: 2 Chain: "K" Number of atoms: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2787 Classifications: {'peptide': 356} Link IDs: {'PTRANS': 18, 'TRANS': 337} Chain breaks: 3 Chain: "L" Number of atoms: 4151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 4151 Classifications: {'peptide': 521} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 502} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 2918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2918 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 18, 'TRANS': 343} Chain breaks: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "N" Number of atoms: 2085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2085 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 8, 'TRANS': 246} Chain breaks: 3 Chain: "a" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 58 Classifications: {'peptide': 12} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 10} Link IDs: {'TRANS': 11} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'UNK:plan-1': 12} Unresolved non-hydrogen planarities: 12 Chain: "O" Number of atoms: 2354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2354 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 15, 'TRANS': 281} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "P" Number of atoms: 3174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3174 Classifications: {'peptide': 385} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 19, 'TRANS': 365} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "Q" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 739 Classifications: {'peptide': 91} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 89} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "R" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 366 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 2, 'TRANS': 41} Chain: "S" Number of atoms: 1738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1738 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 13, 'TRANS': 199} Chain breaks: 2 Chain: "T" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 110 Classifications: {'peptide': 22} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'TRANS': 21} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'UNK:plan-1': 22} Unresolved non-hydrogen planarities: 22 Chain: "U" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 92 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "V" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 420 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'TRANS': 83} Chain breaks: 3 Unresolved non-hydrogen bonds: 168 Unresolved non-hydrogen angles: 252 Unresolved non-hydrogen dihedrals: 84 Planarities with less than four sites: {'UNK:plan-1': 84} Unresolved non-hydrogen planarities: 84 Chain: "X" Number of atoms: 3360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 3360 Classifications: {'DNA': 165} Link IDs: {'rna3p': 164} Chain: "Y" Number of atoms: 3405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 3405 Classifications: {'DNA': 165} Link IDs: {'rna3p': 164} Chain: "W" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 120 Classifications: {'peptide': 24} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'TRANS': 23} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'UNK:plan-1': 24} Unresolved non-hydrogen planarities: 24 Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 20.32, per 1000 atoms: 0.47 Number of scatterers: 43109 At special positions: 0 Unit cell: (160.08, 188.094, 249.458, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 174 16.00 P 332 15.00 Mg 1 11.99 F 3 9.00 O 8709 8.00 N 7753 7.00 C 26136 6.00 Be 1 4.00 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 18.28 Conformation dependent library (CDL) restraints added in 5.8 seconds 8642 Ramachandran restraints generated. 4321 Oldfield, 0 Emsley, 4321 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8742 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 190 helices and 14 sheets defined 55.9% alpha, 3.6% beta 153 base pairs and 247 stacking pairs defined. Time for finding SS restraints: 16.44 Creating SS restraints... Processing helix chain 'A' and resid 45 through 56 Processing helix chain 'A' and resid 64 through 75 Processing helix chain 'A' and resid 86 through 113 Processing helix chain 'A' and resid 121 through 131 Processing helix chain 'B' and resid 31 through 40 Processing helix chain 'B' and resid 48 through 75 removed outlier: 3.671A pdb=" N TYR B 51 " --> pdb=" O GLY B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 92 Processing helix chain 'C' and resid 17 through 20 No H-bonds generated for 'chain 'C' and resid 17 through 20' Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.488A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASP C 72 " --> pdb=" O ASN C 68 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 89 Processing helix chain 'C' and resid 91 through 96 Processing helix chain 'D' and resid 38 through 48 Processing helix chain 'D' and resid 56 through 83 Processing helix chain 'D' and resid 91 through 101 Processing helix chain 'D' and resid 104 through 123 Processing helix chain 'E' and resid 45 through 56 removed outlier: 3.687A pdb=" N ARG E 49 " --> pdb=" O THR E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 78 removed outlier: 3.768A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 113 Processing helix chain 'E' and resid 121 through 131 Processing helix chain 'F' and resid 25 through 28 Processing helix chain 'F' and resid 31 through 40 Processing helix chain 'F' and resid 48 through 75 removed outlier: 4.805A pdb=" N THR F 54 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ARG F 67 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL F 70 " --> pdb=" O ARG F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 93 Processing helix chain 'G' and resid 17 through 21 Processing helix chain 'G' and resid 27 through 36 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.118A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 89 Processing helix chain 'G' and resid 91 through 96 Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'H' and resid 38 through 48 Processing helix chain 'H' and resid 56 through 83 Processing helix chain 'H' and resid 91 through 101 Processing helix chain 'H' and resid 104 through 123 removed outlier: 3.634A pdb=" N HIS H 109 " --> pdb=" O LEU H 106 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER H 123 " --> pdb=" O LYS H 120 " (cutoff:3.500A) Processing helix chain 'Z' and resid 116 through 124 Processing helix chain 'Z' and resid 130 through 139 Processing helix chain 'I' and resid 366 through 385 removed outlier: 3.514A pdb=" N ALA I 379 " --> pdb=" O GLN I 375 " (cutoff:3.500A) Processing helix chain 'I' and resid 395 through 422 removed outlier: 4.171A pdb=" N PHE I 412 " --> pdb=" O ARG I 408 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLN I 415 " --> pdb=" O ASN I 411 " (cutoff:3.500A) Processing helix chain 'I' and resid 446 through 531 Processing helix chain 'I' and resid 550 through 569 removed outlier: 3.548A pdb=" N GLN I 555 " --> pdb=" O ALA I 551 " (cutoff:3.500A) Processing helix chain 'I' and resid 756 through 770 Processing helix chain 'I' and resid 785 through 798 Processing helix chain 'I' and resid 812 through 825 removed outlier: 4.494A pdb=" N SER I 816 " --> pdb=" O LEU I 812 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ASN I 817 " --> pdb=" O SER I 813 " (cutoff:3.500A) Processing helix chain 'I' and resid 838 through 850 removed outlier: 3.717A pdb=" N PHE I 844 " --> pdb=" O ALA I 840 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N VAL I 845 " --> pdb=" O ARG I 841 " (cutoff:3.500A) Proline residue: I 846 - end of helix Processing helix chain 'I' and resid 860 through 865 Processing helix chain 'I' and resid 867 through 872 Processing helix chain 'I' and resid 883 through 886 Processing helix chain 'I' and resid 892 through 899 Processing helix chain 'I' and resid 918 through 928 Processing helix chain 'I' and resid 937 through 940 No H-bonds generated for 'chain 'I' and resid 937 through 940' Processing helix chain 'I' and resid 958 through 970 removed outlier: 3.556A pdb=" N ILE I 964 " --> pdb=" O THR I 961 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LYS I 970 " --> pdb=" O ARG I 967 " (cutoff:3.500A) Processing helix chain 'I' and resid 981 through 984 No H-bonds generated for 'chain 'I' and resid 981 through 984' Processing helix chain 'I' and resid 1002 through 1011 Processing helix chain 'I' and resid 1040 through 1047 Processing helix chain 'I' and resid 1049 through 1051 No H-bonds generated for 'chain 'I' and resid 1049 through 1051' Processing helix chain 'I' and resid 1053 through 1062 removed outlier: 5.314A pdb=" N HIS I1062 " --> pdb=" O SER I1058 " (cutoff:3.500A) Processing helix chain 'I' and resid 1080 through 1095 Proline residue: I1090 - end of helix removed outlier: 3.831A pdb=" N THR I1095 " --> pdb=" O LYS I1091 " (cutoff:3.500A) Processing helix chain 'I' and resid 1106 through 1119 removed outlier: 4.007A pdb=" N ILE I1111 " --> pdb=" O SER