Starting phenix.real_space_refine on Fri Apr 12 06:55:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r57_18903/04_2024/8r57_18903_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r57_18903/04_2024/8r57_18903.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r57_18903/04_2024/8r57_18903_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r57_18903/04_2024/8r57_18903_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r57_18903/04_2024/8r57_18903_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r57_18903/04_2024/8r57_18903.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r57_18903/04_2024/8r57_18903.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r57_18903/04_2024/8r57_18903_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r57_18903/04_2024/8r57_18903_updated.pdb" } resolution = 2.55 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= 0.003 sd= 0.087 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 K 6 8.98 5 Zn 2 6.06 5 P 458 5.49 5 Mg 20 5.21 5 S 81 5.16 5 C 13763 2.51 5 N 4474 2.21 5 O 6244 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K GLU 10": "OE1" <-> "OE2" Residue "K GLU 53": "OE1" <-> "OE2" Residue "K GLU 57": "OE1" <-> "OE2" Residue "M ARG 49": "NH1" <-> "NH2" Residue "M GLU 50": "OE1" <-> "OE2" Residue "M GLU 129": "OE1" <-> "OE2" Residue "F GLU 23": "OE1" <-> "OE2" Residue "F GLU 28": "OE1" <-> "OE2" Residue "F ARG 40": "NH1" <-> "NH2" Residue "F GLU 47": "OE1" <-> "OE2" Residue "F GLU 81": "OE1" <-> "OE2" Residue "F ARG 106": "NH1" <-> "NH2" Residue "F ARG 124": "NH1" <-> "NH2" Residue "P ARG 123": "NH1" <-> "NH2" Residue "P GLU 172": "OE1" <-> "OE2" Residue "Q GLU 48": "OE1" <-> "OE2" Residue "Q ARG 63": "NH1" <-> "NH2" Residue "Q GLU 105": "OE1" <-> "OE2" Residue "Q ARG 117": "NH1" <-> "NH2" Residue "U GLU 41": "OE1" <-> "OE2" Residue "U GLU 119": "OE1" <-> "OE2" Residue "T GLU 26": "OE1" <-> "OE2" Residue "T GLU 42": "OE1" <-> "OE2" Residue "T ARG 142": "NH1" <-> "NH2" Residue "c ARG 62": "NH1" <-> "NH2" Residue "g GLU 6": "OE1" <-> "OE2" Residue "g TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 61": "OE1" <-> "OE2" Residue "g GLU 96": "OE1" <-> "OE2" Residue "g ARG 98": "NH1" <-> "NH2" Residue "g ARG 110": "NH1" <-> "NH2" Residue "g ARG 128": "NH1" <-> "NH2" Residue "g ARG 137": "NH1" <-> "NH2" Residue "g ARG 187": "NH1" <-> "NH2" Residue "S GLU 8": "OE1" <-> "OE2" Residue "S GLU 58": "OE1" <-> "OE2" Residue "S GLU 63": "OE1" <-> "OE2" Residue "S PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 39": "OE1" <-> "OE2" Residue "R GLU 82": "OE1" <-> "OE2" Residue "R GLU 96": "OE1" <-> "OE2" Residue "R TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 36": "OE1" <-> "OE2" Residue "f GLU 45": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 25048 Number of models: 1 Model: "" Number of chains: 29 Chain: "K" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 718 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain: "M" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 887 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "F" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1652 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 9, 'TRANS': 201} Chain: "P" Number of atoms: 1453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1453 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 176} Chain breaks: 1 Chain: "Q" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1153 Classifications: {'peptide': 145} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 136} Chain: "U" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 806 Classifications: {'peptide': 103} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 97} Chain: "T" Number of atoms: 1099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1099 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 8, 'TRANS': 131} Chain: "Z" Number of atoms: 570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 570 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "c" Number of atoms: 498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 498 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 60} Chain: "d" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 436 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain: "g" Number of atoms: 2424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2424 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain breaks: 1 Chain: "S" Number of atoms: 1147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1147 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 2, 'TRANS': 137} Chain: "R" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 953 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 9, 'TRANS': 109} Chain: "h" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 587 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 1, 'TRANS': 69} Chain: "A" Number of atoms: 9766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 9766 Classifications: {'RNA': 458} Modifications used: {'rna2p': 2, 'rna2p_pur': 38, 'rna2p_pyr': 42, 'rna3p': 25, 'rna3p_pur': 188, 'rna3p_pyr': 161} Link IDs: {'rna2p': 82, 'rna3p': 375} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 6 Chain: "f" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 514 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 1, 'TRANS': 62} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Unusual residues: {' K': 5, ' MG': 19} Classifications: {'undetermined': 24} Link IDs: {None: 23} Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "P" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "Q" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "U" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "T" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "d" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 308 Classifications: {'water': 308} Link IDs: {None: 307} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8988 SG CYS d 21 81.259 42.457 73.880 1.00 12.85 S ATOM 9012 SG CYS d 24 80.672 39.513 75.625 1.00 14.37 S ATOM 9124 SG CYS d 39 84.298 41.119 75.706 1.00 11.44 S ATOM 9150 SG CYS d 42 83.360 39.546 72.596 1.00 12.29 S ATOM 24474 SG CYS f 51 35.861 52.721 82.190 1.00 54.44 S ATOM 24594 SG CYS f 66 35.307 50.432 85.602 1.00 56.63 S ATOM 24613 SG CYS f 69 37.501 53.067 85.615 1.00 57.10 S Time building chain proxies: 13.57, per 1000 atoms: 0.54 Number of scatterers: 25048 At special positions: 0 Unit cell: (174.58, 123.84, 141.9, 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) Zn 2 29.99 K 6 19.00 S 81 16.00 P 458 15.00 Mg 20 11.99 O 6244 8.00 N 4474 7.00 C 13763 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.44 Conformation dependent library (CDL) restraints added in 3.