Starting phenix.real_space_refine on Wed Mar 20 13:44:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uig_26545/03_2024/7uig_26545.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uig_26545/03_2024/7uig_26545.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uig_26545/03_2024/7uig_26545.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uig_26545/03_2024/7uig_26545.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uig_26545/03_2024/7uig_26545.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uig_26545/03_2024/7uig_26545.pdb" } resolution = 4.3 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= 0.000 sd= 0.004 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: 4 Type Number sf(0) Gaussians S 107 5.16 5 C 17575 2.51 5 N 4634 2.21 5 O 5264 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "a TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 9": "OE1" <-> "OE2" Residue "a GLU 16": "OE1" <-> "OE2" Residue "a TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 29": "OE1" <-> "OE2" Residue "a GLU 41": "OE1" <-> "OE2" Residue "a GLU 45": "OE1" <-> "OE2" Residue "a GLU 46": "OE1" <-> "OE2" Residue "a GLU 50": "OE1" <-> "OE2" Residue "a TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 97": "OE1" <-> "OE2" Residue "a GLU 99": "OE1" <-> "OE2" Residue "a TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 170": "OE1" <-> "OE2" Residue "a TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 209": "OE1" <-> "OE2" Residue "a GLU 218": "OE1" <-> "OE2" Residue "a GLU 219": "OE1" <-> "OE2" Residue "a TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 230": "OE1" <-> "OE2" Residue "a TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 236": "OE1" <-> "OE2" Residue "a GLU 243": "OE1" <-> "OE2" Residue "a GLU 246": "OE1" <-> "OE2" Residue "a GLU 257": "OE1" <-> "OE2" Residue "a PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 275": "OE1" <-> "OE2" Residue "a PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 281": "OE1" <-> "OE2" Residue "a PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 340": "OE1" <-> "OE2" Residue "a GLU 534": "OE1" <-> "OE2" Residue "a GLU 544": "OE1" <-> "OE2" Residue "a GLU 559": "OE1" <-> "OE2" Residue "a PHE 561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 35": "OD1" <-> "OD2" Residue "d GLU 82": "OE1" <-> "OE2" Residue "d GLU 89": "OE1" <-> "OE2" Residue "d PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 114": "OE1" <-> "OE2" Residue "f TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 180": "OE1" <-> "OE2" Residue "h GLU 124": "OE1" <-> "OE2" Residue "i PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 88": "OE1" <-> "OE2" Residue "n TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 637": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 811": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v GLU 8": "OE1" <-> "OE2" Residue "w TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w GLU 105": "OE1" <-> "OE2" Residue "z TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 27580 Number of models: 1 Model: "" Number of chains: 17 Chain: "a" Number of atoms: 3008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 3008 Classifications: {'peptide': 365} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 356} Chain breaks: 3 Chain: "d" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1388 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 6, 'TRANS': 164} Chain breaks: 2 Chain: "f" Number of atoms: 1407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1407 Classifications: {'peptide': 169} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 159} Chain breaks: 2 Chain: "g" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1409 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 11, 'TRANS': 157} Chain breaks: 4 Chain: "h" Number of atoms: 1126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1126 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 5, 'TRANS': 130} Chain breaks: 1 Chain: "i" Number of atoms: 709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 709 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain breaks: 1 Chain: "j" Number of atoms: 1173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1173 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 7, 'TRANS': 138} Chain breaks: 1 Chain: "k" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 876 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain breaks: 1 Chain: "n" Number of atoms: 5139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 5139 Classifications: {'peptide': 625} Link IDs: {'PTRANS': 18, 'TRANS': 606} Chain breaks: 6 Chain: "q" Number of atoms: 4182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 4182 Classifications: {'peptide': 515} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 497} Chain breaks: 4 Chain: "r" Number of atoms: 1995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1995 Classifications: {'peptide': 253} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 242} Chain breaks: 1 Chain: "s" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 657 Classifications: {'peptide': 81} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 77} Chain breaks: 1 Chain: "t" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1609 Classifications: {'peptide': 210} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 202} Chain: "u" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 978 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain breaks: 2 Chain: "v" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 869 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 1, 'TRANS': 107} Chain breaks: 1 Chain: "w" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 871 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 95} Chain breaks: 1 Chain: "z" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 184 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 6, 'TRANS': 18} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N PRO z 8 " occ=0.70 ... (5 atoms not shown) pdb=" CD PRO z 8 " occ=0.70 residue: pdb=" N SER z 9 " occ=0.70 ... (4 atoms not shown) pdb=" OG SER z 9 " occ=0.70 Time building chain proxies: 13.57, per 1000 atoms: 0.49 Number of scatterers: 27580 At special positions: 0 Unit cell: (158.7, 253.92, 230.