I1107 " (cutoff:3.500A) Processing helix chain 'I' and resid 1132 through 1143 removed outlier: 3.983A pdb=" N GLY I1136 " --> pdb=" O ALA I1132 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N MET I1137 " --> pdb=" O GLU I1133 " (cutoff:3.500A) Processing helix chain 'I' and resid 1180 through 1189 Processing helix chain 'I' and resid 1210 through 1231 removed outlier: 3.987A pdb=" N VAL I1228 " --> pdb=" O VAL I1224 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ALA I1231 " --> pdb=" O LYS I1227 " (cutoff:3.500A) Processing helix chain 'I' and resid 1245 through 1252 Processing helix chain 'I' and resid 1299 through 1306 Processing helix chain 'I' and resid 1310 through 1329 removed outlier: 3.980A pdb=" N ASP I1314 " --> pdb=" O GLU I1310 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ARG I1329 " --> pdb=" O ARG I1325 " (cutoff:3.500A) Processing helix chain 'J' and resid 3 through 5 No H-bonds generated for 'chain 'J' and resid 3 through 5' Processing helix chain 'J' and resid 55 through 63 removed outlier: 4.002A pdb=" N ARG J 62 " --> pdb=" O GLN J 59 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLY J 63 " --> pdb=" O SER J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 97 removed outlier: 4.578A pdb=" N ASN J 92 " --> pdb=" O HIS J 88 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N GLU J 93 " --> pdb=" O THR J 89 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 127 removed outlier: 4.189A pdb=" N THR J 120 " --> pdb=" O ARG J 116 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR J 126 " --> pdb=" O ILE J 122 " (cutoff:3.500A) Processing helix chain 'J' and resid 137 through 145 Processing helix chain 'J' and resid 182 through 196 Processing helix chain 'J' and resid 203 through 214 removed outlier: 5.272A pdb=" N ARG J 210 " --> pdb=" O ARG J 206 " (cutoff:3.500A) Processing helix chain 'J' and resid 223 through 230 removed outlier: 3.563A pdb=" N ALA J 230 " --> pdb=" O GLU J 226 " (cutoff:3.500A) Processing helix chain 'J' and resid 234 through 236 No H-bonds generated for 'chain 'J' and resid 234 through 236' Processing helix chain 'J' and resid 252 through 256 Processing helix chain 'J' and resid 258 through 260 No H-bonds generated for 'chain 'J' and resid 258 through 260' Processing helix chain 'J' and resid 275 through 283 Processing helix chain 'J' and resid 288 through 295 removed outlier: 3.681A pdb=" N LEU J 293 " --> pdb=" O ARG J 290 " (cutoff:3.500A) Processing helix chain 'J' and resid 309 through 320 Processing helix chain 'J' and resid 338 through 348 Processing helix chain 'J' and resid 353 through 355 No H-bonds generated for 'chain 'J' and resid 353 through 355' Processing helix chain 'J' and resid 359 through 362 No H-bonds generated for 'chain 'J' and resid 359 through 362' Processing helix chain 'J' and resid 366 through 370 removed outlier: 3.644A pdb=" N ILE J 369 " --> pdb=" O GLY J 366 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N VAL J 370 " --> pdb=" O PRO J 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 366 through 370' Processing helix chain 'K' and resid 72 through 74 No H-bonds generated for 'chain 'K' and resid 72 through 74' Processing helix chain 'K' and resid 96 through 110 Processing helix chain 'K' and resid 130 through 144 Processing helix chain 'K' and resid 154 through 161 Processing helix chain 'K' and resid 189 through 191 No H-bonds generated for 'chain 'K' and resid 189 through 191' Processing helix chain 'K' and resid 199 through 207 Processing helix chain 'K' and resid 253 through 263 Processing helix chain 'K' and resid 326 through 333 Processing helix chain 'K' and resid 341 through 347 Processing helix chain 'K' and resid 354 through 356 No H-bonds generated for 'chain 'K' and resid 354 through 356' Processing helix chain 'K' and resid 362 through 371 Processing helix chain 'K' and resid 383 through 385 No H-bonds generated for 'chain 'K' and resid 383 through 385' Processing helix chain 'K' and resid 387 through 401 removed outlier: 4.307A pdb=" N SER K 393 " --> pdb=" O ARG K 390 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE K 395 " --> pdb=" O SER K 392 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE K 399 " --> pdb=" O GLY K 396 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU K 400 " --> pdb=" O GLY K 397 " (cutoff:3.500A) Processing helix chain 'K' and resid 404 through 408 removed outlier: 4.492A pdb=" N GLN K 408 " --> pdb=" O GLY K 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 404 through 408' Processing helix chain 'K' and resid 413 through 415 No H-bonds generated for 'chain 'K' and resid 413 through 415' Processing helix chain 'L' and resid 11 through 30 removed outlier: 5.415A pdb=" N ALA L 18 " --> pdb=" O ARG L 14 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N PHE L 19 " --> pdb=" O LYS L 15 " (cutoff:3.500A) Processing helix chain 'L' and resid 47 through 56 Processing helix chain 'L' and resid 60 through 66 removed outlier: 4.551A pdb=" N GLU L 65 " --> pdb=" O ALA L 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 69 through 76 removed outlier: 4.146A pdb=" N GLU L 74 " --> pdb=" O GLY L 70 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLU L 75 " --> pdb=" O GLU L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 86 through 96 Processing helix chain 'L' and resid 101 through 104 No H-bonds generated for 'chain 'L' and resid 101 through 104' Processing helix chain 'L' and resid 141 through 145 removed outlier: 3.907A pdb=" N SER L 145 " --> pdb=" O TYR L 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 141 through 145' Processing helix chain 'L' and resid 157 through 166 Processing helix chain 'L' and resid 170 through 184 Processing helix chain 'L' and resid 193 through 195 No H-bonds generated for 'chain 'L' and resid 193 through 195' Processing helix chain 'L' and resid 198 through 207 removed outlier: 3.921A pdb=" N ALA L 207 " --> pdb=" O LEU L 203 " (cutoff:3.500A) Processing helix chain 'L' and resid 217 through 223 removed outlier: 3.606A pdb=" N GLU L 223 " --> pdb=" O VAL L 220 " (cutoff:3.500A) Processing helix chain 'L' and resid 234 through 239 Processing helix chain 'L' and resid 244 through 250 Processing helix chain 'L' and resid 281 through 298 removed outlier: 3.778A pdb=" N PHE L 298 " --> pdb=" O ARG L 294 " (cutoff:3.500A) Processing helix chain 'L' and resid 300 through 308 removed outlier: 4.287A pdb=" N LYS L 304 " --> pdb=" O GLU L 300 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU L 305 " --> pdb=" O GLY L 301 " (cutoff:3.500A) Processing helix chain 'L' and resid 311 through 321 Processing helix chain 'L' and resid 325 through 341 removed outlier: 4.078A pdb=" N ALA L 340 " --> pdb=" O GLY L 336 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N GLU L 341 " --> pdb=" O ASN L 337 " (cutoff:3.500A) Processing helix chain 'L' and resid 350 through 363 Processing helix chain 'L' and resid 368 through 383 removed outlier: 3.754A pdb=" N CYS L 382 " --> pdb=" O LEU L 378 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LYS L 383 " --> pdb=" O GLY L 379 " (cutoff:3.500A) Processing helix chain 'L' and resid 388 through 394 Processing helix chain 'L' and resid 397 through 407 removed outlier: 3.976A pdb=" N LEU L 407 " --> pdb=" O ILE L 403 " (cutoff:3.500A) Processing helix chain 'L' and resid 412 through 426 Processing helix chain 'L' and resid 430 through 437 Processing helix chain 'L' and resid 442 through 451 removed outlier: 3.550A pdb=" N VAL L 450 " --> pdb=" O LEU L 446 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N SER L 451 " --> pdb=" O VAL L 447 " (cutoff:3.500A) Processing helix chain 'L' and resid 454 through 456 No H-bonds generated for 'chain 'L' and resid 454 through 456' Processing helix chain 'L' and resid 469 through 479 Processing helix chain 'L' and resid 1763 through 1782 removed outlier: 3.925A pdb=" N LEU L1770 " --> pdb=" O LYS L1766 " (cutoff:3.500A) Processing helix chain 'L' and resid 1784 through 1803 removed outlier: 4.727A pdb=" N ASN L1795 " --> pdb=" O LYS L1791 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ASN L1796 " --> pdb=" O ARG L1792 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL L1799 " --> pdb=" O ASN L1795 " (cutoff:3.500A) Processing helix chain 'L' and resid 1809 through 1820 Processing helix chain 'M' and resid 29 through 36 Processing helix chain 'M' and resid 42 through 45 No H-bonds generated for 'chain 'M' and resid 42 through 45' Processing helix chain 'M' and resid 57 through 66 Processing helix chain 'M' and resid 84 through 86 No H-bonds generated for 'chain 'M' and resid 84 through 86' Processing helix chain 'M' and resid 93 through 101 Processing helix chain 'M' and resid 173 through 181 Processing helix chain 'M' and resid 215 through 226 Processing helix chain 'M' and resid 230 through 246 Proline residue: M 235 - end of helix Processing helix chain 'M' and resid 290 through 301 Processing helix chain 'M' and resid 307 through 322 Processing helix chain 'M' and resid 345 through 349 Processing helix chain 'M' and resid 358 through 380 Processing helix chain 'N' and