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN d 101 " pdb="ZN ZN d 101 " - pdb=" SG CYS d 39 " pdb="ZN ZN d 101 " - pdb=" SG CYS d 24 " pdb="ZN ZN d 101 " - pdb=" SG CYS d 42 " pdb="ZN ZN d 101 " - pdb=" SG CYS d 21 " pdb=" ZN f 100 " pdb="ZN ZN f 100 " - pdb=" SG CYS f 51 " pdb="ZN ZN f 100 " - pdb=" SG CYS f 66 " pdb="ZN ZN f 100 " - pdb=" SG CYS f 69 " Number of angles added : 6 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3484 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 63 helices and 20 sheets defined 32.7% alpha, 15.9% beta 119 base pairs and 237 stacking pairs defined. Time for finding SS restraints: 13.70 Creating SS restraints... Processing helix chain 'K' and resid 5 through 18 Processing helix chain 'K' and resid 39 through 51 Processing helix chain 'K' and resid 70 through 79 removed outlier: 3.535A pdb=" N ARG K 77 " --> pdb=" O ILE K 73 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 41 removed outlier: 3.642A pdb=" N LEU M 33 " --> pdb=" O ALA M 30 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL M 34 " --> pdb=" O LEU M 31 " (cutoff:3.500A) Processing helix chain 'M' and resid 48 through 56 removed outlier: 3.850A pdb=" N LYS M 53 " --> pdb=" O ARG M 49 " (cutoff:3.500A) Processing helix chain 'M' and resid 72 through 84 Processing helix chain 'M' and resid 95 through 101 Processing helix chain 'M' and resid 132 through 142 Processing helix chain 'F' and resid 7 through 28 Processing helix chain 'F' and resid 61 through 77 removed outlier: 6.304A pdb=" N ARG F 65 " --> pdb=" O LYS F 62 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE F 66 " --> pdb=" O GLY F 63 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL F 73 " --> pdb=" O THR F 70 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG F 76 " --> pdb=" O VAL F 73 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N PHE F 77 " --> pdb=" O GLN F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 110 Processing helix chain 'F' and resid 115 through 129 removed outlier: 3.891A pdb=" N TYR F 120 " --> pdb=" O ARG F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 167 Processing helix chain 'P' and resid 14 through 16 No H-bonds generated for 'chain 'P' and resid 14 through 16' Processing helix chain 'P' and resid 29 through 31 No H-bonds generated for 'chain 'P' and resid 29 through 31' Processing helix chain 'P' and resid 39 through 41 No H-bonds generated for 'chain 'P' and resid 39 through 41' Processing helix chain 'P' and resid 59 through 61 No H-bonds generated for 'chain 'P' and resid 59 through 61' Processing helix chain 'P' and resid 64 through 72 removed outlier: 3.617A pdb=" N SER P 71 " --> pdb=" O ARG P 67 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU P 72 " --> pdb=" O LEU P 68 " (cutoff:3.500A) Processing helix chain 'P' and resid 76 through 78 No H-bonds generated for 'chain 'P' and resid 76 through 78' Processing helix chain 'P' and resid 82 through 100 Processing helix chain 'P' and resid 104 through 113 Processing helix chain 'P' and resid 139 through 158 Processing helix chain 'P' and resid 165 through 178 Processing helix chain 'P' and resid 184 through 198 Processing helix chain 'Q' and resid 42 through 44 No H-bonds generated for 'chain 'Q' and resid 42 through 44' Processing helix chain 'Q' and resid 48 through 61 removed outlier: 5.225A pdb=" N LEU Q 52 " --> pdb=" O MET Q 49 " (cutoff:3.500A) Proline residue: Q 57 - end of helix removed outlier: 3.754A pdb=" N ALA Q 61 " --> pdb=" O ILE Q 58 " (cutoff:3.500A) Processing helix chain 'Q' and resid 63 through 66 Processing helix chain 'Q' and resid 82 through 102 Processing helix chain 'Q' and resid 105 through 118 Processing helix chain 'Q' and resid 120 through 122 No H-bonds generated for 'chain 'Q' and resid 120 through 122' Processing helix chain 'U' and resid 37 through 53 Processing helix chain 'U' and resid 103 through 109 Processing helix chain 'T' and resid 19 through 21 No H-bonds generated for 'chain 'T' and resid 19 through 21' Processing helix chain 'T' and resid 24 through 38 removed outlier: 3.560A pdb=" N LYS T 29 " --> pdb=" O HIS T 25 " (cutoff:3.500A) Processing helix chain 'T' and resid 45 through 47 No H-bonds generated for 'chain 'T' and resid 45 through 47' Processing helix chain 'T' and resid 63 through 79 removed outlier: 4.623A pdb=" N TYR T 66 " --> pdb=" O ALA T 63 " (cutoff:3.500A) Processing helix chain 'T' and resid 85 through 91 Processing helix chain 'T' and resid 110 through 121 Processing helix chain 'T' and resid 138 through 150 removed outlier: 4.068A pdb=" N THR T 150 " --> pdb=" O GLN T 146 " (cutoff:3.500A) Processing helix chain 'Z' and resid 45 through 53 Processing helix chain 'Z' and resid 55 through 57 No H-bonds generated for 'chain 'Z' and resid 55 through 57' Processing helix chain 'Z' and resid 63 through 70 Processing helix chain 'Z' and resid 74 through 86 Processing helix chain 'd' and resid 16 through 18 No H-bonds generated for 'chain 'd' and resid 16 through 18' Processing helix chain 'd' and resid 33 through 35 No H-bonds generated for 'chain 'd' and resid 33 through 35' Processing helix chain 'd' and resid 40 through 50 removed outlier: 5.253A pdb=" N LYS d 48 " --> pdb=" O ARG d 44 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N ASP d 49 " --> pdb=" O SER d 45 " (cutoff:3.500A) Processing helix chain 'S' and resid 26 through 32 removed outlier: 3.838A pdb=" N THR S 31 " --> pdb=" O MET S 27 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N SER S 32 " --> pdb=" O PHE S 28 " (cutoff:3.500A) Processing helix chain 'S' and resid 38 through 47 Processing helix chain 'S' and resid 56 through 58 No H-bonds generated for 'chain 'S' and resid 56 through 58' Processing helix chain 'S' and resid 61 through 73 Processing helix chain 'S' and resid 81 through 83 No H-bonds generated for 'chain 'S' and resid 81 through 83' Processing helix chain 'S' and resid 100 through 116 removed outlier: 3.646A pdb=" N ARG S 113 " --> pdb=" O ASP S 110 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS S 116 " --> pdb=" O ARG S 113 " (cutoff:3.500A) Processing helix chain 'S' and resid 120 through 126 Processing helix chain 'R' and resid 30 through 35 Processing helix chain 'R' and resid 38 through 44 removed outlier: 3.853A pdb=" N GLN R 43 " --> pdb=" O GLU R 39 " (cutoff:3.500A) Processing helix chain 'R' and resid 47 through 54 Processing helix chain 'R' and resid 59 through 73 removed outlier: 3.514A pdb=" N LYS R 70 " --> pdb=" O LYS R 66 " (cutoff:3.500A) Processing helix chain 'R' and resid 95 through 97 No H-bonds generated for 'chain 'R' and resid 95 through 97' Processing helix chain 'R' and resid 117 through 119 No H-bonds generated for 'chain 'R' and resid 117 through 119' Processing helix chain 'R' and resid 125 through 127 No H-bonds generated for 'chain 'R' and resid 125 through 127' Processing helix chain 'h' and resid 7 through 19 Processing helix chain 'h' and resid 28 through 34 removed outlier: 3.616A pdb=" N LYS h 33 " --> pdb=" O HIS h 29 " (cutoff:3.500A) Processing helix chain 'h' and resid 44 through 63 removed outlier: 3.836A pdb=" N GLN h 62 " --> pdb=" O MET h 58 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'K' and resid 20 through 24 Processing sheet with id= B, first strand: chain 'M' and resid 63 through 65 removed outlier: 4.300A pdb=" N VAL M 64 " --> pdb=" O VAL M 122 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'F' and resid 36 through 41 removed outlier: 3.762A pdb=" N GLU F 85 " --> pdb=" O THR F 46 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'F' and resid 148 through 155 Processing sheet with id= E, first strand: chain 'P' and resid 119 through 121 Processing sheet with id= F, first strand: chain 'Q' and resid 13 through 19 Processing sheet with id= G, first strand: chain 'U' and resid 93 through 101 Processing sheet with id= H, first strand: chain 'U' and resid 67 through 74 Processing sheet with id= I, first strand: chain 'Z' and resid 91 through 94 removed outlier: 6.939A pdb=" N ILE Z 101 " --> pdb=" O VAL Z 93 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'c' and resid 51 through 54 removed outlier: 6.941A pdb=" N ARG c 27 " --> pdb=" O VAL c 11 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N VAL c 13 " --> pdb=" O GLN c 25 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N GLN c 25 " --> pdb=" O VAL c 13 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'g' and resid 21 through 26 removed outlier: 6.545A pdb=" N SER g 37 " --> pdb=" O THR g 22 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ILE g 24 " --> pdb=" O VAL g 35 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N VAL g 35 " --> pdb=" O ILE g 24 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N THR g 26 " --> pdb=" O PHE g 33 " (cutoff:3.500A) removed outlier: 