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 107 16.00 O 5264 8.00 N 4634 7.00 C 17575 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: 10.19 Conformation dependent library (CDL) restraints added in 4.7 seconds 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6566 Finding SS restraints... Secondary structure from input PDB file: 118 helices and 17 sheets defined 57.3% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.41 Creating SS restraints... Processing helix chain 'a' and resid 6 through 22 Processing helix chain 'a' and resid 27 through 38 Processing helix chain 'a' and resid 102 through 110 Processing helix chain 'a' and resid 114 through 131 Processing helix chain 'a' and resid 163 through 182 removed outlier: 3.801A pdb=" N SER a 172 " --> pdb=" O PHE a 168 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N HIS a 173 " --> pdb=" O THR a 169 " (cutoff:3.500A) Processing helix chain 'a' and resid 279 through 281 No H-bonds generated for 'chain 'a' and resid 279 through 281' Processing helix chain 'a' and resid 297 through 305 Processing helix chain 'a' and resid 331 through 335 Processing helix chain 'a' and resid 336 through 351 removed outlier: 4.257A pdb=" N GLU a 340 " --> pdb=" O ASP a 336 " (cutoff:3.500A) Processing helix chain 'a' and resid 351 through 361 Processing helix chain 'a' and resid 550 through 566 Processing helix chain 'd' and resid 32 through 40 removed outlier: 3.845A pdb=" N VAL d 40 " --> pdb=" O LYS d 36 " (cutoff:3.500A) Processing helix chain 'd' and resid 40 through 62 removed outlier: 4.029A pdb=" N GLU d 44 " --> pdb=" O VAL d 40 " (cutoff:3.500A) Processing helix chain 'd' and resid 66 through 89 removed outlier: 3.560A pdb=" N ALA d 70 " --> pdb=" O ASN d 66 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA d 88 " --> pdb=" O VAL d 84 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU d 89 " --> pdb=" O LYS d 85 " (cutoff:3.500A) Processing helix chain 'd' and resid 92 through 128 Processing helix chain 'd' and resid 132 through 148 removed outlier: 3.520A pdb=" N ILE d 148 " --> pdb=" O GLN d 144 " (cutoff:3.500A) Processing helix chain 'd' and resid 149 through 165 removed outlier: 3.680A pdb=" N LEU d 153 " --> pdb=" O ASN d 149 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LYS d 162 " --> pdb=" O THR d 158 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N PHE d 163 " --> pdb=" O LYS d 159 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS d 165 " --> pdb=" O SER d 161 " (cutoff:3.500A) Processing helix chain 'd' and resid 184 through 191 Processing helix chain 'd' and resid 191 through 199 removed outlier: 4.359A pdb=" N MET d 195 " --> pdb=" O GLY d 191 " (cutoff:3.500A) Processing helix chain 'f' and resid 13 through 20 Processing helix chain 'f' and resid 26 through 33 removed outlier: 4.388A pdb=" N GLU f 33 " --> pdb=" O ASP f 29 " (cutoff:3.500A) Processing helix chain 'f' and resid 41 through 56 removed outlier: 3.718A pdb=" N VAL f 45 " --> pdb=" O SER f 41 " (cutoff:3.500A) Processing helix chain 'f' and resid 89 through 97 removed outlier: 3.876A pdb=" N TYR f 97 " --> pdb=" O ILE f 93 " (cutoff:3.500A) Processing helix chain 'f' and resid 97 through 108 removed outlier: 3.660A pdb=" N MET f 101 " --> pdb=" O TYR f 97 " (cutoff:3.500A) Processing helix chain 'f' and resid 166 through 192 Processing helix chain 'g' and resid 18 through 23 removed outlier: 3.728A pdb=" N PHE g 23 " --> pdb=" O VAL g 20 " (cutoff:3.500A) Processing helix chain 'g' and resid 24 through 43 Proline residue: g 32 - end of helix Processing helix chain 'g' and resid 112 through 140 Processing helix chain 'g' and resid 141 through 143 No H-bonds generated for 'chain 'g' and resid 141 through 143' Processing helix chain 'g' and resid 144 through 166 removed outlier: 3.641A pdb=" N GLU g 149 " --> pdb=" O GLU g 145 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ASN g 150 " --> pdb=" O ARG g 146 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU g 164 " --> pdb=" O HIS g 160 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR g 165 " --> pdb=" O LEU g 161 " (cutoff:3.500A) Processing helix chain 'g' and resid 170 through 213 Processing helix chain 'h' and resid 31 through 55 Processing helix chain 'h' and resid 61 through 86 Processing helix chain 'h' and resid 86 through 93 Processing helix chain 'h' and resid 102 through 115 removed outlier: 6.453A pdb=" N SER h 108 " --> pdb=" O THR h 104 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N LEU h 109 " --> pdb=" O SER h 105 " (cutoff:3.500A) Processing helix chain 'h' and resid 119 through 134 Processing helix chain 'h' and resid 144 through 170 removed outlier: 3.818A pdb=" N HIS h 170 " --> pdb=" O GLU h 166 " (cutoff:3.500A) Processing helix chain 'i' and resid 65 through 79 Processing helix chain 'i' and resid 83 through 108 removed outlier: 3.830A pdb=" N ASN i 108 " --> pdb=" O LEU i 104 " (cutoff:3.500A) Processing helix chain 'i' and resid 108 through 115 removed outlier: 3.628A pdb=" N LYS i 112 " --> pdb=" O ASN i 108 " (cutoff:3.500A) Processing helix chain 'i' and resid 120 through 148 removed outlier: 3.500A pdb=" N GLN i 148 " --> pdb=" O TYR i 144 " (cutoff:3.500A) Processing helix chain 'j' and resid 2 through 38 Processing helix chain 'j' and resid 42 through 68 Processing helix chain 'j' and resid 80 through 87 Processing helix chain 'j' and resid 94 through 133 Processing helix chain 'j' and resid 136 through 148 Processing helix chain 'k' and resid 3 through 40 removed outlier: 3.523A pdb=" N GLN k 7 " --> pdb=" O PRO k 3 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY k 35 " --> pdb=" O THR k 31 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU k 36 " --> pdb=" O PHE k 32 " (cutoff:3.500A) Processing helix chain 'k' and resid 44 through 77 removed outlier: 3.531A pdb=" N PHE k 48 " --> pdb=" O VAL k 44 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU k 49 " --> pdb=" O LYS k 45 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASN k 50 " --> pdb=" O PRO k 46 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER k 62 " --> pdb=" O ARG k 58 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR k 63 " --> pdb=" O LEU k 59 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU k 75 " --> pdb=" O GLN k 71 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL k 77 " --> pdb=" O LEU k 73 " (cutoff:3.500A) Processing helix chain 'k' and resid 89 through 110 removed outlier: 3.996A pdb=" N ASP k 