resid 440 through 445 Processing helix chain 'N' and resid 447 through 451 removed outlier: 3.576A pdb=" N ASN N 451 " --> pdb=" O GLU N 448 " (cutoff:3.500A) Processing helix chain 'N' and resid 459 through 476 removed outlier: 4.141A pdb=" N ASN N 476 " --> pdb=" O THR N 472 " (cutoff:3.500A) Processing helix chain 'N' and resid 483 through 490 Processing helix chain 'N' and resid 494 through 506 Processing helix chain 'N' and resid 604 through 615 Processing helix chain 'N' and resid 623 through 626 No H-bonds generated for 'chain 'N' and resid 623 through 626' Processing helix chain 'N' and resid 632 through 640 Processing helix chain 'N' and resid 672 through 684 removed outlier: 3.571A pdb=" N SER N 682 " --> pdb=" O ALA N 678 " (cutoff:3.500A) Processing helix chain 'N' and resid 859 through 950 Processing helix chain 'O' and resid 441 through 450 Proline residue: O 447 - end of helix Processing helix chain 'O' and resid 459 through 475 removed outlier: 3.879A pdb=" N ALA O 464 " --> pdb=" O GLU O 460 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN O 467 " --> pdb=" O LEU O 463 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR O 473 " --> pdb=" O MET O 469 " (cutoff:3.500A) Processing helix chain 'O' and resid 485 through 488 No H-bonds generated for 'chain 'O' and resid 485 through 488' Processing helix chain 'O' and resid 494 through 506 Processing helix chain 'O' and resid 537 through 539 No H-bonds generated for 'chain 'O' and resid 537 through 539' Processing helix chain 'O' and resid 607 through 615 removed outlier: 5.626A pdb=" N GLU O 614 " --> pdb=" O LEU O 610 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N MET O 615 " --> pdb=" O GLU O 611 " (cutoff:3.500A) Processing helix chain 'O' and resid 621 through 627 removed outlier: 3.508A pdb=" N GLU O 625 " --> pdb=" O ASN O 621 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N HIS O 626 " --> pdb=" O LYS O 622 " (cutoff:3.500A) Processing helix chain 'O' and resid 632 through 641 removed outlier: 3.906A pdb=" N CYS O 635 " --> pdb=" O GLN O 632 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N HIS O 638 " --> pdb=" O CYS O 635 " (cutoff:3.500A) Processing helix chain 'O' and resid 672 through 682 Processing helix chain 'O' and resid 686 through 704 Processing helix chain 'O' and resid 868 through 951 Processing helix chain 'P' and resid 144 through 173 Processing helix chain 'P' and resid 219 through 224 Processing helix chain 'P' and resid 233 through 236 No H-bonds generated for 'chain 'P' and resid 233 through 236' Processing helix chain 'P' and resid 246 through 249 No H-bonds generated for 'chain 'P' and resid 246 through 249' Processing helix chain 'P' and resid 299 through 305 Processing helix chain 'P' and resid 312 through 326 Processing helix chain 'P' and resid 341 through 347 removed outlier: 3.582A pdb=" N GLN P 345 " --> pdb=" O LYS P 341 " (cutoff:3.500A) Processing helix chain 'P' and resid 354 through 364 removed outlier: 4.128A pdb=" N ILE P 357 " --> pdb=" O PHE P 354 " (cutoff:3.500A) Proline residue: P 358 - end of helix removed outlier: 4.857A pdb=" N HIS P 362 " --> pdb=" O GLN P 359 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA P 363 " --> pdb=" O ARG P 360 " (cutoff:3.500A) Processing helix chain 'P' and resid 381 through 383 No H-bonds generated for 'chain 'P' and resid 381 through 383' Processing helix chain 'P' and resid 400 through 446 removed outlier: 3.567A pdb=" N THR P 411 " --> pdb=" O PHE P 407 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA P 418 " --> pdb=" O GLN P 414 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N THR P 419 " --> pdb=" O GLN P 415 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N LEU P 420 " --> pdb=" O GLU P 416 " (cutoff:3.500A) Processing helix chain 'P' and resid 448 through 466 Processing helix chain 'P' and resid 484 through 510 removed outlier: 4.480A pdb=" N GLN P 488 " --> pdb=" O GLN P 484 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N GLU P 489 " --> pdb=" O PRO P 485 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N CYS P 492 " --> pdb=" O GLN P 488 " (cutoff:3.500A) Processing helix chain 'Q' and resid 189 through 207 removed outlier: 3.637A pdb=" N ARG Q 195 " --> pdb=" O ALA Q 192 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ARG Q 198 " --> pdb=" O ARG Q 195 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N HIS Q 200 " --> pdb=" O GLN Q 197 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ARG Q 201 " --> pdb=" O ARG Q 198 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N SER Q 204 " --> pdb=" O ARG Q 201 " (cutoff:3.500A) Processing helix chain 'Q' and resid 221 through 274 Processing helix chain 'R' and resid 197 through 221 Processing helix chain 'S' and resid 135 through 150 removed outlier: 3.619A pdb=" N LYS S 150 " --> pdb=" O GLN S 146 " (cutoff:3.500A) Processing helix chain 'S' and resid 168 through 171 No H-bonds generated for 'chain 'S' and resid 168 through 171' Processing helix chain 'S' and resid 178 through 186 Processing helix chain 'S' and resid 193 through 210 Processing helix chain 'S' and resid 216 through 231 Processing helix chain 'S' and resid 406 through 408 No H-bonds generated for 'chain 'S' and resid 406 through 408' Processing helix chain 'S' and resid 423 through 432 Processing helix chain 'S' and resid 537 through 564 Processing helix chain 'S' and resid 580 through 598 Processing helix chain 'U' and resid 1517 through 1523 Processing helix chain 'V' and resid 3 through 10 Processing helix chain 'V' and resid 19 through 32 Processing helix chain 'V' and resid 1003 through 1016 Processing helix chain 'V' and resid 1033 through 1041 removed outlier: 4.118A pdb=" N UNK V1036 " --> pdb=" O UNK V1033 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N UNK V1037 " --> pdb=" O UNK V1034 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N UNK V1038 " --> pdb=" O UNK V1035 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N UNK V1041 " --> pdb=" O UNK V1038 " (cutoff:3.500A) Processing helix chain 'W' and resid 4 through 9 removed outlier: 3.766A pdb=" N UNK W 8 " --> pdb=" O UNK W 4 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'I' and resid 877 through 880 removed outlier: 3.701A pdb=" N ILE I 879 " --> pdb=" O LEU I 807 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL I 832 " --> pdb=" O VAL I 855 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU I 857 " --> pdb=" O VAL I 832 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'I' and resid 992 through 998 removed outlier: 3.788A pdb=" N CYS I1205 " --> pdb=" O ILE I 996 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU I1100 " --> pdb=" O ILE I1172 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'J' and resid 8 through 10 Processing sheet with id= D, first strand: chain 'J' and resid 103 through 107 Processing sheet with id= E, first strand: chain 'J' and resid 161 through 165 removed outlier: 3.738A pdb=" N MET J 153 " --> pdb=" O VAL J 298 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER J 155 " --> pdb=" O SER J 300 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N LYS J 328 " --> pdb=" O THR J 297 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N LEU J 299 " --> pdb=" O LYS J 328 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N ILE J 330 " --> pdb=" O LEU J 299 " (cutoff:3.500A) removed outlier: 9.742A pdb=" N GLY J 301 " --> pdb=" O ILE J 330 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'K' and resid 14 through 17 Processing sheet with id= G, first strand: chain 'K' and resid 179 through 182 Processing sheet with id= H, first strand: chain 'M' and resid 52 through 54 removed outlier: 4.165A pdb=" N GLU M 24 " --> pdb=" O GLU M 20 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLU M 20 " --> pdb=" O GLU M 24 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N TYR M 26 " --> pdb=" O GLN M 18 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N GLN M 18 " --> pdb=" O TYR M 26 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ILE M 28 " --> pdb=" O LYS M 16 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N LYS M 16 " --> pdb=" O ILE M 28 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'M' and resid 186 through 191 Processing sheet with id= J, first strand: chain 'M' and resid 262 through 267 Processing sheet with id= K, first strand: chain 'P' and resid 185 through 188 removed outlier: 4.488A pdb=" N TRP P 207 " --> pdb=" O ARG P 274 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ARG P 274 " --> pdb=" O TRP P 207 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N VAL P 272 " --> pdb=" O LEU P 209 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'P' and resid 257 through 259 removed outlier: 3.770A pdb=" N TRP P 258 " --> pdb=" O LEU P 240 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N MET P 287 " --> pdb=" O LYS P 238 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N LEU P 240 " --> pdb=" O LEU P 285 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LEU P 285 " --> pdb=" O LEU P 240 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N ILE P 242 " --> pdb=" O THR P 283 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N THR P 283 " --> pdb=" O ILE P 242 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL P 280 " --> pdb=" O ILE P 377 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'P' and resid 294 through 296 Processing sheet with id= N, first strand: chain 'P' and resid 178 through 180 removed outlier: 6.295A pdb=" N ARG P 180 " --> pdb=" O GLU P 395 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N GLU P 395 " --> pdb=" O ARG P 180 " (cutoff:3.500A) 1707 hydrogen bonds defined for protein. 