8.738A pdb=" N PHE g 33 " --> pdb=" O THR g 26 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE g 34 " --> pdb=" O TRP g 46 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N ASP g 47 " --> pdb=" O PRO g 65 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'g' and resid 76 through 81 removed outlier: 6.747A pdb=" N GLY g 91 " --> pdb=" O GLN g 77 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N VAL g 79 " --> pdb=" O LEU g 89 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU g 89 " --> pdb=" O VAL g 79 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N LEU g 81 " --> pdb=" O PHE g 87 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N PHE g 87 " --> pdb=" O LEU g 81 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG g 109 " --> pdb=" O LEU g 99 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ASP g 101 " --> pdb=" O THR g 107 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR g 107 " --> pdb=" O ASP g 101 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'g' and resid 139 through 143 Processing sheet with id= N, first strand: chain 'g' and resid 179 through 184 removed outlier: 4.069A pdb=" N SER g 188 " --> pdb=" O SER g 184 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N CYS g 201 " --> pdb=" O VAL g 191 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N ASN g 193 " --> pdb=" O LEU g 199 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N LEU g 199 " --> pdb=" O ASN g 193 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'g' and resid 212 through 215 Processing sheet with id= P, first strand: chain 'g' and resid 251 through 256 removed outlier: 6.530A pdb=" N ALA g 266 " --> pdb=" O ASN g 252 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LEU g 254 " --> pdb=" O CYS g 264 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N CYS g 264 " --> pdb=" O LEU g 254 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N PHE g 256 " --> pdb=" O TRP g 262 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N TRP g 262 " --> pdb=" O PHE g 256 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN g 283 " --> pdb=" O ILE g 273 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ASP g 275 " --> pdb=" O ILE g 281 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ILE g 281 " --> pdb=" O ASP g 275 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'g' and resid 7 through 15 removed outlier: 3.808A pdb=" N SER g 7 " --> pdb=" O SER g 326 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILE g 322 " --> pdb=" O ALA g 11 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL g 13 " --> pdb=" O ILE g 320 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE g 320 " --> pdb=" O VAL g 13 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N THR g 319 " --> pdb=" O TYR g 315 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'S' and resid 12 through 15 Processing sheet with id= S, first strand: chain 'R' and resid 84 through 86 Processing sheet with id= T, first strand: chain 'f' and resid 57 through 60 542 hydrogen bonds defined for protein. 1383 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 299 hydrogen bonds 466 hydrogen bond angles 0 basepair planarities 119 basepair parallelities 237 stacking parallelities Total time for adding SS restraints: 14.69 Time building geometry restraints manager: 13.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3119 1.32 - 1.44: 9483 1.44 - 1.57: 12427 1.57 - 1.69: 912 1.69 - 1.82: 124 Bond restraints: 26065 Sorted by residual: bond pdb=" C2' A2M A1331 " pdb=" C1' A2M A1331 " ideal model delta sigma weight residual 1.305 1.528 -0.223 2.00e-02 2.50e+03 1.24e+02 bond pdb=" O4' A2M A1582 " pdb=" C1' A2M A1582 " ideal model delta sigma weight residual 1.615 1.397 0.218 2.00e-02 2.50e+03 1.19e+02 bond pdb=" C2' A2M A1582 " pdb=" C1' A2M A1582 " ideal model delta sigma weight residual 1.305 1.503 -0.198 2.00e-02 2.50e+03 9.77e+01 bond pdb=" O4' A2M A1331 " pdb=" C1' A2M A1331 " ideal model delta sigma weight residual 1.615 1.421 0.194 2.00e-02 2.50e+03 9.45e+01 bond pdb=" C2 4AC A1285 " pdb=" N3 4AC A1285 " ideal model delta sigma weight residual 1.486 1.317 0.169 2.00e-02 2.50e+03 7.10e+01 ... (remaining 26060 not shown) Histogram of bond angle deviations from ideal: 98.42 - 105.90: 2640 105.90 - 113.38: 15111 113.38 - 120.86: 11644 120.86 - 128.34: 7262 128.34 - 135.83: 697 Bond angle restraints: 37354 Sorted by residual: angle pdb=" C1' A2M A1331 " pdb=" N9 A2M A1331 " pdb=" C8 A2M A1331 " ideal model delta sigma weight residual 88.50 127.56 -39.06 3.00e+00 1.11e-01 1.70e+02 angle pdb=" C1' A2M A1582 " pdb=" N9 A2M A1582 " pdb=" C8 A2M A1582 " ideal model delta sigma weight residual 88.50 124.56 -36.06 3.00e+00 1.11e-01 1.44e+02 angle pdb=" N6 A2M A1582 " pdb=" C6 A2M A1582 " pdb=" N1 A2M A1582 " ideal model delta sigma weight residual 92.14 122.56 -30.42 3.00e+00 1.11e-01 1.03e+02 angle pdb=" N6 A2M A1331 " pdb=" C6 A2M A1331 " pdb=" N1 A2M A1331 " ideal model delta sigma weight residual 92.14 118.56 -26.42 3.00e+00 1.11e-01 7.75e+01 angle pdb=" C1' OMG A1435 " pdb=" N9 OMG A1435 " pdb=" C8 OMG A1435 " ideal model delta sigma weight residual 142.82 124.05 18.77 3.00e+00 1.11e-01 3.92e+01 ... (remaining 37349 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.38: 14926 35.38 - 70.75: 1320 70.75 - 106.13: 162 106.13 - 141.51: 5 141.51 - 176.89: 6 Dihedral angle restraints: 16419 sinusoidal: 11013 harmonic: 5406 Sorted by residual: dihedral pdb=" O4' U A1263 " pdb=" C1' U A1263 " pdb=" N1 U A1263 " pdb=" C2 U A1263 " ideal model delta sinusoidal sigma weight residual -160.00 5.57 -165.57 1 1.50e+01 4.44e-03 8.40e+01 dihedral pdb=" O4' C A1396 " pdb=" C1' C A1396 " pdb=" N1 C A1396 " pdb=" C2 C A1396 " ideal model delta sinusoidal sigma weight residual 200.00 73.12 126.88 1 1.50e+01 4.44e-03 6.83e+01 dihedral pdb=" O4' C A1479 " pdb=" C1' C A1479 " pdb=" N1 C A1479 " pdb=" C2 C A1479 " ideal model delta sinusoidal sigma weight residual -128.00 48.89 -176.89 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 16416 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 4091 0.091 - 0.183: 375 0.183 - 0.274: 37 0.274 - 0.366: 0 0.366 - 0.457: 2 Chirality restraints: 4505 Sorted by residual: chirality pdb=" C1* PSU A1480 " pdb=" O4* PSU A1480 " pdb=" C2* PSU A1480 " pdb=" C5 PSU A1480 " both_signs ideal model delta sigma weight residual False 2.60 2.14 0.46 2.00e-01 2.50e+01 5.22e+00 chirality pdb=" C2' A2M A1331 " pdb=" C3' A2M A1331 " pdb=" O2' A2M A1331 " pdb=" C1' A2M A1331 " both_signs ideal model delta sigma weight residual False -2.39 -2.77 0.37 2.00e-01 2.50e+01 3.49e+00 chirality pdb=" C1* PSU A1407 " pdb=" O4* PSU A1407 " pdb=" C2* PSU A1407 " pdb=" C5 PSU A1407 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 4502 not shown) Planarity restraints: 3056 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMC A1337 " -0.073 2.00e-02 2.50e+03 6.11e-01 8.40e+03 pdb=" C4' OMC A1337 " -0.432 2.00e-02 2.50e+03 pdb=" O4' OMC A1337 " -0.650 2.00e-02 2.50e+03 pdb=" C3' OMC A1337 " 0.618 2.00e-02 2.50e+03 pdb=" O3' OMC A1337 " 0.659 2.00e-02 2.50e+03 pdb=" C2' OMC A1337 " 0.183 2.00e-02 2.50e+03 pdb=" O2' OMC A1337 " -1.009 2.00e-02 2.50e+03 pdb=" C1' OMC A1337 " -0.211 2.00e-02 2.50e+03 pdb=" N1 OMC A1337 " 0.914 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMC A1220 " 0.033 2.00e-02 2.50e+03 5.87e-01 7.76e+03 pdb=" C4' OMC A1220 " 0.444 2.00e-02 2.50e+03 pdb=" O4' OMC A1220 " 0.685 2.00e-02 2.50e+03 pdb=" C3' OMC A1220 " -0.590 2.00e-02 2.50e+03 pdb=" O3' OMC A1220 " -0.587 2.00e-02 2.50e+03 pdb=" C2' OMC A1220 " -0.212 2.00e-02 2.50e+03 pdb=" O2' OMC A1220 " 0.914 2.00e-02 2.50e+03 pdb=" C1' OMC A1220 " 0.216 2.00e-02 2.50e+03 pdb=" N1 OMC A1220 " -0.903 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 