94 " --> pdb=" O ALA k 90 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N THR k 95 " --> pdb=" O LEU k 91 " (cutoff:3.500A) Processing helix chain 'k' and resid 111 through 114 removed outlier: 3.718A pdb=" N SER k 114 " --> pdb=" O PRO k 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 111 through 114' Processing helix chain 'n' and resid 91 through 117 Processing helix chain 'n' and resid 122 through 154 removed outlier: 3.613A pdb=" N LYS n 126 " --> pdb=" O PRO n 122 " (cutoff:3.500A) Processing helix chain 'n' and resid 161 through 191 Processing helix chain 'n' and resid 241 through 260 Processing helix chain 'n' and resid 263 through 267 Processing helix chain 'n' and resid 344 through 359 Processing helix chain 'n' and resid 365 through 393 removed outlier: 3.700A pdb=" N ASN n 391 " --> pdb=" O LEU n 387 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLY n 392 " --> pdb=" O LYS n 388 " (cutoff:3.500A) Processing helix chain 'n' and resid 444 through 450 Processing helix chain 'n' and resid 459 through 486 removed outlier: 6.468A pdb=" N GLU n 465 " --> pdb=" O VAL n 461 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N GLY n 466 " --> pdb=" O SER n 462 " (cutoff:3.500A) Processing helix chain 'n' and resid 530 through 542 Processing helix chain 'n' and resid 545 through 571 Processing helix chain 'n' and resid 684 through 711 removed outlier: 4.010A pdb=" N LEU n 696 " --> pdb=" O GLN n 692 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ASN n 697 " --> pdb=" O ARG n 693 " (cutoff:3.500A) Processing helix chain 'n' and resid 719 through 725 Processing helix chain 'n' and resid 729 through 734 Processing helix chain 'n' and resid 749 through 753 Processing helix chain 'n' and resid 756 through 760 removed outlier: 3.853A pdb=" N LEU n 759 " --> pdb=" O SER n 756 " (cutoff:3.500A) Processing helix chain 'n' and resid 788 through 792 Processing helix chain 'n' and resid 795 through 798 Processing helix chain 'n' and resid 818 through 820 No H-bonds generated for 'chain 'n' and resid 818 through 820' Processing helix chain 'n' and resid 821 through 832 Processing helix chain 'q' and resid 91 through 97 Processing helix chain 'q' and resid 98 through 111 Proline residue: q 104 - end of helix Processing helix chain 'q' and resid 120 through 133 Processing helix chain 'q' and resid 198 through 226 removed outlier: 3.736A pdb=" N GLU q 217 " --> pdb=" O LEU q 213 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER q 218 " --> pdb=" O ALA q 214 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU q 220 " --> pdb=" O ASN q 216 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA q 221 " --> pdb=" O GLU q 217 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU q 222 " --> pdb=" O SER q 218 " (cutoff:3.500A) Processing helix chain 'q' and resid 226 through 233 removed outlier: 3.823A pdb=" N SER q 230 " --> pdb=" O SER q 226 " (cutoff:3.500A) Processing helix chain 'q' and resid 233 through 239 removed outlier: 4.450A pdb=" N SER q 239 " --> pdb=" O SER q 235 " (cutoff:3.500A) Processing helix chain 'q' and resid 242 through 249 removed outlier: 3.546A pdb=" N VAL q 249 " --> pdb=" O LEU q 245 " (cutoff:3.500A) Processing helix chain 'q' and resid 265 through 316 removed outlier: 4.437A pdb=" N TYR q 269 " --> pdb=" O THR q 265 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE q 270 " --> pdb=" O LYS q 266 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLU q 271 " --> pdb=" O LYS q 267 " (cutoff:3.500A) Processing helix chain 'q' and resid 341 through 345 removed outlier: 3.818A pdb=" N GLY q 345 " --> pdb=" O GLU q 342 " (cutoff:3.500A) Processing helix chain 'q' and resid 380 through 386 Processing helix chain 'q' and resid 417 through 422 Processing helix chain 'q' and resid 424 through 450 Processing helix chain 'q' and resid 451 through 455 removed outlier: 4.946A pdb=" N SER q 454 " --> pdb=" O LEU q 451 " (cutoff:3.500A) Processing helix chain 'q' and resid 497 through 526 removed outlier: 3.639A pdb=" N SER q 526 " --> pdb=" O SER q 522 " (cutoff:3.500A) Processing helix chain 'q' and resid 541 through 566 removed outlier: 4.459A pdb=" N ILE q 545 " --> pdb=" O ILE q 541 " (cutoff:3.500A) Processing helix chain 'q' and resid 593 through 605 removed outlier: 3.567A pdb=" N THR q 597 " --> pdb=" O ASP q 593 " (cutoff:3.500A) Processing helix chain 'q' and resid 606 through 611 Processing helix chain 'q' and resid 666 through 686 Processing helix chain 'r' and resid 15 through 28 Processing helix chain 'r' and resid 71 through 75 Processing helix chain 'r' and resid 86 through 93 removed outlier: 3.607A pdb=" N ILE r 89 " --> pdb=" O ASN r 86 " (cutoff:3.500A) Processing helix chain 'r' and resid 101 through 109 Processing helix chain 'r' and resid 199 through 208 Processing helix chain 'r' and resid 225 through 227 No H-bonds generated for 'chain 'r' and resid 225 through 227' Processing helix chain 'r' and resid 264 through 282 removed outlier: 3.865A pdb=" N ILE r 268 " --> pdb=" O ASP r 264 " (cutoff:3.500A) Processing helix chain 's' and resid 41 through 47 Processing helix chain 's' and resid 64 through 68 Processing helix chain 's' and resid 134 through 148 Processing helix chain 't' and resid 15 through 24 Processing helix chain 't' and resid 83 through 87 removed outlier: 3.873A pdb=" N ILE t 87 " --> pdb=" O ALA t 84 " (cutoff:3.500A) Processing helix chain 't' and resid 88 through 95 removed outlier: 3.607A pdb=" N VAL t 92 " --> pdb=" O PRO t 88 " (cutoff:3.500A) Processing helix chain 't' and resid 103 through 111 removed outlier: 3.545A pdb=" N ILE t 107 " --> pdb=" O SER t 103 " (cutoff:3.500A) Processing helix chain 't' and resid 162 through 177 removed outlier: 3.647A pdb=" N ILE t 177 " --> pdb=" O HIS t 173 " (cutoff:3.500A) Processing helix chain 't' and resid 195 through 209 Processing helix chain 'u' and resid 3 through 30 Processing helix chain 'u' and resid 51 through 78 Processing helix chain 'u' and resid 86 through 138 removed outlier: 3.600A pdb=" N GLN u 90 " --> pdb=" O SER u 86 " (cutoff:3.500A) Processing helix chain 'v' and resid 2 through 29 Processing helix chain 'v' and resid 46 through 87 removed outlier: 4.072A pdb=" N ALA v 51 " --> pdb=" O GLU v 47 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLN v 87 " --> pdb=" O TRP v 83 " (cutoff:3.500A) Processing helix chain 'v' and