4599 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 393 hydrogen bonds 786 hydrogen bond angles 0 basepair planarities 153 basepair parallelities 247 stacking parallelities Total time for adding SS restraints: 19.27 Time building geometry restraints manager: 19.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 10817 1.33 - 1.45: 9261 1.45 - 1.57: 23531 1.57 - 1.69: 661 1.69 - 1.81: 295 Bond restraints: 44565 Sorted by residual: bond pdb=" BE BEF I1703 " pdb=" F2 BEF I1703 " ideal model delta sigma weight residual 1.476 1.564 -0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" BE BEF I1703 " pdb=" F3 BEF I1703 " ideal model delta sigma weight residual 1.476 1.544 -0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" BE BEF I1703 " pdb=" F1 BEF I1703 " ideal model delta sigma weight residual 1.476 1.533 -0.057 2.00e-02 2.50e+03 8.12e+00 bond pdb=" N GLY B 9 " pdb=" CA GLY B 9 " ideal model delta sigma weight residual 1.451 1.492 -0.041 1.60e-02 3.91e+03 6.47e+00 bond pdb=" N GLY K 12 " pdb=" CA GLY K 12 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.22e+00 ... (remaining 44560 not shown) Histogram of bond angle deviations from ideal: 99.26 - 106.64: 2992 106.64 - 114.03: 25359 114.03 - 121.41: 23104 121.41 - 128.79: 9673 128.79 - 136.18: 464 Bond angle restraints: 61592 Sorted by residual: angle pdb=" N PRO O 543 " pdb=" CA PRO O 543 " pdb=" CB PRO O 543 " ideal model delta sigma weight residual 103.25 111.67 -8.42 1.05e+00 9.07e-01 6.43e+01 angle pdb=" N PRO O 643 " pdb=" CA PRO O 643 " pdb=" CB PRO O 643 " ideal model delta sigma weight residual 103.25 110.82 -7.57 1.05e+00 9.07e-01 5.20e+01 angle pdb=" N PRO O 647 " pdb=" CA PRO O 647 " pdb=" CB PRO O 647 " ideal model delta sigma weight residual 103.25 110.49 -7.24 1.05e+00 9.07e-01 4.75e+01 angle pdb=" F2 BEF I1703 " pdb=" BE BEF I1703 " pdb=" F3 BEF I1703 " ideal model delta sigma weight residual 119.96 107.78 12.18 3.00e+00 1.11e-01 1.65e+01 angle pdb=" N HIS O 439 " pdb=" CA HIS O 439 " pdb=" C HIS O 439 " ideal model delta sigma weight residual 109.69 115.29 -5.60 1.44e+00 4.82e-01 1.51e+01 ... (remaining 61587 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.44: 24580 33.44 - 66.88: 1645 66.88 - 100.31: 54 100.31 - 133.75: 1 133.75 - 167.19: 3 Dihedral angle restraints: 26283 sinusoidal: 12859 harmonic: 13424 Sorted by residual: dihedral pdb=" O1B ADP I1701 " pdb=" O3A ADP I1701 " pdb=" PB ADP I1701 " pdb=" PA ADP I1701 " ideal model delta sinusoidal sigma weight residual -60.00 -177.48 117.48 1 2.00e+01 2.50e-03 3.51e+01 dihedral pdb=" CA ARG M 341 " pdb=" C ARG M 341 " pdb=" N ASN M 342 " pdb=" CA ASN M 342 " ideal model delta harmonic sigma weight residual -180.00 -155.80 -24.20 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA LYS M 73 " pdb=" C LYS M 73 " pdb=" N PRO M 74 " pdb=" CA PRO M 74 " ideal model delta harmonic sigma weight residual -180.00 -157.15 -22.85 0 5.00e+00 4.00e-02 2.09e+01 ... (remaining 26280 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 6228 0.062 - 0.125: 677 0.125 - 0.187: 12 0.187 - 0.250: 4 0.250 - 0.312: 2 Chirality restraints: 6923 Sorted by residual: chirality pdb=" CA SER O 437 " pdb=" N SER O 437 " pdb=" C SER O 437 " pdb=" CB SER O 437 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" CA VAL O 542 " pdb=" N VAL O 542 " pdb=" C VAL O 542 " pdb=" CB VAL O 542 " both_signs ideal model delta sigma weight residual False 2.44 2.16 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CA PRO O 643 " pdb=" N PRO O 643 " pdb=" C PRO O 643 " pdb=" CB PRO O 643 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 6920 not shown) Planarity restraints: 6764 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN O 436 " -0.013 2.00e-02 2.50e+03 2.62e-02 6.85e+00 pdb=" C ASN O 436 " 0.045 2.00e-02 2.50e+03 pdb=" O ASN O 436 " -0.018 2.00e-02 2.50e+03 pdb=" N SER O 437 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA X 60 " 0.021 2.00e-02 2.50e+03 9.94e-03 2.72e+00 pdb=" N9 DA X 60 " -0.023 2.00e-02 2.50e+03 pdb=" C8 DA X 60 " -0.004 2.00e-02 2.50e+03 pdb=" N7 DA X 60 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DA X 60 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DA X 60 " 0.004 2.00e-02 2.50e+03 pdb=" N6 DA X 60 " 0.007 2.00e-02 2.50e+03 pdb=" N1 DA X 60 " -0.004 2.00e-02 2.50e+03 pdb=" C2 DA X 60 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DA X 60 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DA X 60 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS L 470 " -0.027 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO L 471 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO L 471 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO L 471 " -0.023 5.00e-02 4.00e+02 ... (remaining 6761 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 222 2.52 - 3.11: 34250 3.11 - 3.71: 69948 3.71 - 4.30: 94964 4.30 - 4.90: 147269 Nonbonded interactions: 346653 Sorted by model distance: nonbonded pdb=" OG1 THR J 186 " pdb=" O ARG J 206 " model vdw 1.920 2.440 nonbonded pdb=" OE1 GLU I 365 " pdb=" OG1 THR Q 191 " model vdw 1.973 2.440 nonbonded pdb=" OH TYR O 473 " pdb=" OD2 ASP O 515 " model vdw 2.001 2.440 nonbonded pdb=" OH TYR G 39 " pdb=" OE1 GLU H 71 " model vdw 2.048 2.440 nonbonded pdb=" OG1 THR J 149 " pdb=" OD2 ASP J 292 " model vdw 2.066 2.440 ... (remaining 346648 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 'A' and resid 38 through 135) selection = chain 'E' } ncs_group { reference = (chain 'B' and (resid 16 through 101 or (resid 102 and (name N or name CA or nam \ e C or name O )))) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 14 through 117) } ncs_group { reference = (chain 'D' and resid 31 through 124) selection = chain 'H' } ncs_group { reference = (chain 'N' and (resid 423 through 641 or (resid 642 through 647 and (name N or n \ ame CA or name C or name O or name CB )) or resid 671 through 686 or resid 862 t \ hrough 952)) selection = (chain 'O' and (resid 423 through 515 or resid 602 through 647 or resid 671 thro \ ugh 686 or resid 691 through 693 or resid 696 through 697 or resid 867 through 9 \ 52)) } ncs_group { reference = chain 'T' selection = (chain 'W' and resid 3 through 24) } 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=0.21 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.820 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: 0.030 Extract box with map and model: 12.250 Check model and map are aligned: 0.580 Set scattering table: 0.360 Process input model: 116.690 Find NCS groups from input model: 1.520 Set up NCS constraints: 0.190 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 137.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5469 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 : 0.003 0.088 44565 Z= 0.166 Angle : 0.544 12.178 61592 Z= 0.335 Chirality : 0.036 0.312 6923 Planarity : 0.002 0.040 6764 Dihedral : 18.475 167.188 17541 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.05 % Favored : 94.86 % Rotamer: Outliers : 0.05 % Allowed : 1.14 % Favored : 98.80 % 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: -1.79 (0.12), residues: 4321 helix: -0.11 (0.10), residues: 2408 sheet: -3.01 (0.30), residues: 200 loop : -2.53 (0.14), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP P 320 HIS 0.006 0.000 HIS L 27 PHE 0.015 0.001 PHE I1313 TYR 0.023 0.001 TYR R 225 ARG 0.004 0.000 ARG I1318 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8642 Ramachandran restraints generated. 4321 Oldfield, 0 Emsley, 4321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8642 Ramachandran restraints generated. 4321 Oldfield, 0 Emsley, 4321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 715 residues out of total 3874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 713 time to evaluate : 4.099 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 PHE cc_start: 0.7191 (m-80) cc_final: 0.6739 (m-10) REVERT: B 84 MET cc_start: 0.6083 (mmm) cc_final: 0.5835 (mmm) REVERT: D 98 VAL cc_start: 0.9347 (m) cc_final: 0.8860 (p) REVERT: E 78 PHE cc_start: 0.7475 (m-10) cc_final: 0.7166 (m-10) REVERT: F 22 LEU cc_start: 0.7509 (mp) cc_final: 0.7298 (pt) REVERT: F 60 VAL cc_start: 0.8898 (t) cc_final: 0.8451 (t) REVERT: F 66 ILE cc_start: 0.9130 (mt) cc_final: 0.8693 (tp) REVERT: K 376 MET cc_start: -0.0219 (ptt) cc_final: -0.1248 (ppp) REVERT: L 162 VAL cc_start: 0.9546 (t) cc_final: 0.9282 (t) REVERT: L 211 ASP cc_start: 0.6417 (t0) cc_final: 0.6186 (t70) REVERT: L 332 LEU cc_start: 0.9278 (mm) cc_final: 0.8819 (tp) REVERT: L 372 MET cc_start: 0.8974 (mtt) cc_final: 0.8503 (mtp) REVERT: L 393 GLU cc_start: 0.9036 (pt0) cc_final: 0.8635 (tm-30) REVERT: L 445 MET cc_start: 0.8861 (mtp) cc_final: 0.8459 (mtt) REVERT: M 217 MET cc_start: 0.7688 (mtp) cc_final: 0.7451 (mtp) REVERT: M 301 LEU cc_start: 0.7184 (mm) cc_final: 0.6982 (mm) REVERT: N 936 MET cc_start: 0.8867 (mmp) cc_final: 0.8562 (tmm) REVERT: P 157 LEU cc_start: 0.8797 (tt) cc_final: 0.8569 (tp) REVERT: P 164 LYS cc_start: 0.9043 (mmmt) cc_final: 0.8797 (tmtt) REVERT: P 258 TRP cc_start: 0.2453 (t60) cc_final: 0.0852 (m-10) REVERT: U 1521 TYR cc_start: 0.7383 (t80) cc_final: 0.7101 (m-10) outliers start: 2 outliers final: 1 residues processed: 715 average time/residue: 0.6246 time to fit residues: 697.0604 Evaluate side-chains 385 residues out of total 3874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 384 time to evaluate : 5.