7MG A1584 " 0.008 2.00e-02 2.50e+03 5.53e-01 6.87e+03 pdb=" C4' 7MG A1584 " 0.431 2.00e-02 2.50e+03 pdb=" O4' 7MG A1584 " 0.639 2.00e-02 2.50e+03 pdb=" C3' 7MG A1584 " -0.585 2.00e-02 2.50e+03 pdb=" O3' 7MG A1584 " -0.517 2.00e-02 2.50e+03 pdb=" C2' 7MG A1584 " -0.234 2.00e-02 2.50e+03 pdb=" O2' 7MG A1584 " 0.864 2.00e-02 2.50e+03 pdb=" C1' 7MG A1584 " 0.226 2.00e-02 2.50e+03 pdb=" N9 7MG A1584 " -0.832 2.00e-02 2.50e+03 ... (remaining 3053 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.47: 299 2.47 - 3.14: 19509 3.14 - 3.80: 56558 3.80 - 4.47: 84436 4.47 - 5.14: 117224 Nonbonded interactions: 278026 Sorted by model distance: nonbonded pdb=" O6 G A1462 " pdb="MG MG A1911 " model vdw 1.799 2.170 nonbonded pdb="MG MG A1909 " pdb=" O HOH A2276 " model vdw 1.836 2.170 nonbonded pdb="MG MG A1915 " pdb=" O HOH A2096 " model vdw 1.839 2.170 nonbonded pdb="MG MG A1913 " pdb=" O HOH A2217 " model vdw 1.845 2.170 nonbonded pdb="MG MG A1913 " pdb=" O HOH A2222 " model vdw 1.848 2.170 ... (remaining 278021 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.870 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: 22.660 Check model and map are aligned: 0.470 Set scattering table: 0.240 Process input model: 89.560 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.080 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:13.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 136.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 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 : 0.009 0.223 26065 Z= 0.528 Angle : 0.990 39.062 37354 Z= 0.559 Chirality : 0.053 0.457 4505 Planarity : 0.026 0.611 3056 Dihedral : 21.805 176.885 12935 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 17.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 1.11 % Allowed : 20.58 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.06 % 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: -1.66 (0.19), residues: 1844 helix: -0.57 (0.20), residues: 606 sheet: -0.90 (0.29), residues: 315 loop : -1.50 (0.20), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP P 18 HIS 0.016 0.001 HIS M 88 PHE 0.033 0.002 PHE g 176 TYR 0.028 0.002 TYR g 10 ARG 0.011 0.001 ARG d 40 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 383 time to evaluate : 1.995 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: P 164 THR cc_start: 0.8324 (m) cc_final: 0.8047 (p) REVERT: d 44 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.8022 (ttp-110) REVERT: S 118 ARG cc_start: 0.7103 (mmm160) cc_final: 0.6146 (tmt-80) REVERT: f 56 PHE cc_start: 0.8250 (m-80) cc_final: 0.7996 (m-80) outliers start: 18 outliers final: 10 residues processed: 396 average time/residue: 1.6332 time to fit residues: 733.7285 Evaluate side-chains 346 residues out of total 1623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 335 time to evaluate : 2.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain U residue 112 ILE Chi-restraints excluded: chain Z residue 37 VAL Chi-restraints excluded: chain Z residue 41 VAL Chi-restraints excluded: chain c residue 54 LEU Chi-restraints excluded: chain d residue 18 SER Chi-restraints excluded: chain d residue 44 ARG Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 64 VAL Chi-restraints excluded: chain R residue 65 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 59 optimal weight: 0.5980 chunk 116 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 178 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 133 optimal weight: 3.9990 chunk 207 optimal weight: 0.5980 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 34 GLN ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 57 ASN F 74 GLN F 145 GLN P 78 ASN ** P 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 103 ASN P 114 ASN Q 100 GLN T 96 GLN T 121 GLN ** Z 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 25 GLN g 86 GLN g 127 ASN ** g 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 24 GLN R 111 ASN ** f 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 26065 Z= 0.260 Angle : 0.807 17.683 37354 Z= 0.433 Chirality : 0.042 0.380 4505 Planarity : 0.008 0.125 3056 Dihedral : 22.579 176.393 9222 Min Nonbonded Distance : 1.745 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 4.19 % Allowed : 20.89 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.06 % 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: -1.27 (0.19), residues: 1844 helix: -0.25 (0.20), residues: 613 sheet: -0.80 (0.28), residues: 323 loop : -1.21 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP P 18 HIS 0.010 0.001 HIS M 88 PHE 0.017 0.002 PHE d 43 TYR 0.028 0.002 TYR R 105 ARG 0.007 0.001 ARG P 17 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 350 time to evaluate : 2.186 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: S 118 ARG cc_start: 0.7170 (mmm160) cc_final: 0.6189 (tmt-80) REVERT: R 58 LYS cc_start: 0.6095 (OUTLIER) cc_final: 0.5399 (mmtp) REVERT: f 56 PHE cc_start: 0.8266 (m-80) cc_final: 0.8017 (m-80) REVERT: f 65 TYR cc_start: 0.7424 (t80) cc_final: 0.7173 (t80) outliers start: 68 outliers final: 31 residues processed: 388 average time/residue: 1.5960 time to fit residues: 707.3229 Evaluate side-chains 361 residues out of total 1623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 329 time to evaluate : 2.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 58 THR Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 159 SER Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain Q residue 34 LEU Chi-restraints excluded: chain Q residue 113 GLU Chi-restraints excluded: chain U residue 58 VAL Chi-restraints excluded: chain T residue 32 SER Chi-restraints excluded: chain Z residue 37 VAL Chi-restraints excluded: chain c residue 14 MET Chi-restraints excluded: chain c residue 54 LEU Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 64 VAL Chi-restraints excluded: chain g residue 117 ASP Chi-restraints excluded: chain g residue 168 CYS Chi-restraints excluded: chain g residue 197 CYS Chi-restraints excluded: chain g residue 234 TRP Chi-restraints excluded: chain g residue 282 VAL Chi-restraints excluded: chain g residue 300 THR Chi-restraints excluded: chain g residue 303 SER Chi-restraints excluded: chain S residue 12 ILE Chi-restraints excluded: chain R residue 58 LYS Chi-restraints excluded: chain R residue 91 MET Chi-restraints excluded: chain R residue 100 SER Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 104 ILE Chi-restraints excluded: chain h residue 66 VAL Chi-restraints excluded: chain f residue 34 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 115 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 chunk 172 optimal weight: 0.9990 chunk 140 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 chunk 224 optimal weight: 20.0000 chunk 184 optimal weight: 6.9990 chunk 205 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 166 optimal weight: 5.