resid 101 through 119 Processing helix chain 'w' and resid 21 through 33 Processing helix chain 'w' and resid 35 through 45 removed outlier: 3.628A pdb=" N GLN w 45 " --> pdb=" O TYR w 41 " (cutoff:3.500A) Processing helix chain 'w' and resid 45 through 51 removed outlier: 4.091A pdb=" N TRP w 49 " --> pdb=" O GLN w 45 " (cutoff:3.500A) Processing helix chain 'w' and resid 51 through 61 removed outlier: 4.167A pdb=" N LYS w 55 " --> pdb=" O SER w 51 " (cutoff:3.500A) Processing helix chain 'w' and resid 62 through 66 removed outlier: 4.136A pdb=" N ASN w 66 " --> pdb=" O TYR w 63 " (cutoff:3.500A) Processing helix chain 'w' and resid 68 through 73 removed outlier: 3.530A pdb=" N ILE w 73 " --> pdb=" O SER w 70 " (cutoff:3.500A) Processing helix chain 'w' and resid 76 through 89 removed outlier: 3.933A pdb=" N PHE w 80 " --> pdb=" O PRO w 76 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS w 83 " --> pdb=" O LEU w 79 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N MET w 89 " --> pdb=" O LEU w 85 " (cutoff:3.500A) Processing helix chain 'w' and resid 105 through 126 Proline residue: w 115 - end of helix Processing sheet with id=AA1, first strand: chain 'a' and resid 41 through 46 removed outlier: 6.789A pdb=" N VAL a 62 " --> pdb=" O LEU a 79 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LEU a 79 " --> pdb=" O VAL a 62 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ASP a 64 " --> pdb=" O VAL a 77 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL a 77 " --> pdb=" O ASP a 64 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ASP a 66 " --> pdb=" O GLN a 75 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 187 through 190 removed outlier: 6.381A pdb=" N ILE a 198 " --> pdb=" O LYS a 214 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LYS a 214 " --> pdb=" O ILE a 198 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ILE a 200 " --> pdb=" O LEU a 212 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'a' and resid 252 through 258 current: chain 'a' and resid 322 through 329 Processing sheet with id=AA3, first strand: chain 'a' and resid 227 through 229 Processing sheet with id=AA4, first strand: chain 'a' and resid 232 through 234 removed outlier: 3.652A pdb=" N SER a 239 " --> pdb=" O SER a 234 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'a' and resid 312 through 316 Processing sheet with id=AA6, first strand: chain 'f' and resid 113 through 121 removed outlier: 3.887A pdb=" N GLN f 131 " --> pdb=" O GLU f 114 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL f 127 " --> pdb=" O SER f 118 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N VAL f 120 " --> pdb=" O PHE f 125 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N PHE f 125 " --> pdb=" O VAL f 120 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N TRP f 126 " --> pdb=" O TYR f 154 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N TYR f 154 " --> pdb=" O TRP f 126 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N ILE f 128 " --> pdb=" O ASP f 152 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ASP f 152 " --> pdb=" O ILE f 128 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N LYS f 130 " --> pdb=" O LEU f 150 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'f' and resid 193 through 195 Processing sheet with id=AA8, first strand: chain 'g' and resid 76 through 78 Processing sheet with id=AA9, first strand: chain 'n' and resid 269 through 272 removed outlier: 6.066A pdb=" N SER n 289 " --> pdb=" O PHE n 299 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N PHE n 299 " --> pdb=" O SER n 289 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'n' and resid 400 through 405 removed outlier: 3.786A pdb=" N GLY n 425 " --> pdb=" O TYR n 415 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LYS n 426 " --> pdb=" O ASP n 443 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'n' and resid 490 through 491 Processing sheet with id=AB3, first strand: chain 'n' and resid 575 through 577 removed outlier: 4.871A pdb=" N PHE n 626 " --> pdb=" O SER n 577 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ILE n 655 " --> pdb=" O LEU n 670 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N LEU n 670 " --> pdb=" O ILE n 655 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LYS n 657 " --> pdb=" O LYS n 668 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'n' and resid 715 through 717 removed outlier: 6.841A pdb=" N SER n 766 " --> pdb=" O LYS n 783 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N LYS n 783 " --> pdb=" O SER n 766 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'q' and resid 321 through 326 removed outlier: 4.504A pdb=" N VAL q 321 " --> pdb=" O LYS q 338 " (cutoff:3.500A) removed outlier: 14.007A pdb=" N LYS q 333 " --> pdb=" O ASN q 359 " (cutoff:3.500A) removed outlier: 10.211A pdb=" N ASN q 359 " --> pdb=" O LYS q 333 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N LEU q 335 " --> pdb=" O ILE q 357 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'q' and resid 403 through 408 removed outlier: 6.011A pdb=" N LEU q 405 " --> pdb=" O THR q 395 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N THR q 395 " --> pdb=" O LEU q 405 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LYS q 464 " --> pdb=" O GLU q 460 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'q' and resid 574 through 578 Processing sheet with id=AB8, first strand: chain 'r' and resid 2 through 12 WARNING: can't find start of bonding for strands! previous: chain 'r' and resid 2 through 12 current: chain 'r' and resid 64 through 68 WARNING: can't find start of bonding for strands! previous: chain 'r' and resid 181 through 195 current: chain 'r' and resid 229 through 239 WARNING: can't find start of bonding for strands! previous: chain 'r' and resid 242 through 245 current: chain 't' and resid 56 through 62 WARNING: can't find start of bonding for strands! previous: chain 't' and resid 76 through 81 current: chain 't' and resid 135 through 143 removed outlier: 7.048A pdb=" N THR t 136 " --> pdb=" O LEU t 155 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N LEU t 155 " --> pdb=" O THR t 136 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ARG t 138 " --> pdb=" O ILE t 153 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ILE t 153 " --> pdb=" O ARG t 138 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N VAL t 140 " --> pdb=" O LEU t 151 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N LEU t 151 " --> pdb=" O VAL t 140 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LEU t 142 " --> pdb=" O LYS t 149 " (cutoff:3.500A) 1633 hydrogen bonds defined for protein. 