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 404 optimal weight: 0.5980 chunk 363 optimal weight: 0.7980 chunk 201 optimal weight: 20.0000 chunk 124 optimal weight: 20.0000 chunk 244 optimal weight: 0.9980 chunk 193 optimal weight: 6.9990 chunk 375 optimal weight: 9.9990 chunk 145 optimal weight: 5.9990 chunk 228 optimal weight: 9.9990 chunk 279 optimal weight: 30.0000 chunk 434 optimal weight: 30.0000 overall best weight: 3.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS C 38 ASN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN G 104 GLN H 84 ASN ** I 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 570 GLN I 745 GLN I 888 ASN I1230 GLN ** J 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 296 ASN K 105 HIS K 189 GLN ** K 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 263 GLN K 294 ASN L 105 HIS ** L 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 406 HIS M 103 ASN M 123 GLN M 140 HIS ** N 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 439 HIS N 467 ASN N 513 GLN N 935 HIS ** O 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 145 GLN P 326 HIS ** P 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 231 HIS S 199 ASN S 206 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5753 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 44565 Z= 0.261 Angle : 0.650 14.446 61592 Z= 0.348 Chirality : 0.039 0.229 6923 Planarity : 0.006 0.114 6764 Dihedral : 22.408 171.848 8596 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.04 % Favored : 93.89 % Rotamer: Outliers : 0.21 % Allowed : 4.29 % Favored : 95.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.83 (0.13), residues: 4321 helix: 0.50 (0.10), residues: 2432 sheet: -2.43 (0.34), residues: 176 loop : -1.87 (0.15), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP M 321 HIS 0.017 0.001 HIS O 638 PHE 0.018 0.002 PHE L 217 TYR 0.027 0.002 TYR N 941 ARG 0.023 0.001 ARG P 274 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8642 Ramachandran restraints generated. 4321 Oldfield, 0 Emsley, 4321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8642 Ramachandran restraints generated. 4321 Oldfield, 0 Emsley, 4321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 3874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 460 time to evaluate : 4.934 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 PHE cc_start: 0.7050 (m-80) cc_final: 0.6783 (m-10) REVERT: D 83 TYR cc_start: 0.7958 (m-10) cc_final: 0.7638 (m-80) REVERT: E 104 PHE cc_start: 0.7505 (m-80) cc_final: 0.7026 (m-10) REVERT: F 59 LYS cc_start: 0.8833 (tmtt) cc_final: 0.8542 (tptp) REVERT: F 63 GLU cc_start: 0.7648 (pt0) cc_final: 0.7128 (pt0) REVERT: G 64 GLU cc_start: 0.6084 (tp30) cc_final: 0.5883 (tp30) REVERT: H 59 MET cc_start: 0.7410 (tpp) cc_final: 0.6970 (tpp) REVERT: I 886 MET cc_start: 0.6607 (mtt) cc_final: 0.6234 (mmp) REVERT: I 1109 MET cc_start: 0.6965 (tpp) cc_final: 0.6592 (tpt) REVERT: K 376 MET cc_start: -0.0109 (ptt) cc_final: -0.1094 (ppp) REVERT: L 287 LEU cc_start: 0.8598 (mm) cc_final: 0.8241 (mm) REVERT: L 332 LEU cc_start: 0.9183 (mm) cc_final: 0.8635 (tp) REVERT: L 372 MET cc_start: 0.9009 (mtt) cc_final: 0.8663 (mtt) REVERT: L 378 LEU cc_start: 0.8729 (tp) cc_final: 0.8525 (tp) REVERT: M 275 LEU cc_start: 0.5781 (tp) cc_final: 0.5412 (tp) REVERT: N 906 PHE cc_start: 0.7878 (t80) cc_final: 0.7654 (t80) REVERT: N 936 MET cc_start: 0.8935 (mmp) cc_final: 0.8735 (tmm) REVERT: O 615 MET cc_start: 0.7930 (mtt) cc_final: 0.7518 (mmp) REVERT: P 161 ILE cc_start: 0.9385 (mt) cc_final: 0.9182 (mt) REVERT: P 164 LYS cc_start: 0.9163 (mmmt) cc_final: 0.8920 (tmtt) REVERT: P 441 MET cc_start: 0.8857 (mpp) cc_final: 0.8532 (mpp) REVERT: P 474 GLU cc_start: 0.7097 (tm-30) cc_final: 0.6798 (tm-30) REVERT: S 572 MET cc_start: -0.0540 (mmm) cc_final: -0.1520 (mtp) outliers start: 8 outliers final: 4 residues processed: 468 average time/residue: 0.5781 time to fit residues: 436.6494 Evaluate side-chains 333 residues out of total 3874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 329 time to evaluate : 4.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 241 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 362 optimal weight: 10.0000 chunk 296 optimal weight: 8.9990 chunk 119 optimal weight: 10.0000 chunk 435 optimal weight: 30.0000 chunk 470 optimal weight: 6.9990 chunk 388 optimal weight: 6.9990 chunk 432 optimal weight: 6.9990 chunk 148 optimal weight: 3.9990 chunk 349 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 ASN ** I 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 519 ASN ** I 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 969 HIS I1253 HIS ** J 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 296 ASN ** L 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L1796 ASN M 140 HIS M 152 ASN N 422 HIS N 439 HIS ** O 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 604 GLN O 638 HIS ** P 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5921 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 44565 Z= 0.275 Angle : 0.657 9.631 61592 Z= 0.355 Chirality : 0.040 0.221 6923 Planarity : 0.006 0.108 6764 Dihedral : 22.871 170.542 8596 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.80 % Favored : 93.13 % Rotamer: Outliers : 0.16 % Allowed : 4.55 % Favored : 95.29 % 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: -0.76 (0.13), residues: 4321 helix: 0.50 (0.10), residues: 2426 sheet: -2.27 (0.34), residues: 180 loop : -1.74 (0.15), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP M 321 HIS 0.009 0.001 HIS L 136 PHE 0.022 0.002 PHE L 217 TYR 0.031 0.002 TYR R 225 ARG 0.019 0.001 ARG M 376 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8642 Ramachandran restraints generated. 4321 Oldfield, 0 Emsley, 4321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8642 Ramachandran restraints generated. 4321 Oldfield, 0 Emsley, 4321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 3874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 412 time to evaluate : 4.379 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: 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: 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: 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: symmetry clash REVERT: A 104 PHE cc_start: 0.7054 (m-80) cc_final: 0.6808 (m-10) REVERT: B 58 LEU cc_start: 0.9045 (pp) cc_final: 0.8536 (pp) REVERT: B 59 LYS cc_start: 0.8570 (mptt) cc_final: 0.8178 (mmtt) REVERT: D 54 ILE cc_start: 0.8245 (pt) cc_final: 0.7992 (mm) REVERT: E 126 LEU cc_start: 0.8340 (tt) cc_final: 0.7984 (tt) REVERT: F 60 VAL cc_start: 0.9581 (t) cc_final: 0.9359 (t) REVERT: F 63 GLU cc_start: 0.7697 (pt0) cc_final: 0.6824 (pt0) REVERT: H 59 MET cc_start: 0.7236 (tpp) cc_final: 0.6863 (tpp) REVERT: H 100 LEU cc_start: 0.8140 (tp) cc_final: 0.7643 (tp) REVERT: I 1109 MET cc_start: 0.7097 (tpp) cc_final: 0.6713 (tpt) REVERT: J 305 MET cc_start: 0.6768 (mmt) cc_final: 0.5615 (mmp) REVERT: K 376 MET cc_start: -0.0119 (ptt) cc_final: -0.0589 (ppp) REVERT: N 489 ASN cc_start: 0.7587 (m-40) cc_final: 0.7319 (m110) REVERT: N 936 MET cc_start: 0.9034 (mmp) cc_final: 0.8786 (tmm) REVERT: O 896 MET cc_start: 0.7623 (mmt) cc_final: 0.7297 (mmt) REVERT: P 149 ASP cc_start: 0.9044 (t0) cc_final: 0.8346 (t0) REVERT: P 164 LYS cc_start: 0.9282 (mmmt) cc_final: 0.8961 (tmtt) REVERT: P 441 MET cc_start: 0.8762 (mpp) cc_final: 0.8480 (mpp) REVERT: P 474 GLU cc_start: 0.6984 (tm-30) cc_final: 0.6743 (tm-30) REVERT: P 494 TYR cc_start: 0.8824 (t80) cc_final: 0.8496 (t80) REVERT: R 228 LEU cc_start: 0.7041 (tp) cc_final: 0.6787 (mp) REVERT: S 572 MET cc_start: -0.0634 (mmm) cc_final: -0.1522 (mtt) outliers start: 6 outliers final: 4 residues processed: 418 average time/residue: 0.5681 time to fit residues: 387.9190 Evaluate side-chains 306 residues out of total 3874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 302 time to evaluate : 4.