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 34 GLN K 41 GLN M 32 GLN F 57 ASN F 74 GLN F 145 GLN ** P 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 25 GLN g 50 ASN ** g 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 24 GLN R 111 ASN ** f 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 26065 Z= 0.305 Angle : 0.809 17.876 37354 Z= 0.431 Chirality : 0.043 0.349 4505 Planarity : 0.008 0.131 3056 Dihedral : 22.477 176.515 9212 Min Nonbonded Distance : 1.685 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.75 % Favored : 94.20 % Rotamer: Outliers : 4.44 % Allowed : 21.07 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.06 % 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: -1.09 (0.19), residues: 1844 helix: -0.17 (0.20), residues: 615 sheet: -0.55 (0.28), residues: 332 loop : -1.12 (0.20), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP g 142 HIS 0.010 0.001 HIS M 88 PHE 0.019 0.002 PHE d 43 TYR 0.025 0.002 TYR R 105 ARG 0.007 0.001 ARG P 160 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 348 time to evaluate : 2.018 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: K 34 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.6510 (mm110) REVERT: F 27 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.6625 (mmm-85) REVERT: T 17 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.7359 (mtp-110) REVERT: S 46 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8335 (mttp) REVERT: S 118 ARG cc_start: 0.7187 (mmm160) cc_final: 0.6166 (tmt-80) REVERT: f 56 PHE cc_start: 0.8223 (m-80) cc_final: 0.7983 (m-80) REVERT: f 65 TYR cc_start: 0.7572 (t80) cc_final: 0.7081 (t80) outliers start: 72 outliers final: 35 residues processed: 397 average time/residue: 1.6431 time to fit residues: 740.5678 Evaluate side-chains 360 residues out of total 1623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 321 time to evaluate : 2.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 34 GLN Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain K residue 58 THR Chi-restraints excluded: chain F residue 27 ARG Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain Q residue 34 LEU Chi-restraints excluded: chain Q residue 108 LYS Chi-restraints excluded: chain Q residue 113 GLU Chi-restraints excluded: chain T residue 17 ARG Chi-restraints excluded: chain T residue 32 SER Chi-restraints excluded: chain Z residue 37 VAL Chi-restraints excluded: chain Z residue 41 VAL Chi-restraints excluded: chain Z residue 94 SER Chi-restraints excluded: chain c residue 14 MET Chi-restraints excluded: chain c residue 54 LEU Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 64 VAL Chi-restraints excluded: chain g residue 117 ASP Chi-restraints excluded: chain g residue 168 CYS Chi-restraints excluded: chain g residue 197 CYS Chi-restraints excluded: chain g residue 204 ASP Chi-restraints excluded: chain g residue 282 VAL Chi-restraints excluded: chain g residue 300 THR Chi-restraints excluded: chain S residue 12 ILE Chi-restraints excluded: chain S residue 46 LYS Chi-restraints excluded: chain S residue 71 VAL Chi-restraints excluded: chain R residue 91 MET Chi-restraints excluded: chain R residue 100 SER Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 104 ILE Chi-restraints excluded: chain h residue 66 VAL Chi-restraints excluded: chain f residue 34 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 204 optimal weight: 2.9990 chunk 155 optimal weight: 0.5980 chunk 107 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 98 optimal weight: 7.9990 chunk 139 optimal weight: 1.9990 chunk 208 optimal weight: 1.9990 chunk 220 optimal weight: 1.9990 chunk 108 optimal weight: 8.9990 chunk 197 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 41 GLN M 32 GLN F 57 ASN F 74 GLN F 145 GLN ** P 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 28 HIS g 50 ASN S 24 GLN R 111 ASN ** f 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 26065 Z= 0.368 Angle : 0.846 17.656 37354 Z= 0.446 Chirality : 0.045 0.456 4505 Planarity : 0.008 0.132 3056 Dihedral : 22.480 176.595 9212 Min Nonbonded Distance : 1.635 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.75 % Favored : 94.20 % Rotamer: Outliers : 4.87 % Allowed : 21.50 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.06 % 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: -1.11 (0.19), residues: 1844 helix: -0.23 (0.20), residues: 614 sheet: -0.50 (0.28), residues: 331 loop : -1.11 (0.20), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP g 142 HIS 0.008 0.001 HIS M 88 PHE 0.018 0.002 PHE d 43 TYR 0.021 0.002 TYR R 105 ARG 0.008 0.001 ARG R 59 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 332 time to evaluate : 2.340 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: K 1 MET cc_start: 0.7542 (OUTLIER) cc_final: 0.6269 (ptt) REVERT: M 56 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7417 (mp0) REVERT: F 23 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6938 (tm-30) REVERT: F 27 ARG cc_start: 0.8143 (OUTLIER) cc_final: 0.6603 (mmm-85) REVERT: T 17 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.7434 (mtp-110) REVERT: g 295 GLN cc_start: 0.6245 (OUTLIER) cc_final: 0.5530 (mt0) REVERT: S 46 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8358 (mttp) REVERT: S 118 ARG cc_start: 0.7204 (mmm160) cc_final: 0.6416 (tmt-80) REVERT: f 56 PHE cc_start: 0.8236 (m-80) cc_final: 0.8001 (m-80) outliers start: 79 outliers final: 38 residues processed: 381 average time/residue: 1.7078 time to fit residues: 739.5345 Evaluate side-chains 361 residues out of total 1623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 316 time to evaluate : 2.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 58 THR Chi-restraints excluded: chain M residue 56 GLU Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain F residue 23 GLU Chi-restraints excluded: chain F residue 27 ARG Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain P residue 157 SER Chi-restraints excluded: chain P residue 199 ASN Chi-restraints excluded: chain Q residue 34 LEU Chi-restraints excluded: chain Q residue 108 LYS Chi-restraints excluded: chain Q residue 113 GLU Chi-restraints excluded: chain T residue 17 ARG Chi-restraints excluded: chain T residue 32 SER Chi-restraints excluded: chain T residue 47 VAL Chi-restraints excluded: chain Z residue 37 VAL Chi-restraints excluded: chain Z residue 41 VAL Chi-restraints excluded: chain Z residue 94 SER Chi-restraints excluded: chain c residue 14 MET Chi-restraints excluded: chain c residue 26 VAL Chi-restraints excluded: chain c residue 54 LEU Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 64 VAL Chi-restraints excluded: chain g residue 117 ASP Chi-restraints excluded: chain g residue 197 CYS Chi-restraints excluded: chain g residue 204 ASP Chi-restraints excluded: chain g residue 285 LEU Chi-restraints excluded: chain g residue 295 GLN Chi-restraints excluded: chain g residue 300 THR Chi-restraints excluded: chain S residue 12 ILE Chi-restraints excluded: chain S residue 46 LYS Chi-restraints excluded: chain S residue 52 MET Chi-restraints excluded: chain S residue 71 VAL Chi-restraints excluded: chain R residue 91 MET Chi-restraints excluded: chain R residue 100 SER Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 104 ILE Chi-restraints excluded: chain h residue 66 VAL Chi-restraints excluded: chain f residue 34 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 183 optimal weight: 2.9990 chunk 125 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 164 optimal weight: 0.0040 chunk 90 optimal weight: 0.0770 chunk 188 optimal weight: 2.9990 chunk 152 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 112 optimal weight: 0.6980 chunk 197 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.4150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 34 GLN K 41 GLN F 57 ASN F 74 GLN F 145 GLN P 91 HIS c 25 GLN d 28 HIS g 50 ASN ** g 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 24 GLN R 111 ASN ** f 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26065 Z= 0.162 Angle : 0.730 17.322 37354 Z= 0.400 Chirality : 0.039 0.401 4505 Planarity : 0.007 0.123 3056 Dihedral : 22.209 177.632 9212 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.94 % Allowed : 22.80 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.06 % 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: -0.69 (0.19), residues: 1844 helix: 0.26 (0.20), residues: 620 sheet: -0.28 (0.28), residues: 324 loop : -0.97 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP g 142 HIS 0.006 0.001 HIS h 56 PHE 0.015 0.001 PHE T 55 TYR 0.014 0.001 TYR R 105 ARG 0.006 0.000 ARG K 56 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 1623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 359 time to evaluate : 2.259 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: K 1 MET cc_start: 0.7299 (OUTLIER) cc_final: 0.6537 (ptt) REVERT: F 162 GLN cc_start: 0.7767 (tp40) cc_final: 0.7565 (mm-40) REVERT: P 164 THR cc_start: 0.8273 (m) cc_final: 0.8061 (p) REVERT: d 12 LYS cc_start: 0.7997 (mptp) cc_final: 0.7537 (mmmt) REVERT: S 46 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.8335 (mttp) REVERT: S 118 ARG cc_start: 0.7191 (mmm160) cc_final: 0.6142 (tmt-80) REVERT: f 56 PHE cc_start: 0.8161 (m-80) cc_final: 0.7960 (m-80) REVERT: f 64 HIS cc_start: 0.6782 (m170) cc_final: 0.6528 (m-70) REVERT: f 65 TYR cc_start: 0.7527 (t80) cc_final: 0.7221 (t80) outliers start: 64 outliers final: 27 residues processed: 397 average time/residue: 1.5969 time to fit residues: 720.1314 Evaluate side-chains 362 residues out of total 1623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 333 time to evaluate : 2.