4740 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.44 Time building geometry restraints manager: 11.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5275 1.33 - 1.45: 6402 1.45 - 1.57: 16178 1.57 - 1.70: 1 1.70 - 1.82: 183 Bond restraints: 28039 Sorted by residual: bond pdb=" CZ ARG a 189 " pdb=" NH2 ARG a 189 " ideal model delta sigma weight residual 1.330 1.292 0.038 1.30e-02 5.92e+03 8.60e+00 bond pdb=" CZ ARG a 349 " pdb=" NH2 ARG a 349 " ideal model delta sigma weight residual 1.330 1.294 0.036 1.30e-02 5.92e+03 7.76e+00 bond pdb=" CZ ARG a 33 " pdb=" NH2 ARG a 33 " ideal model delta sigma weight residual 1.330 1.296 0.034 1.30e-02 5.92e+03 6.99e+00 bond pdb=" ND1 HIS a 536 " pdb=" CE1 HIS a 536 " ideal model delta sigma weight residual 1.321 1.347 -0.026 1.00e-02 1.00e+04 6.76e+00 bond pdb=" CD2 HIS a 173 " pdb=" NE2 HIS a 173 " ideal model delta sigma weight residual 1.374 1.401 -0.027 1.10e-02 8.26e+03 6.04e+00 ... (remaining 28034 not shown) Histogram of bond angle deviations from ideal: 98.99 - 106.11: 588 106.11 - 113.23: 15457 113.23 - 120.35: 10743 120.35 - 127.47: 10845 127.47 - 134.58: 204 Bond angle restraints: 37837 Sorted by residual: angle pdb=" CA PRO g 16 " pdb=" N PRO g 16 " pdb=" CD PRO g 16 " ideal model delta sigma weight residual 112.00 104.16 7.84 1.40e+00 5.10e-01 3.14e+01 angle pdb=" C PRO a 298 " pdb=" N ILE a 299 " pdb=" CA ILE a 299 " ideal model delta sigma weight residual 120.56 127.50 -6.94 1.26e+00 6.30e-01 3.03e+01 angle pdb=" OE1 GLN a 529 " pdb=" CD GLN a 529 " pdb=" NE2 GLN a 529 " ideal model delta sigma weight residual 122.60 117.16 5.44 1.00e+00 1.00e+00 2.96e+01 angle pdb=" OD1 ASN a 324 " pdb=" CG ASN a 324 " pdb=" ND2 ASN a 324 " ideal model delta sigma weight residual 122.60 117.49 5.11 1.00e+00 1.00e+00 2.61e+01 angle pdb=" C LYS a 22 " pdb=" N PRO a 23 " pdb=" CA PRO a 23 " ideal model delta sigma weight residual 119.56 124.73 -5.17 1.02e+00 9.61e-01 2.56e+01 ... (remaining 37832 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 15716 17.44 - 34.87: 1361 34.87 - 52.31: 177 52.31 - 69.75: 30 69.75 - 87.18: 16 Dihedral angle restraints: 17300 sinusoidal: 7267 harmonic: 10033 Sorted by residual: dihedral pdb=" CA SER a 295 " pdb=" C SER a 295 " pdb=" N SER a 296 " pdb=" CA SER a 296 " ideal model delta harmonic sigma weight residual 180.00 154.70 25.30 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA ASN j 92 " pdb=" C ASN j 92 " pdb=" N PRO j 93 " pdb=" CA PRO j 93 " ideal model delta harmonic sigma weight residual -180.00 -156.41 -23.59 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA SER q 252 " pdb=" C SER q 252 " pdb=" N SER q 253 " pdb=" CA SER q 253 " ideal model delta harmonic sigma weight residual -180.00 -156.81 -23.19 0 5.00e+00 4.00e-02 2.15e+01 ... (remaining 17297 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 3256 0.049 - 0.097: 791 0.097 - 0.146: 250 0.146 - 0.194: 37 0.194 - 0.243: 7 Chirality restraints: 4341 Sorted by residual: chirality pdb=" CG LEU i 73 " pdb=" CB LEU i 73 " pdb=" CD1 LEU i 73 " pdb=" CD2 LEU i 73 " both_signs ideal model delta sigma weight residual False -2.59 -2.83 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CG LEU a 352 " pdb=" CB LEU a 352 " pdb=" CD1 LEU a 352 " pdb=" CD2 LEU a 352 " both_signs ideal model delta sigma weight residual False -2.59 -2.80 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CG LEU d 53 " pdb=" CB LEU d 53 " pdb=" CD1 LEU d 53 " pdb=" CD2 LEU d 53 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 4338 not shown) Planarity restraints: 4801 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR a 216 " 0.109 2.00e-02 2.50e+03 6.74e-02 9.09e+01 pdb=" CG TYR a 216 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR a 216 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR a 216 " -0.064 2.00e-02 2.50e+03 pdb=" CE1 TYR a 216 " -0.063 2.00e-02 2.50e+03 pdb=" CE2 TYR a 216 " -0.041 2.00e-02 2.50e+03 pdb=" CZ TYR a 216 " -0.011 2.00e-02 2.50e+03 pdb=" OH TYR a 216 " 0.116 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP a 344 " -0.088 2.00e-02 2.50e+03 4.64e-02 5.37e+01 pdb=" CG TRP a 344 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP a 344 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP a 344 " 0.033 2.00e-02 2.50e+03 pdb=" NE1 TRP a 344 " 0.042 2.00e-02 2.50e+03 pdb=" CE2 TRP a 344 " -0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP a 344 " 0.040 2.00e-02 2.50e+03 pdb=" CZ2 TRP a 344 " -0.079 2.00e-02 2.50e+03 pdb=" CZ3 TRP a 344 " 0.033 2.00e-02 2.50e+03 pdb=" CH2 TRP a 344 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR a 67 " 0.055 2.00e-02 2.50e+03 4.40e-02 3.87e+01 pdb=" CG TYR a 67 " 0.011 2.00e-02 2.50e+03 pdb=" CD1 TYR a 67 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR a 67 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR a 67 " -0.042 2.00e-02 2.50e+03 pdb=" CE2 TYR a 67 " -0.040 2.00e-02 2.50e+03 pdb=" CZ TYR a 67 " -0.023 2.00e-02 2.50e+03 pdb=" OH TYR a 67 " 0.085 2.00e-02 2.50e+03 ... (remaining 4798 not shown) Histogram of nonbonded interaction distances: 0.85 - 1.66: 6 1.66 - 2.47: 134 2.47 - 3.28: 30230 3.28 - 4.09: 67192 4.09 - 4.90: 117380 Warning: very small nonbonded interaction distances. Nonbonded interactions: 214942 Sorted by model distance: nonbonded pdb=" CD2 TYR a 21 " pdb=" NZ LYS d 71 " model vdw 0.850 3.420 nonbonded pdb=" CE2 TYR a 21 " pdb=" NZ LYS d 71 " model vdw 1.176 3.420 nonbonded pdb=" CG TYR a 21 " pdb=" NZ LYS d 71 " model vdw 1.304 3.340 nonbonded pdb=" CZ TYR a 21 " pdb=" CE LYS d 71 " model vdw 1.461 3.660 nonbonded pdb=" CE1 TYR a 21 " pdb=" CE LYS d 71 " model vdw 1.614 3.740 ... (remaining 214937 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=0.30 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.730 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: 0.020 Extract box with map and model: 10.850 Check model and map are aligned: 0.390 Set scattering table: 0.230 Process input model: 65.350 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4689 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 : 0.005 0.097 28039 Z= 0.314 Angle : 0.800 12.469 37837 Z= 0.474 Chirality : 0.048 0.243 4341 Planarity : 0.006 0.147 4801 Dihedral : 12.884 87.182 10734 Min Nonbonded Distance : 0.850 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.34 % Favored : 98.54 % Rotamer: Outliers : 0.09 % Allowed : 0.47 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.15), residues: 3294 helix: 1.77 (0.12), residues: 1759 sheet: 0.80 (0.24), residues: 486 loop : -0.06 (0.20), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.088 0.005 TRP a 344 HIS 0.014 0.001 HIS a 536 PHE 0.055 0.003 PHE a 356 TYR 0.116 0.003 TYR a 216 ARG 0.011 0.001 ARG h 130 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 3163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 215 time to evaluate : 3.