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 430 optimal weight: 6.9990 chunk 327 optimal weight: 0.7980 chunk 226 optimal weight: 0.9980 chunk 48 optimal weight: 8.9990 chunk 207 optimal weight: 0.0670 chunk 292 optimal weight: 2.9990 chunk 437 optimal weight: 20.0000 chunk 463 optimal weight: 6.9990 chunk 228 optimal weight: 9.9990 chunk 414 optimal weight: 30.0000 chunk 124 optimal weight: 3.9990 overall best weight: 1.7722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 ASN I 375 GLN ** I 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 570 GLN ** I 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 296 ASN ** L 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 140 HIS N 439 HIS ** O 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 211 ASN S 394 ASN ** S 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5888 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 44565 Z= 0.181 Angle : 0.596 11.288 61592 Z= 0.319 Chirality : 0.038 0.183 6923 Planarity : 0.004 0.044 6764 Dihedral : 22.918 161.911 8596 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.60 % Favored : 93.33 % Rotamer: Outliers : 0.08 % Allowed : 3.25 % Favored : 96.67 % 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: -0.45 (0.13), residues: 4321 helix: 0.74 (0.10), residues: 2412 sheet: -1.94 (0.33), residues: 203 loop : -1.58 (0.15), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP M 321 HIS 0.008 0.001 HIS N 905 PHE 0.020 0.001 PHE K 309 TYR 0.038 0.001 TYR R 225 ARG 0.009 0.000 ARG I1189 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8642 Ramachandran restraints generated. 4321 Oldfield, 0 Emsley, 4321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8642 Ramachandran restraints generated. 4321 Oldfield, 0 Emsley, 4321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 3874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 404 time to evaluate : 4.784 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: 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: 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: 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: symmetry clash REVERT: A 104 PHE cc_start: 0.6973 (m-80) cc_final: 0.6612 (m-10) REVERT: B 58 LEU cc_start: 0.9149 (pp) cc_final: 0.8645 (pp) REVERT: B 59 LYS cc_start: 0.8695 (mptt) cc_final: 0.8174 (mmtt) REVERT: E 74 ILE cc_start: 0.8819 (pt) cc_final: 0.8299 (pt) REVERT: H 59 MET cc_start: 0.7013 (tpp) cc_final: 0.6679 (tpp) REVERT: H 71 GLU cc_start: 0.7527 (pp20) cc_final: 0.7301 (pp20) REVERT: H 100 LEU cc_start: 0.7978 (tp) cc_final: 0.7592 (tp) REVERT: I 1109 MET cc_start: 0.7427 (tpp) cc_final: 0.7052 (tpt) REVERT: J 305 MET cc_start: 0.5372 (mmp) cc_final: 0.4883 (mmp) REVERT: K 376 MET cc_start: -0.0131 (ptt) cc_final: -0.0552 (ppp) REVERT: L 287 LEU cc_start: 0.8756 (mm) cc_final: 0.8431 (mm) REVERT: N 936 MET cc_start: 0.9085 (mmp) cc_final: 0.8819 (tmm) REVERT: P 149 ASP cc_start: 0.9015 (t0) cc_final: 0.8523 (t0) REVERT: P 162 MET cc_start: 0.8653 (mmm) cc_final: 0.8116 (mmm) REVERT: P 164 LYS cc_start: 0.9300 (mmmt) cc_final: 0.8995 (tmtt) REVERT: P 494 TYR cc_start: 0.8763 (t80) cc_final: 0.8372 (t80) REVERT: S 572 MET cc_start: -0.0671 (mmm) cc_final: -0.1501 (mtt) outliers start: 3 outliers final: 2 residues processed: 406 average time/residue: 0.5485 time to fit residues: 363.0540 Evaluate side-chains 308 residues out of total 3874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 306 time to evaluate : 4.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 385 optimal weight: 9.9990 chunk 262 optimal weight: 0.0870 chunk 6 optimal weight: 5.9990 chunk 344 optimal weight: 20.0000 chunk 191 optimal weight: 5.9990 chunk 395 optimal weight: 1.9990 chunk 320 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 236 optimal weight: 10.0000 chunk 415 optimal weight: 0.0270 chunk 116 optimal weight: 7.9990 overall best weight: 1.7220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 570 GLN ** I 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 296 ASN ** K 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 140 HIS N 422 HIS N 439 HIS N 454 ASN ** O 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 211 ASN S 592 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5907 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 44565 Z= 0.179 Angle : 0.586 11.256 61592 Z= 0.314 Chirality : 0.038 0.213 6923 Planarity : 0.004 0.045 6764 Dihedral : 22.889 157.886 8596 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.94 % Favored : 92.99 % Rotamer: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % 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: -0.38 (0.13), residues: 4321 helix: 0.76 (0.10), residues: 2437 sheet: -1.76 (0.33), residues: 215 loop : -1.55 (0.16), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 321 HIS 0.008 0.001 HIS O 905 PHE 0.023 0.001 PHE K 289 TYR 0.023 0.001 TYR N 922 ARG 0.009 0.000 ARG L 95 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8642 Ramachandran restraints generated. 4321 Oldfield, 0 Emsley, 4321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8642 Ramachandran restraints generated. 4321 Oldfield, 0 Emsley, 4321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 3874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 388 time to evaluate : 5.006 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: 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: 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: 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 94 GLU cc_start: 0.7608 (tp30) cc_final: 0.7322 (tp30) REVERT: B 58 LEU cc_start: 0.9216 (pp) cc_final: 0.8715 (pp) REVERT: B 59 LYS cc_start: 0.8632 (mptt) cc_final: 0.8126 (mmtt) REVERT: B 97 LEU cc_start: 0.8064 (tp) cc_final: 0.7851 (tp) REVERT: D 83 TYR cc_start: 0.7932 (m-80) cc_final: 0.7125 (m-80) REVERT: E 74 ILE cc_start: 0.8783 (pt) cc_final: 0.8350 (pt) REVERT: H 59 MET cc_start: 0.7046 (tpp) cc_final: 0.6736 (tpp) REVERT: H 98 VAL cc_start: 0.8802 (t) cc_final: 0.8544 (t) REVERT: I 1109 MET cc_start: 0.7575 (tpp) cc_final: 0.7122 (tpt) REVERT: J 123 MET cc_start: 0.5016 (mmm) cc_final: 0.4614 (mmm) REVERT: J 153 MET cc_start: 0.1583 (tpt) cc_final: 0.0588 (tpp) REVERT: J 305 MET cc_start: 0.5278 (mmp) cc_final: 0.4813 (mmp) REVERT: K 254 MET cc_start: 0.1656 (mmp) cc_final: 0.1051 (mmp) REVERT: K 376 MET cc_start: -0.0100 (ptt) cc_final: -0.0516 (ppp) REVERT: L 287 LEU cc_start: 0.8796 (mm) cc_final: 0.8446 (mm) REVERT: M 275 LEU cc_start: 0.6151 (tp) cc_final: 0.5735 (tp) REVERT: M 301 LEU cc_start: 0.7473 (mm) cc_final: 0.7232 (mm) REVERT: N 936 MET cc_start: 0.9100 (mmp) cc_final: 0.8853 (tmm) REVERT: O 896 MET cc_start: 0.7423 (mtp) cc_final: 0.6387 (mmt) REVERT: P 149 ASP cc_start: 0.8524 (t0) cc_final: 0.7694 (t0) REVERT: P 161 ILE cc_start: 0.9376 (tt) cc_final: 0.8763 (pt) REVERT: P 162 MET cc_start: 0.8694 (mmm) cc_final: 0.8101 (mmm) REVERT: P 164 LYS cc_start: 0.9295 (mmmt) cc_final: 0.8973 (tmtt) REVERT: P 441 MET cc_start: 0.8929 (mpp) cc_final: 0.8585 (mpp) REVERT: P 494 TYR cc_start: 0.8778 (t80) cc_final: 0.8406 (t80) REVERT: Q 205 GLU cc_start: 0.5804 (tp30) cc_final: 0.5571 (tp30) REVERT: S 181 MET cc_start: -0.0709 (ptp) cc_final: -0.1009 (mtp) REVERT: S 572 MET cc_start: -0.0645 (mmm) cc_final: -0.1444 (mtt) outliers start: 0 outliers final: 0 residues processed: 388 average time/residue: 0.5534 time to fit residues: 355.1285 Evaluate side-chains 299 residues out of total 3874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 299 time to evaluate : 4.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 155 optimal weight: 0.8980 chunk 416 optimal weight: 0.0470 chunk 91 optimal weight: 20.0000 chunk 271 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 463 optimal weight: 6.9990 chunk 384 optimal weight: 0.9980 chunk 214 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 153 optimal weight: 8.9990 chunk 243 optimal weight: 6.9990 overall best weight: 1.1480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 ASN ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 92 ASN ** J 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 140 HIS ** M 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 439 HIS ** O 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 252 HIS R 211 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5891 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 44565 Z= 0.163 Angle : 0.585 11.820 61592 Z= 0.311 Chirality : 0.038 0.208 6923 Planarity : 0.004 0.080 6764 Dihedral : 22.850 156.237 8596 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.78 % Favored : 93.15 % Rotamer: Outliers : 0.05 % Allowed : 1.82 % Favored : 98.13 % 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: -0.32 (0.13), residues: 4321 helix: 0.79 (0.10), residues: 2440 sheet: -1.51 (0.35), residues: 203 loop : -1.53 (0.16), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 321 HIS 0.011 0.001 HIS H 49 PHE 0.022 0.001 PHE P 153 TYR 0.023 0.001 TYR N 922 ARG 0.010 0.000 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8642 Ramachandran restraints generated. 4321 Oldfield, 0 Emsley, 4321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8642 Ramachandran restraints generated. 