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 58 THR Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain M residue 127 TYR Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 157 MET Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain Q residue 34 LEU Chi-restraints excluded: chain Q residue 45 ILE Chi-restraints excluded: chain Q residue 108 LYS Chi-restraints excluded: chain Q residue 113 GLU Chi-restraints excluded: chain Z residue 37 VAL Chi-restraints excluded: chain Z residue 41 VAL Chi-restraints excluded: chain c residue 14 MET Chi-restraints excluded: chain c residue 26 VAL Chi-restraints excluded: chain c residue 54 LEU Chi-restraints excluded: chain g residue 117 ASP Chi-restraints excluded: chain g residue 197 CYS Chi-restraints excluded: chain g residue 204 ASP Chi-restraints excluded: chain g residue 282 VAL Chi-restraints excluded: chain S residue 12 ILE Chi-restraints excluded: chain S residue 46 LYS Chi-restraints excluded: chain R residue 91 MET Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 104 ILE Chi-restraints excluded: chain h residue 66 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 74 optimal weight: 0.7980 chunk 198 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 129 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 220 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 18 optimal weight: 0.5980 chunk 72 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 41 GLN F 57 ASN F 145 GLN P 114 ASN ** Z 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 25 GLN d 28 HIS g 50 ASN g 86 GLN ** g 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 24 GLN R 111 ASN ** f 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 26065 Z= 0.255 Angle : 0.774 17.359 37354 Z= 0.415 Chirality : 0.041 0.363 4505 Planarity : 0.007 0.129 3056 Dihedral : 22.247 176.388 9210 Min Nonbonded Distance : 1.703 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 3.64 % Allowed : 24.15 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.06 % 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: -0.67 (0.19), residues: 1844 helix: 0.29 (0.20), residues: 613 sheet: -0.26 (0.28), residues: 327 loop : -0.97 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP g 142 HIS 0.006 0.001 HIS h 56 PHE 0.019 0.002 PHE K 49 TYR 0.017 0.002 TYR T 78 ARG 0.012 0.001 ARG h 23 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 338 time to evaluate : 2.898 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: F 127 MET cc_start: 0.8674 (mmm) cc_final: 0.8073 (mmm) REVERT: T 80 ARG cc_start: 0.7403 (OUTLIER) cc_final: 0.6789 (ttm170) REVERT: g 196 ASN cc_start: 0.7420 (p0) cc_final: 0.6921 (p0) REVERT: g 295 GLN cc_start: 0.6018 (OUTLIER) cc_final: 0.5352 (mt0) REVERT: S 46 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8240 (mttp) REVERT: S 118 ARG cc_start: 0.7199 (mmm160) cc_final: 0.6401 (tmt-80) REVERT: R 92 ILE cc_start: 0.9025 (OUTLIER) cc_final: 0.8820 (mm) REVERT: h 5 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7050 (mmt90) REVERT: f 56 PHE cc_start: 0.8195 (m-80) cc_final: 0.7875 (m-10) REVERT: f 64 HIS cc_start: 0.6808 (m170) cc_final: 0.6560 (m-70) REVERT: f 65 TYR cc_start: 0.7637 (t80) cc_final: 0.7235 (t80) outliers start: 59 outliers final: 33 residues processed: 373 average time/residue: 1.6992 time to fit residues: 718.1659 Evaluate side-chains 365 residues out of total 1623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 327 time to evaluate : 2.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain K residue 58 THR Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain M residue 127 TYR Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 157 MET Chi-restraints excluded: chain P residue 157 SER Chi-restraints excluded: chain Q residue 34 LEU Chi-restraints excluded: chain Q residue 108 LYS Chi-restraints excluded: chain Q residue 113 GLU Chi-restraints excluded: chain U residue 121 GLU Chi-restraints excluded: chain T residue 47 VAL Chi-restraints excluded: chain T residue 80 ARG Chi-restraints excluded: chain Z residue 37 VAL Chi-restraints excluded: chain Z residue 41 VAL Chi-restraints excluded: chain c residue 14 MET Chi-restraints excluded: chain c residue 26 VAL Chi-restraints excluded: chain c residue 54 LEU Chi-restraints excluded: chain g residue 117 ASP Chi-restraints excluded: chain g residue 181 VAL Chi-restraints excluded: chain g residue 197 CYS Chi-restraints excluded: chain g residue 204 ASP Chi-restraints excluded: chain g residue 282 VAL Chi-restraints excluded: chain g residue 295 GLN Chi-restraints excluded: chain g residue 300 THR Chi-restraints excluded: chain S residue 12 ILE Chi-restraints excluded: chain S residue 46 LYS Chi-restraints excluded: chain R residue 91 MET Chi-restraints excluded: chain R residue 92 ILE Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 104 ILE Chi-restraints excluded: chain h residue 5 ARG Chi-restraints excluded: chain h residue 66 VAL Chi-restraints excluded: chain f residue 34 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 125 optimal weight: 0.6980 chunk 161 optimal weight: 0.5980 chunk 124 optimal weight: 0.2980 chunk 185 optimal weight: 3.9990 chunk 123 optimal weight: 0.6980 chunk 219 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 133 optimal weight: 6.9990 chunk 101 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 57 ASN F 145 GLN ** Z 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 50 ASN ** g 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 24 GLN R 111 ASN ** f 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 26065 Z= 0.218 Angle : 0.753 17.229 37354 Z= 0.408 Chirality : 0.040 0.368 4505 Planarity : 0.007 0.127 3056 Dihedral : 22.209 176.740 9210 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 4.07 % Allowed : 23.78 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.06 % 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: -0.56 (0.19), residues: 1844 helix: 0.34 (0.20), residues: 626 sheet: -0.12 (0.28), residues: 326 loop : -0.93 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP g 142 HIS 0.006 0.001 HIS h 56 PHE 0.016 0.002 PHE R 53 TYR 0.015 0.001 TYR T 78 ARG 0.012 0.001 ARG h 23 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 339 time to evaluate : 2.144 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: F 127 MET cc_start: 0.8654 (mmm) cc_final: 0.8116 (mmm) REVERT: T 17 ARG cc_start: 0.7827 (OUTLIER) cc_final: 0.7409 (mtp-110) REVERT: T 80 ARG cc_start: 0.7425 (OUTLIER) cc_final: 0.6854 (ttm170) REVERT: d 12 LYS cc_start: 0.7991 (mptp) cc_final: 0.7557 (mmmt) REVERT: S 46 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8349 (mttp) REVERT: S 118 ARG cc_start: 0.7201 (mmm160) cc_final: 0.6403 (tmt-80) REVERT: R 92 ILE cc_start: 0.9013 (OUTLIER) cc_final: 0.8783 (mm) REVERT: f 56 PHE cc_start: 0.8073 (m-80) cc_final: 0.7865 (m-10) REVERT: f 64 HIS cc_start: 0.6853 (m170) cc_final: 0.6608 (m-70) REVERT: f 65 TYR cc_start: 0.7607 (t80) cc_final: 0.7264 (t80) outliers start: 66 outliers final: 40 residues processed: 381 average time/residue: 1.6288 time to fit residues: 705.3148 Evaluate side-chains 376 residues out of total 1623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 332 time to evaluate : 1.