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 195 MET cc_start: 0.4780 (mpp) cc_final: 0.4212 (mpp) REVERT: k 1 MET cc_start: 0.3740 (tpt) cc_final: 0.2639 (tpt) REVERT: n 510 MET cc_start: 0.0877 (tpt) cc_final: -0.1328 (mmt) REVERT: n 565 LEU cc_start: 0.7462 (pp) cc_final: 0.7168 (pp) REVERT: n 790 MET cc_start: -0.4515 (ppp) cc_final: -0.6643 (tpt) REVERT: t 200 LEU cc_start: 0.6137 (tp) cc_final: 0.5270 (tp) REVERT: u 1 MET cc_start: 0.0534 (pmm) cc_final: -0.0500 (mpp) outliers start: 3 outliers final: 1 residues processed: 218 average time/residue: 0.4229 time to fit residues: 143.8711 Evaluate side-chains 125 residues out of total 3163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 124 time to evaluate : 3.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 279 optimal weight: 8.9990 chunk 250 optimal weight: 10.0000 chunk 139 optimal weight: 8.9990 chunk 85 optimal weight: 20.0000 chunk 169 optimal weight: 9.9990 chunk 134 optimal weight: 40.0000 chunk 259 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 157 optimal weight: 0.3980 chunk 193 optimal weight: 2.9990 chunk 300 optimal weight: 0.1980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 118 HIS ** a 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 182 ASN ** f 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 173 ASN ** n 715 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 45 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4789 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 28039 Z= 0.155 Angle : 0.547 10.985 37837 Z= 0.285 Chirality : 0.041 0.213 4341 Planarity : 0.004 0.084 4801 Dihedral : 4.023 24.603 3628 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.70 % Favored : 98.27 % Rotamer: Outliers : 0.38 % Allowed : 3.41 % Favored : 96.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.15), residues: 3294 helix: 2.13 (0.12), residues: 1795 sheet: 1.00 (0.24), residues: 463 loop : 0.08 (0.20), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP n 181 HIS 0.011 0.001 HIS n 116 PHE 0.037 0.001 PHE d 136 TYR 0.023 0.001 TYR h 128 ARG 0.005 0.000 ARG h 130 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 3163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 142 time to evaluate : 3.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: k 1 MET cc_start: 0.4158 (tpt) cc_final: 0.3434 (tpt) REVERT: n 510 MET cc_start: 0.0906 (tpt) cc_final: -0.1273 (mmt) REVERT: n 565 LEU cc_start: 0.7548 (pp) cc_final: 0.7078 (pp) REVERT: n 790 MET cc_start: -0.4438 (ppp) cc_final: -0.6633 (tpt) REVERT: u 1 MET cc_start: 0.0366 (pmm) cc_final: -0.0539 (mpp) outliers start: 12 outliers final: 7 residues processed: 154 average time/residue: 0.4076 time to fit residues: 99.5146 Evaluate side-chains 122 residues out of total 3163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 115 time to evaluate : 3.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 167 optimal weight: 10.0000 chunk 93 optimal weight: 9.9990 chunk 250 optimal weight: 1.9990 chunk 204 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 301 optimal weight: 6.9990 chunk 325 optimal weight: 8.9990 chunk 268 optimal weight: 30.0000 chunk 298 optimal weight: 3.9990 chunk 102 optimal weight: 8.9990 chunk 241 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 324 ASN d 122 HIS ** d 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 70 ASN ** h 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 502 GLN q 310 ASN r 53 ASN t 203 GLN ** u 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 68 ASN ** w 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4954 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 28039 Z= 0.211 Angle : 0.560 10.611 37837 Z= 0.295 Chirality : 0.040 0.193 4341 Planarity : 0.004 0.070 4801 Dihedral : 3.971 24.642 3628 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.73 % Favored : 98.24 % Rotamer: Outliers : 0.16 % Allowed : 3.86 % Favored : 95.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.15), residues: 3294 helix: 1.98 (0.12), residues: 1803 sheet: 0.90 (0.24), residues: 467 loop : 0.10 (0.20), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP r 41 HIS 0.009 0.001 HIS n 116 PHE 0.028 0.002 PHE s 145 TYR 0.031 0.001 TYR f 100 ARG 0.009 0.001 ARG u 92 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 3163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 136 time to evaluate : 3.431 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: d 195 MET cc_start: 0.5654 (mpp) cc_final: 0.4749 (mmt) REVERT: n 510 MET cc_start: 0.1091 (tpt) cc_final: -0.1705 (mmt) REVERT: n 565 LEU cc_start: 0.7583 (pp) cc_final: 0.7270 (pp) REVERT: n 790 MET cc_start: -0.4569 (ppp) cc_final: -0.6974 (tpt) outliers start: 5 outliers final: 4 residues processed: 141 average time/residue: 0.3890 time to fit residues: 89.5096 Evaluate side-chains 115 residues out of total 3163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 111 time to evaluate : 3.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 297 optimal weight: 20.0000 chunk 226 optimal weight: 0.8980 chunk 156 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 143 optimal weight: 2.9990 chunk 202 optimal weight: 8.9990 chunk 302 optimal weight: 3.9990 chunk 319 optimal weight: 0.0870 chunk 157 optimal weight: 10.0000 chunk 286 optimal weight: 0.1980 chunk 86 optimal weight: 2.9990 overall best weight: 1.4362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 118 GLN ** u 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 86 ASN w 113 GLN w 116 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4901 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 28039 Z= 0.135 Angle : 0.526 9.019 37837 Z= 0.270 Chirality : 0.040 0.159 4341 Planarity : 0.004 0.077 4801 Dihedral : 3.870 24.828 3628 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.58 % Favored : 98.39 % Rotamer: Outliers : 0.03 % Allowed : 2.28 % Favored : 97.