4321 Oldfield, 0 Emsley, 4321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 3874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 391 time to evaluate : 4.348 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.7633 (tp30) cc_final: 0.7366 (tp30) REVERT: A 97 GLU cc_start: 0.6902 (mt-10) cc_final: 0.6541 (mm-30) REVERT: E 74 ILE cc_start: 0.8854 (pt) cc_final: 0.8368 (pt) REVERT: G 62 ILE cc_start: 0.8394 (pt) cc_final: 0.8058 (pt) REVERT: G 87 ILE cc_start: 0.8730 (pt) cc_final: 0.8494 (pt) REVERT: G 95 LYS cc_start: 0.8250 (pttp) cc_final: 0.7911 (ttpp) REVERT: H 59 MET cc_start: 0.6996 (tpp) cc_final: 0.6636 (tpp) REVERT: I 1109 MET cc_start: 0.7683 (tpp) cc_final: 0.7355 (mmt) REVERT: J 305 MET cc_start: 0.5314 (mmp) cc_final: 0.4800 (mmp) REVERT: K 254 MET cc_start: 0.1687 (mmp) cc_final: 0.1186 (mmp) REVERT: L 65 GLU cc_start: 0.9086 (mp0) cc_final: 0.8877 (mp0) REVERT: L 317 LEU cc_start: 0.9491 (mt) cc_final: 0.9266 (pp) REVERT: M 275 LEU cc_start: 0.6073 (tp) cc_final: 0.5854 (tp) REVERT: N 936 MET cc_start: 0.9097 (mmp) cc_final: 0.8854 (tmm) REVERT: O 896 MET cc_start: 0.7283 (mtp) cc_final: 0.6538 (mmt) REVERT: P 149 ASP cc_start: 0.8574 (t0) cc_final: 0.7921 (t0) REVERT: P 157 LEU cc_start: 0.9533 (mt) cc_final: 0.9175 (pp) REVERT: P 161 ILE cc_start: 0.9431 (tt) cc_final: 0.8793 (pt) REVERT: P 162 MET cc_start: 0.8767 (mmm) cc_final: 0.8193 (mmm) REVERT: P 164 LYS cc_start: 0.9295 (mmmt) cc_final: 0.8972 (tmtt) REVERT: P 404 MET cc_start: 0.8753 (mtm) cc_final: 0.8535 (mtp) REVERT: P 441 MET cc_start: 0.8922 (mpp) cc_final: 0.8556 (mpp) REVERT: P 494 TYR cc_start: 0.8712 (t80) cc_final: 0.8330 (t80) REVERT: S 572 MET cc_start: -0.0650 (mmm) cc_final: -0.1424 (mtt) outliers start: 2 outliers final: 1 residues processed: 393 average time/residue: 0.5523 time to fit residues: 359.6166 Evaluate side-chains 305 residues out of total 3874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 304 time to evaluate : 4.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 446 optimal weight: 10.0000 chunk 52 optimal weight: 8.9990 chunk 264 optimal weight: 0.0270 chunk 338 optimal weight: 8.9990 chunk 262 optimal weight: 2.9990 chunk 390 optimal weight: 2.9990 chunk 258 optimal weight: 9.9990 chunk 461 optimal weight: 20.0000 chunk 288 optimal weight: 4.9990 chunk 281 optimal weight: 6.9990 chunk 213 optimal weight: 1.9990 overall best weight: 2.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 915 GLN ** J 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 73 ASN K 110 HIS ** K 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 140 HIS ** M 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 422 HIS N 439 HIS ** O 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 211 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5984 moved from start: 0.4586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.134 44565 Z= 0.220 Angle : 0.610 11.988 61592 Z= 0.327 Chirality : 0.038 0.206 6923 Planarity : 0.004 0.070 6764 Dihedral : 22.919 155.550 8596 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.24 % Favored : 92.69 % Rotamer: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % 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: -0.29 (0.13), residues: 4321 helix: 0.79 (0.10), residues: 2433 sheet: -1.46 (0.36), residues: 199 loop : -1.47 (0.16), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 206 HIS 0.019 0.001 HIS J 73 PHE 0.020 0.001 PHE O 951 TYR 0.047 0.002 TYR D 83 ARG 0.008 0.000 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8642 Ramachandran restraints generated. 4321 Oldfield, 0 Emsley, 4321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8642 Ramachandran restraints generated. 4321 Oldfield, 0 Emsley, 4321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 3874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 365 time to evaluate : 4.538 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: 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: 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 94 GLU cc_start: 0.7612 (tp30) cc_final: 0.7397 (tp30) REVERT: A 97 GLU cc_start: 0.6925 (mt-10) cc_final: 0.6579 (mm-30) REVERT: E 74 ILE cc_start: 0.8946 (pt) cc_final: 0.8431 (pt) REVERT: G 62 ILE cc_start: 0.8568 (pt) cc_final: 0.8273 (pt) REVERT: G 95 LYS cc_start: 0.8205 (pttp) cc_final: 0.7870 (ttpp) REVERT: H 59 MET cc_start: 0.7098 (tpp) cc_final: 0.6714 (tpp) REVERT: I 1109 MET cc_start: 0.7771 (tpp) cc_final: 0.7426 (mmt) REVERT: J 305 MET cc_start: 0.5519 (mmp) cc_final: 0.4969 (mmp) REVERT: L 287 LEU cc_start: 0.8947 (mm) cc_final: 0.8705 (mm) REVERT: M 38 MET cc_start: -0.0104 (ptm) cc_final: -0.0313 (ptm) REVERT: M 275 LEU cc_start: 0.6206 (tp) cc_final: 0.5954 (tp) REVERT: P 148 MET cc_start: 0.9213 (mpp) cc_final: 0.8957 (mpp) REVERT: P 161 ILE cc_start: 0.9456 (tt) cc_final: 0.8832 (pt) REVERT: P 162 MET cc_start: 0.8844 (mmm) cc_final: 0.8239 (mmm) REVERT: P 494 TYR cc_start: 0.8702 (t80) cc_final: 0.8366 (t80) REVERT: S 572 MET cc_start: -0.0729 (mmm) cc_final: -0.1783 (mtp) outliers start: 0 outliers final: 0 residues processed: 365 average time/residue: 0.5404 time to fit residues: 328.2520 Evaluate side-chains 281 residues out of total 3874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 281 time to evaluate : 4.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 285 optimal weight: 6.9990 chunk 184 optimal weight: 50.0000 chunk 275 optimal weight: 40.0000 chunk 139 optimal weight: 1.9990 chunk 90 optimal weight: 9.9990 chunk 89 optimal weight: 7.9990 chunk 293 optimal weight: 1.9990 chunk 314 optimal weight: 9.9990 chunk 228 optimal weight: 8.9990 chunk 43 optimal weight: 0.6980 chunk 362 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: ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 380 HIS ** I 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 847 GLN I1104 GLN I1187 GLN J 73 HIS ** J 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 192 GLN M 140 HIS ** M 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 318 GLN M 380 ASN N 422 HIS ** N 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 875 HIS ** O 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 200 HIS ** R 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 213 ASN S 142 GLN S 561 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6135 moved from start: 0.5446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 44565 Z= 0.282 Angle : 0.689 13.178 61592 Z= 0.370 Chirality : 0.040 0.203 6923 Planarity : 0.005 0.104 6764 Dihedral : 23.349 155.043 8596 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 20.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.87 % Favored : 92.06 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.60 (0.13), residues: 4321 helix: 0.49 (0.10), residues: 2406 sheet: -1.46 (0.37), residues: 208 loop : -1.50 (0.15), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP M 206 HIS 0.010 0.001 HIS J 73 PHE 0.030 0.002 PHE E 104 TYR 0.066 0.002 TYR O 922 ARG 0.012 0.001 ARG P 180 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8642 Ramachandran restraints generated. 4321 Oldfield, 0 Emsley, 4321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8642 Ramachandran restraints generated. 4321 Oldfield, 0 Emsley, 4321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 358 time to evaluate : 4.303 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.7718 (tp30) cc_final: 0.7455 (tp30) REVERT: D 79 ARG cc_start: 0.7974 (ptp-110) cc_final: 0.7623 (ptp90) REVERT: E 74 ILE cc_start: 0.8905 (pt) cc_final: 0.8388 (pt) REVERT: G 62 ILE cc_start: 0.8698 (pt) cc_final: 0.8472 (pt) REVERT: G 95 LYS cc_start: 0.8022 (pttp) cc_final: 0.7610 (ttpp) REVERT: H 59 MET cc_start: 0.7076 (tpp) cc_final: 0.6820 (tpp) REVERT: I 749 MET cc_start: 0.3938 (tpp) cc_final: 0.3471 (tpt) REVERT: I 1011 MET cc_start: 0.6865 (mmt) cc_final: 0.6341 (mmt) REVERT: I 1109 MET cc_start: 0.7873 (tpp) cc_final: 0.7501 (mmt) REVERT: J 123 MET cc_start: 0.5332 (mmm) cc_final: 0.4999 (mmm) REVERT: J 305 MET cc_start: 0.5636 (mmp) cc_final: 0.5162 (mmp) REVERT: L 477 MET cc_start: 0.8808 (ppp) cc_final: 0.8006 (mmp) REVERT: M 275 LEU cc_start: 0.6353 (tp) cc_final: 0.6022 (tp) REVERT: N 489 ASN cc_start: 0.7655 (m-40) cc_final: 0.7352 (m110) REVERT: P 149 ASP cc_start: 0.8906 (t70) cc_final: 0.8060 (t0) REVERT: P 161 ILE cc_start: 0.9490 (tt) cc_final: 0.8830 (pt) REVERT: P 162 MET cc_start: 0.8930 (mmm) cc_final: 0.8327 (mmm) REVERT: P 366 MET cc_start: 0.6742 (mmp) cc_final: 0.6537 (mmm) REVERT: P 494 TYR cc_start: 0.8731 (t80) cc_final: 0.8422 (t80) REVERT: Q 205 GLU cc_start: 0.6422 (tp30) cc_final: 0.5782 (pt0) REVERT: S 572 MET cc_start: -0.0477 (mmm) cc_final: -0.1590 (mtp) outliers start: 0 outliers final: 0 residues processed: 358 average time/residue: 0.5334 time to fit residues: 315.3357 Evaluate side-chains 260 residues out of total 3874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 260 time to evaluate : 4.