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain K residue 58 THR Chi-restraints excluded: chain M residue 28 MET Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain M residue 127 TYR Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 157 MET Chi-restraints excluded: chain P residue 157 SER Chi-restraints excluded: chain Q residue 34 LEU Chi-restraints excluded: chain Q residue 108 LYS Chi-restraints excluded: chain Q residue 113 GLU Chi-restraints excluded: chain U residue 121 GLU Chi-restraints excluded: chain T residue 17 ARG Chi-restraints excluded: chain T residue 32 SER Chi-restraints excluded: chain T residue 36 LYS Chi-restraints excluded: chain T residue 47 VAL Chi-restraints excluded: chain T residue 80 ARG Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain Z residue 37 VAL Chi-restraints excluded: chain Z residue 41 VAL Chi-restraints excluded: chain Z residue 94 SER Chi-restraints excluded: chain c residue 14 MET Chi-restraints excluded: chain c residue 53 THR Chi-restraints excluded: chain g residue 117 ASP Chi-restraints excluded: chain g residue 168 CYS Chi-restraints excluded: chain g residue 181 VAL Chi-restraints excluded: chain g residue 197 CYS Chi-restraints excluded: chain g residue 204 ASP Chi-restraints excluded: chain g residue 282 VAL Chi-restraints excluded: chain g residue 300 THR Chi-restraints excluded: chain S residue 12 ILE Chi-restraints excluded: chain S residue 46 LYS Chi-restraints excluded: chain R residue 91 MET Chi-restraints excluded: chain R residue 92 ILE Chi-restraints excluded: chain R residue 100 SER Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 104 ILE Chi-restraints excluded: chain h residue 66 VAL Chi-restraints excluded: chain f residue 34 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 135 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 139 optimal weight: 0.9990 chunk 149 optimal weight: 0.6980 chunk 108 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 172 optimal weight: 4.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 57 ASN F 145 GLN Z 60 GLN ** Z 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 25 GLN ** d 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 50 ASN g 86 GLN S 24 GLN R 111 ASN ** f 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 26065 Z= 0.263 Angle : 0.776 17.352 37354 Z= 0.417 Chirality : 0.041 0.380 4505 Planarity : 0.007 0.129 3056 Dihedral : 22.241 176.369 9208 Min Nonbonded Distance : 1.704 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 4.31 % Allowed : 23.54 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.06 % 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: -0.57 (0.19), residues: 1844 helix: 0.31 (0.20), residues: 621 sheet: -0.12 (0.28), residues: 338 loop : -0.92 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP g 274 HIS 0.006 0.001 HIS h 56 PHE 0.017 0.002 PHE R 53 TYR 0.016 0.002 TYR T 78 ARG 0.014 0.001 ARG h 23 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 329 time to evaluate : 2.097 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: F 127 MET cc_start: 0.8664 (mmm) cc_final: 0.8138 (mmm) REVERT: U 52 LYS cc_start: 0.8136 (mtmm) cc_final: 0.7904 (mtmm) REVERT: T 17 ARG cc_start: 0.7855 (OUTLIER) cc_final: 0.7424 (mtp-110) REVERT: T 80 ARG cc_start: 0.7491 (OUTLIER) cc_final: 0.6918 (ttm170) REVERT: S 46 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8214 (mttp) REVERT: S 118 ARG cc_start: 0.7202 (mmm160) cc_final: 0.6401 (tmt-80) REVERT: h 5 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.7054 (mmt90) REVERT: h 14 ARG cc_start: 0.7914 (mtt-85) cc_final: 0.7596 (mtt180) REVERT: f 65 TYR cc_start: 0.7635 (t80) cc_final: 0.7247 (t80) outliers start: 70 outliers final: 40 residues processed: 375 average time/residue: 1.6815 time to fit residues: 712.3669 Evaluate side-chains 370 residues out of total 1623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 326 time to evaluate : 2.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain M residue 28 MET Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 73 ASP Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain M residue 127 TYR Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain P residue 157 SER Chi-restraints excluded: chain Q residue 34 LEU Chi-restraints excluded: chain Q residue 108 LYS Chi-restraints excluded: chain Q residue 113 GLU Chi-restraints excluded: chain U residue 101 SER Chi-restraints excluded: chain U residue 121 GLU Chi-restraints excluded: chain T residue 17 ARG Chi-restraints excluded: chain T residue 32 SER Chi-restraints excluded: chain T residue 36 LYS Chi-restraints excluded: chain T residue 47 VAL Chi-restraints excluded: chain T residue 80 ARG Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain Z residue 37 VAL Chi-restraints excluded: chain Z residue 41 VAL Chi-restraints excluded: chain Z residue 94 SER Chi-restraints excluded: chain c residue 53 THR Chi-restraints excluded: chain d residue 44 ARG Chi-restraints excluded: chain g residue 117 ASP Chi-restraints excluded: chain g residue 168 CYS Chi-restraints excluded: chain g residue 181 VAL Chi-restraints excluded: chain g residue 197 CYS Chi-restraints excluded: chain g residue 204 ASP Chi-restraints excluded: chain g residue 282 VAL Chi-restraints excluded: chain g residue 300 THR Chi-restraints excluded: chain S residue 12 ILE Chi-restraints excluded: chain S residue 46 LYS Chi-restraints excluded: chain R residue 91 MET Chi-restraints excluded: chain R residue 100 SER Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 104 ILE Chi-restraints excluded: chain h residue 5 ARG Chi-restraints excluded: chain h residue 66 VAL Chi-restraints excluded: chain f residue 34 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 199 optimal weight: 3.9990 chunk 210 optimal weight: 2.9990 chunk 192 optimal weight: 2.9990 chunk 204 optimal weight: 2.9990 chunk 123 optimal weight: 0.0870 chunk 89 optimal weight: 0.0030 chunk 160 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 185 optimal weight: 3.9990 chunk 193 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 overall best weight: 1.4174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 57 ASN F 145 GLN F 174 HIS Z 60 GLN ** Z 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 4 GLN ** d 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 24 GLN R 111 ASN ** f 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 26065 Z= 0.314 Angle : 0.809 17.377 37354 Z= 0.430 Chirality : 0.043 0.401 4505 Planarity : 0.008 0.131 3056 Dihedral : 22.281 176.421 9208 Min Nonbonded Distance : 1.673 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 3.14 % Allowed : 25.20 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.06 % 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: -0.62 (0.19), residues: 1844 helix: 0.22 (0.20), residues: 620 sheet: -0.12 (0.28), residues: 341 loop : -0.92 (0.21), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP g 274 HIS 0.011 0.001 HIS M 88 PHE 0.028 0.002 PHE f 56 TYR 0.016 0.002 TYR R 105 ARG 0.014 0.001 ARG h 23 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 331 time to evaluate : 2.410 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: F 127 MET cc_start: 0.8657 (mmm) cc_final: 0.8147 (mmm) REVERT: U 52 LYS cc_start: 0.8105 (mtmm) cc_final: 0.7879 (mtmm) REVERT: T 17 ARG cc_start: 0.7884 (OUTLIER) cc_final: 0.7477 (mtp-110) REVERT: d 12 LYS cc_start: 0.8020 (mptp) cc_final: 0.7591 (mmmt) REVERT: S 118 ARG cc_start: 0.7208 (mmm160) cc_final: 0.6402 (tmt-80) REVERT: h 5 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7015 (mmt90) REVERT: h 14 ARG cc_start: 0.7908 (mtt-85) cc_final: 0.7594 (mtt180) REVERT: f 65 TYR cc_start: 0.7643 (t80) cc_final: 0.7240 (t80) outliers start: 51 outliers final: 39 residues processed: 365 average time/residue: 1.7506 time to fit residues: 720.7299 Evaluate side-chains 367 residues out of total 1623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 326 time to evaluate : 2.