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.15), residues: 3294 helix: 2.12 (0.12), residues: 1801 sheet: 0.97 (0.24), residues: 468 loop : 0.12 (0.20), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP r 41 HIS 0.008 0.001 HIS n 116 PHE 0.024 0.001 PHE d 81 TYR 0.022 0.001 TYR t 204 ARG 0.013 0.000 ARG j 59 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 3163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 130 time to evaluate : 3.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 195 MET cc_start: 0.5743 (mpp) cc_final: 0.4682 (mmt) REVERT: n 510 MET cc_start: 0.0813 (tpt) cc_final: -0.1623 (mmt) REVERT: n 565 LEU cc_start: 0.7726 (pp) cc_final: 0.7289 (pp) REVERT: n 722 MET cc_start: -0.1390 (tpt) cc_final: -0.2277 (ttt) REVERT: n 790 MET cc_start: -0.4599 (ppp) cc_final: -0.6980 (tpt) REVERT: t 200 LEU cc_start: 0.6384 (tp) cc_final: 0.5816 (tp) REVERT: w 116 GLN cc_start: 0.4267 (OUTLIER) cc_final: 0.3950 (pm20) outliers start: 1 outliers final: 0 residues processed: 131 average time/residue: 0.3919 time to fit residues: 85.6580 Evaluate side-chains 115 residues out of total 3163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 114 time to evaluate : 3.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 266 optimal weight: 0.1980 chunk 181 optimal weight: 50.0000 chunk 4 optimal weight: 0.8980 chunk 238 optimal weight: 9.9990 chunk 132 optimal weight: 5.9990 chunk 273 optimal weight: 30.0000 chunk 221 optimal weight: 8.9990 chunk 0 optimal weight: 30.0000 chunk 163 optimal weight: 2.9990 chunk 287 optimal weight: 8.9990 chunk 80 optimal weight: 5.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 151 GLN ** j 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 173 ASN n 399 ASN ** r 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 60 ASN ** w 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 119 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4982 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28039 Z= 0.161 Angle : 0.530 8.535 37837 Z= 0.275 Chirality : 0.040 0.155 4341 Planarity : 0.003 0.056 4801 Dihedral : 3.847 25.128 3628 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.79 % Favored : 98.18 % Rotamer: Outliers : 0.09 % Allowed : 2.43 % Favored : 97.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.15), residues: 3294 helix: 2.06 (0.12), residues: 1813 sheet: 0.96 (0.24), residues: 459 loop : 0.14 (0.20), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP r 41 HIS 0.007 0.001 HIS n 116 PHE 0.020 0.001 PHE k 55 TYR 0.027 0.001 TYR t 204 ARG 0.013 0.000 ARG u 92 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 3163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 131 time to evaluate : 3.446 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: d 195 MET cc_start: 0.5948 (mpp) cc_final: 0.4645 (mmt) REVERT: n 472 MET cc_start: 0.7053 (mmp) cc_final: 0.6727 (mmt) REVERT: n 510 MET cc_start: 0.1268 (tpt) cc_final: -0.1362 (mmt) REVERT: n 767 MET cc_start: -0.1270 (mpp) cc_final: -0.3393 (mpp) REVERT: n 790 MET cc_start: -0.4866 (ppp) cc_final: -0.7007 (tpt) REVERT: v 1 MET cc_start: 0.7333 (ppp) cc_final: 0.6909 (ppp) outliers start: 3 outliers final: 0 residues processed: 134 average time/residue: 0.3975 time to fit residues: 87.8692 Evaluate side-chains 109 residues out of total 3163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 3.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 107 optimal weight: 6.9990 chunk 288 optimal weight: 20.0000 chunk 63 optimal weight: 40.0000 chunk 187 optimal weight: 30.0000 chunk 78 optimal weight: 30.0000 chunk 320 optimal weight: 9.9990 chunk 265 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 105 optimal weight: 7.9990 chunk 168 optimal weight: 7.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 529 GLN d 98 GLN d 199 HIS f 10 GLN ** g 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 151 GLN h 165 ASN ** i 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 14 ASN ** k 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 173 ASN n 622 GLN n 631 HIS q 310 ASN ** q 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 258 ASN t 48 ASN ** u 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 119 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5227 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 28039 Z= 0.301 Angle : 0.689 10.592 37837 Z= 0.362 Chirality : 0.043 0.212 4341 Planarity : 0.005 0.064 4801 Dihedral : 4.375 24.991 3628 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 19.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.49 % Favored : 97.48 % Rotamer: Outliers : 0.06 % Allowed : 2.97 % Favored : 96.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.14), residues: 3294 helix: 1.38 (0.12), residues: 1819 sheet: 0.56 (0.25), residues: 442 loop : -0.06 (0.20), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP t 35 HIS 0.011 0.002 HIS q 91 PHE 0.028 0.002 PHE w 80 TYR 0.033 0.002 TYR z 17 ARG 0.010 0.001 ARG d 75 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 3163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 118 time to evaluate : 3.289 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: d 195 MET cc_start: 0.6432 (mpp) cc_final: 0.5494 (mmt) REVERT: n 510 MET cc_start: 0.2239 (tpt) cc_final: -0.1319 (mmt) REVERT: n 767 MET cc_start: -0.0839 (mpp) cc_final: -0.3139 (mpp) REVERT: v 1 MET cc_start: 0.7692 (ppp) cc_final: 0.7272 (ppp) outliers start: 2 outliers final: 2 residues processed: 120 average time/residue: 0.3981 time to fit residues: 78.0161 Evaluate side-chains 102 residues out of total 3163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 100 time to evaluate : 3.