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 419 optimal weight: 6.9990 chunk 442 optimal weight: 20.0000 chunk 403 optimal weight: 0.5980 chunk 430 optimal weight: 5.9990 chunk 258 optimal weight: 0.8980 chunk 187 optimal weight: 2.9990 chunk 337 optimal weight: 4.9990 chunk 132 optimal weight: 6.9990 chunk 388 optimal weight: 50.0000 chunk 406 optimal weight: 2.9990 chunk 428 optimal weight: 0.6980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 HIS ** I 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 121 GLN ** J 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 140 HIS ** M 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 875 HIS ** O 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 213 ASN S 142 GLN ** S 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6059 moved from start: 0.5484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 44565 Z= 0.184 Angle : 0.629 12.869 61592 Z= 0.333 Chirality : 0.039 0.185 6923 Planarity : 0.004 0.067 6764 Dihedral : 23.338 153.454 8596 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.31 % Favored : 92.62 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % 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: -0.42 (0.13), residues: 4321 helix: 0.66 (0.10), residues: 2409 sheet: -1.30 (0.38), residues: 194 loop : -1.48 (0.16), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP L 237 HIS 0.007 0.001 HIS L 28 PHE 0.022 0.001 PHE G 25 TYR 0.030 0.002 TYR O 922 ARG 0.009 0.000 ARG C 29 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8642 Ramachandran restraints generated. 4321 Oldfield, 0 Emsley, 4321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8642 Ramachandran restraints generated. 4321 Oldfield, 0 Emsley, 4321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 3874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 364 time to evaluate : 4.453 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.7614 (tp30) cc_final: 0.7398 (tp30) REVERT: E 74 ILE cc_start: 0.8899 (pt) cc_final: 0.8462 (pt) REVERT: E 104 PHE cc_start: 0.7006 (m-10) cc_final: 0.6781 (m-10) REVERT: G 64 GLU cc_start: 0.6594 (tp30) cc_final: 0.6334 (tp30) REVERT: H 59 MET cc_start: 0.6862 (tpp) cc_final: 0.6548 (tpp) REVERT: H 100 LEU cc_start: 0.8621 (tp) cc_final: 0.8300 (tp) REVERT: I 1109 MET cc_start: 0.7926 (tpp) cc_final: 0.7569 (mmt) REVERT: J 123 MET cc_start: 0.5666 (mmm) cc_final: 0.5173 (mmm) REVERT: J 153 MET cc_start: 0.1857 (tpt) cc_final: 0.1161 (tpp) REVERT: J 305 MET cc_start: 0.5547 (mmp) cc_final: 0.5124 (mmp) REVERT: K 254 MET cc_start: 0.2067 (mmp) cc_final: 0.1410 (mmp) REVERT: L 317 LEU cc_start: 0.9527 (mt) cc_final: 0.9292 (pp) REVERT: M 156 MET cc_start: 0.7554 (tmm) cc_final: 0.7270 (tmm) REVERT: M 275 LEU cc_start: 0.5819 (tp) cc_final: 0.5352 (tp) REVERT: N 489 ASN cc_start: 0.7668 (m-40) cc_final: 0.7314 (m110) REVERT: N 674 MET cc_start: 0.4303 (mpp) cc_final: 0.2212 (ttt) REVERT: P 148 MET cc_start: 0.9184 (mpp) cc_final: 0.8958 (mpp) REVERT: P 161 ILE cc_start: 0.9521 (tt) cc_final: 0.8869 (pt) REVERT: P 162 MET cc_start: 0.8801 (mmm) cc_final: 0.8149 (mmm) REVERT: P 494 TYR cc_start: 0.8688 (t80) cc_final: 0.8306 (t80) REVERT: Q 205 GLU cc_start: 0.6610 (tp30) cc_final: 0.6399 (tp30) REVERT: S 572 MET cc_start: -0.0384 (mmm) cc_final: -0.1545 (mtp) outliers start: 0 outliers final: 0 residues processed: 364 average time/residue: 0.5475 time to fit residues: 333.4345 Evaluate side-chains 277 residues out of total 3874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 277 time to evaluate : 4.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 282 optimal weight: 0.9990 chunk 454 optimal weight: 7.9990 chunk 277 optimal weight: 7.9990 chunk 215 optimal weight: 0.9990 chunk 316 optimal weight: 7.9990 chunk 477 optimal weight: 30.0000 chunk 439 optimal weight: 20.0000 chunk 380 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 293 optimal weight: 0.7980 chunk 233 optimal weight: 4.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 ASN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 915 GLN ** J 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 73 ASN ** K 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 159 ASN M 140 HIS ** M 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 422 HIS ** N 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 875 HIS O 423 HIS ** O 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 211 ASN S 561 ASN ** S 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6036 moved from start: 0.5594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 44565 Z= 0.173 Angle : 0.620 12.888 61592 Z= 0.329 Chirality : 0.038 0.194 6923 Planarity : 0.004 0.064 6764 Dihedral : 23.186 154.627 8596 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.17 % Favored : 92.76 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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: -0.32 (0.13), residues: 4321 helix: 0.74 (0.11), residues: 2403 sheet: -1.17 (0.38), residues: 194 loop : -1.42 (0.16), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 237 HIS 0.006 0.001 HIS P 308 PHE 0.032 0.001 PHE P 153 TYR 0.037 0.001 TYR D 83 ARG 0.008 0.000 ARG C 29 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8642 Ramachandran restraints generated. 4321 Oldfield, 0 Emsley, 4321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8642 Ramachandran restraints generated. 4321 Oldfield, 0 Emsley, 4321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 3874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 361 time to evaluate : 4.286 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.7638 (tp30) cc_final: 0.7374 (tp30) REVERT: E 70 LEU cc_start: 0.8710 (tp) cc_final: 0.8378 (tt) REVERT: E 74 ILE cc_start: 0.8953 (pt) cc_final: 0.8420 (pt) REVERT: G 62 ILE cc_start: 0.8429 (pt) cc_final: 0.8181 (pt) REVERT: H 59 MET cc_start: 0.6975 (tpp) cc_final: 0.6709 (tpp) REVERT: H 100 LEU cc_start: 0.8569 (tp) cc_final: 0.8280 (tp) REVERT: H 106 LEU cc_start: 0.7771 (tt) cc_final: 0.7489 (tt) REVERT: I 1109 MET cc_start: 0.7993 (tpp) cc_final: 0.7578 (tpt) REVERT: J 123 MET cc_start: 0.5641 (mmm) cc_final: 0.5207 (mmm) REVERT: J 153 MET cc_start: 0.1099 (tpt) cc_final: 0.0536 (tpp) REVERT: J 227 MET cc_start: 0.1836 (mmt) cc_final: 0.1324 (mmm) REVERT: J 305 MET cc_start: 0.5845 (mmp) cc_final: 0.5338 (mmp) REVERT: K 254 MET cc_start: 0.1963 (mmp) cc_final: 0.1393 (mmp) REVERT: K 335 MET cc_start: 0.7551 (ptt) cc_final: 0.7296 (ptt) REVERT: L 315 PHE cc_start: 0.8668 (t80) cc_final: 0.8411 (t80) REVERT: L 317 LEU cc_start: 0.9511 (mt) cc_final: 0.9308 (pp) REVERT: M 156 MET cc_start: 0.7383 (tmm) cc_final: 0.7075 (tmm) REVERT: M 275 LEU cc_start: 0.5682 (tp) cc_final: 0.5303 (tp) REVERT: N 674 MET cc_start: 0.4530 (mpp) cc_final: 0.4263 (mpp) REVERT: N 896 MET cc_start: 0.9138 (mmp) cc_final: 0.8929 (mmm) REVERT: P 148 MET cc_start: 0.9257 (mpp) cc_final: 0.8994 (mpp) REVERT: P 157 LEU cc_start: 0.9495 (mt) cc_final: 0.9084 (pp) REVERT: P 161 ILE cc_start: 0.9496 (tt) cc_final: 0.8882 (pt) REVERT: P 162 MET cc_start: 0.8808 (mmm) cc_final: 0.8123 (mmm) REVERT: P 441 MET cc_start: 0.8968 (mpp) cc_final: 0.8292 (mpp) REVERT: P 494 TYR cc_start: 0.8669 (t80) cc_final: 0.8272 (t80) REVERT: Q 205 GLU cc_start: 0.6119 (tp30) cc_final: 0.5892 (pt0) REVERT: S 572 MET cc_start: -0.0069 (mmm) cc_final: -0.1660 (mtp) outliers start: 0 outliers final: 0 residues processed: 361 average time/residue: 0.5169 time to fit residues: 314.3871 Evaluate side-chains 278 residues out of total 3874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 278 time to evaluate : 4.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 301 optimal weight: 0.9990 chunk 404 optimal weight: 10.0000 chunk 116 optimal weight: 0.8980 chunk 350 optimal weight: 10.0000 chunk 56 optimal weight: 0.8980 chunk 105 optimal weight: 0.0980 chunk 380 optimal weight: 10.0000 chunk 159 optimal weight: 8.9990 chunk 390 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 HIS C 38 ASN ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN D 67 ASN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 140 HIS ** M 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 875 HIS ** O 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.065112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.045302 restraints weight = 451594.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.046353 restraints weight = 243706.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.047113 restraints weight = 162338.662| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3280 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3280 r_free = 0.3280 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3280 r_free = 0.3280 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3280 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.5619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 44565 Z= 0.163 Angle : 0.619 12.773 61592 Z= 0.325 Chirality : 0.038 0.271 6923 Planarity : 0.004 0.063 6764 Dihedral : 23.080 154.529 8596 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.92 % Favored : 93.03 % 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: -0.31 (0.13), residues: 4321 helix: 0.73 (0.11), residues: 2405 sheet: -1.08 (0.38), residues: 192 loop : -1.42 (0.16), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 237 HIS 0.006 0.001 HIS P 308 PHE 0.021 0.001 PHE G 25 TYR 0.033 0.001 TYR O 922 ARG 0.011 0.000 ARG R 216 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8622.16 seconds wall clock time: 157 minutes 8.01 seconds (9428.01 seconds total)