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain M residue 28 MET Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain M residue 127 TYR Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 157 MET Chi-restraints excluded: chain P residue 157 SER Chi-restraints excluded: chain Q residue 34 LEU Chi-restraints excluded: chain Q residue 108 LYS Chi-restraints excluded: chain Q residue 113 GLU Chi-restraints excluded: chain U residue 101 SER Chi-restraints excluded: chain U residue 121 GLU Chi-restraints excluded: chain T residue 17 ARG Chi-restraints excluded: chain T residue 32 SER Chi-restraints excluded: chain T residue 47 VAL Chi-restraints excluded: chain T residue 80 ARG Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain Z residue 37 VAL Chi-restraints excluded: chain Z residue 41 VAL Chi-restraints excluded: chain Z residue 94 SER Chi-restraints excluded: chain c residue 53 THR Chi-restraints excluded: chain d residue 44 ARG Chi-restraints excluded: chain g residue 117 ASP Chi-restraints excluded: chain g residue 168 CYS Chi-restraints excluded: chain g residue 181 VAL Chi-restraints excluded: chain g residue 197 CYS Chi-restraints excluded: chain g residue 204 ASP Chi-restraints excluded: chain g residue 282 VAL Chi-restraints excluded: chain g residue 300 THR Chi-restraints excluded: chain S residue 12 ILE Chi-restraints excluded: chain R residue 91 MET Chi-restraints excluded: chain R residue 100 SER Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 104 ILE Chi-restraints excluded: chain h residue 5 ARG Chi-restraints excluded: chain h residue 66 VAL Chi-restraints excluded: chain f residue 34 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 102 optimal weight: 0.4980 chunk 150 optimal weight: 0.8980 chunk 227 optimal weight: 3.9990 chunk 209 optimal weight: 3.9990 chunk 180 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 143 optimal weight: 0.4980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 57 ASN F 145 GLN Z 60 GLN ** Z 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 24 GLN R 111 ASN ** f 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 26065 Z= 0.308 Angle : 0.816 17.281 37354 Z= 0.434 Chirality : 0.043 0.400 4505 Planarity : 0.008 0.130 3056 Dihedral : 22.296 177.148 9208 Min Nonbonded Distance : 1.681 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 3.27 % Allowed : 25.02 % Favored : 71.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.06 % 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: -0.66 (0.19), residues: 1844 helix: 0.14 (0.20), residues: 619 sheet: -0.10 (0.28), residues: 341 loop : -0.93 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP g 274 HIS 0.006 0.001 HIS h 56 PHE 0.020 0.002 PHE R 53 TYR 0.017 0.002 TYR R 105 ARG 0.014 0.001 ARG h 23 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 341 time to evaluate : 1.884 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: F 127 MET cc_start: 0.8646 (mmm) cc_final: 0.8164 (mmm) REVERT: U 52 LYS cc_start: 0.8101 (mtmm) cc_final: 0.7863 (mtmm) REVERT: T 17 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.7479 (mtp-110) REVERT: d 12 LYS cc_start: 0.8065 (mptp) cc_final: 0.7651 (mmmt) REVERT: S 118 ARG cc_start: 0.7189 (mmm160) cc_final: 0.6394 (tmt-80) REVERT: R 92 ILE cc_start: 0.9033 (OUTLIER) cc_final: 0.8797 (mm) REVERT: h 5 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.7034 (mmt90) REVERT: f 65 TYR cc_start: 0.7625 (t80) cc_final: 0.7229 (t80) outliers start: 53 outliers final: 37 residues processed: 376 average time/residue: 1.7139 time to fit residues: 726.1411 Evaluate side-chains 365 residues out of total 1623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 325 time to evaluate : 1.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain M residue 28 MET Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain M residue 127 TYR Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 157 MET Chi-restraints excluded: chain P residue 157 SER Chi-restraints excluded: chain Q residue 34 LEU Chi-restraints excluded: chain Q residue 108 LYS Chi-restraints excluded: chain Q residue 113 GLU Chi-restraints excluded: chain T residue 17 ARG Chi-restraints excluded: chain T residue 32 SER Chi-restraints excluded: chain T residue 47 VAL Chi-restraints excluded: chain T residue 80 ARG Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain Z residue 37 VAL Chi-restraints excluded: chain Z residue 41 VAL Chi-restraints excluded: chain Z residue 94 SER Chi-restraints excluded: chain c residue 53 THR Chi-restraints excluded: chain d residue 44 ARG Chi-restraints excluded: chain g residue 117 ASP Chi-restraints excluded: chain g residue 168 CYS Chi-restraints excluded: chain g residue 181 VAL Chi-restraints excluded: chain g residue 197 CYS Chi-restraints excluded: chain g residue 204 ASP Chi-restraints excluded: chain g residue 282 VAL Chi-restraints excluded: chain g residue 300 THR Chi-restraints excluded: chain S residue 12 ILE Chi-restraints excluded: chain R residue 91 MET Chi-restraints excluded: chain R residue 92 ILE Chi-restraints excluded: chain R residue 100 SER Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 104 ILE Chi-restraints excluded: chain h residue 5 ARG Chi-restraints excluded: chain h residue 66 VAL Chi-restraints excluded: chain f residue 34 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 166 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 181 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 186 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 33 optimal weight: 0.0670 chunk 159 optimal weight: 0.0050 overall best weight: 0.5132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 32 GLN ** M 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 57 ASN F 145 GLN ** d 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 24 GLN R 111 ASN ** f 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.181289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 109)---------------| | r_work = 0.3819 r_free = 0.3819 target = 0.143788 restraints weight = 23804.418| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 1.08 r_work: 0.3608 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3524 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26065 Z= 0.178 Angle : 0.746 17.477 37354 Z= 0.408 Chirality : 0.039 0.376 4505 Planarity : 0.007 0.124 3056 Dihedral : 22.150 177.260 9208 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.65 % Allowed : 25.94 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.06 % 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: -0.44 (0.19), residues: 1844 helix: 0.33 (0.20), residues: 623 sheet: 0.13 (0.28), residues: 341 loop : -0.85 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP g 274 HIS 0.007 0.001 HIS f 64 PHE 0.019 0.001 PHE R 53 TYR 0.025 0.001 TYR F 156 ARG 0.014 0.001 ARG h 23 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10842.74 seconds wall clock time: 196 minutes 35.78 seconds (11795.78 seconds total)