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 308 optimal weight: 6.9990 chunk 36 optimal weight: 20.0000 chunk 182 optimal weight: 0.6980 chunk 233 optimal weight: 30.0000 chunk 181 optimal weight: 20.0000 chunk 269 optimal weight: 0.0060 chunk 178 optimal weight: 8.9990 chunk 319 optimal weight: 3.9990 chunk 199 optimal weight: 5.9990 chunk 194 optimal weight: 8.9990 chunk 147 optimal weight: 1.9990 overall best weight: 2.5402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 177 GLN ** f 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 151 GLN ** j 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 173 ASN n 399 ASN ** r 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 4 GLN ** v 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 113 GLN w 119 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5122 moved from start: 0.4088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 28039 Z= 0.158 Angle : 0.562 8.662 37837 Z= 0.291 Chirality : 0.041 0.185 4341 Planarity : 0.004 0.053 4801 Dihedral : 4.112 24.555 3628 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.91 % Favored : 98.06 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.15), residues: 3294 helix: 1.71 (0.12), residues: 1824 sheet: 0.55 (0.25), residues: 441 loop : -0.01 (0.20), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP w 64 HIS 0.007 0.001 HIS n 116 PHE 0.029 0.002 PHE j 39 TYR 0.016 0.001 TYR z 17 ARG 0.009 0.000 ARG u 92 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 3163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 3.343 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: d 195 MET cc_start: 0.6240 (mpp) cc_final: 0.5670 (mmt) REVERT: n 510 MET cc_start: 0.1740 (tpt) cc_final: 0.0915 (mmt) REVERT: n 767 MET cc_start: -0.0888 (mpp) cc_final: -0.3096 (mpp) REVERT: v 1 MET cc_start: 0.7298 (ppp) cc_final: 0.6977 (ppp) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.3939 time to fit residues: 78.2387 Evaluate side-chains 104 residues out of total 3163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 3.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 197 optimal weight: 0.7980 chunk 127 optimal weight: 10.0000 chunk 190 optimal weight: 50.0000 chunk 96 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 61 optimal weight: 30.0000 chunk 202 optimal weight: 9.9990 chunk 217 optimal weight: 30.0000 chunk 157 optimal weight: 0.0170 chunk 29 optimal weight: 9.9990 chunk 250 optimal weight: 6.9990 overall best weight: 2.9222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 529 GLN ** d 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 173 ASN ** r 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 86 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5130 moved from start: 0.4255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 28039 Z= 0.160 Angle : 0.553 9.615 37837 Z= 0.288 Chirality : 0.041 0.160 4341 Planarity : 0.004 0.063 4801 Dihedral : 4.036 25.120 3628 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.22 % Favored : 97.75 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.15), residues: 3294 helix: 1.80 (0.12), residues: 1823 sheet: 0.57 (0.25), residues: 441 loop : 0.02 (0.20), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP w 125 HIS 0.007 0.001 HIS n 116 PHE 0.029 0.002 PHE j 39 TYR 0.018 0.001 TYR f 100 ARG 0.008 0.000 ARG u 92 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 3163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 3.347 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: d 195 MET cc_start: 0.6202 (mpp) cc_final: 0.5698 (mmt) REVERT: n 510 MET cc_start: 0.1710 (tpt) cc_final: -0.0422 (mmt) REVERT: n 767 MET cc_start: -0.0866 (mpp) cc_final: -0.3105 (mpp) REVERT: v 1 MET cc_start: 0.7338 (ppp) cc_final: 0.7069 (ppp) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.3740 time to fit residues: 74.9509 Evaluate side-chains 105 residues out of total 3163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 3.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 290 optimal weight: 9.9990 chunk 305 optimal weight: 6.9990 chunk 278 optimal weight: 10.0000 chunk 297 optimal weight: 10.0000 chunk 178 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 233 optimal weight: 9.9990 chunk 91 optimal weight: 0.0770 chunk 268 optimal weight: 6.9990 chunk 281 optimal weight: 8.9990 chunk 296 optimal weight: 5.9990 overall best weight: 4.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 25 GLN n 173 ASN n 177 ASN ** r 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 26 GLN ** u 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5182 moved from start: 0.4594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28039 Z= 0.188 Angle : 0.584 9.481 37837 Z= 0.307 Chirality : 0.041 0.178 4341 Planarity : 0.004 0.051 4801 Dihedral : 4.109 25.204 3628 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.58 % Favored : 97.39 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.15), residues: 3294 helix: 1.70 (0.12), residues: 1827 sheet: 0.55 (0.25), residues: 436 loop : -0.07 (0.20), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP h 62 HIS 0.012 0.001 HIS g 160 PHE 0.024 0.002 PHE j 39 TYR 0.019 0.001 TYR z 17 ARG 0.011 0.001 ARG g 166 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 3163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 4.212 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: d 195 MET cc_start: 0.6078 (mpp) cc_final: 0.5758 (mmt) REVERT: n 510 MET cc_start: 0.1755 (tpt) cc_final: 0.0957 (mmt) REVERT: n 767 MET cc_start: -0.0313 (mpp) cc_final: -0.2678 (mpp) REVERT: v 1 MET cc_start: 0.7420 (ppp) cc_final: 0.7156 (ppp) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.3969 time to fit residues: 76.6541 Evaluate side-chains 102 residues out of total 3163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 3.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 195 optimal weight: 0.0870 chunk 314 optimal weight: 5.9990 chunk 191 optimal weight: 0.4980 chunk 149 optimal weight: 7.9990 chunk 218 optimal weight: 40.0000 chunk 329 optimal weight: 6.9990 chunk 303 optimal weight: 0.0000 chunk 262 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 202 optimal weight: 3.9990 chunk 161 optimal weight: 8.9990 overall best weight: 1.7166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 173 ASN ** r 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 226 HIS ** u 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 18 GLN ** u 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5129 moved from start: 0.4631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 28039 Z= 0.143 Angle : 0.553 10.132 37837 Z= 0.287 Chirality : 0.041 0.169 4341 Planarity : 0.003 0.050 4801 Dihedral : 3.998 25.504 3628 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.28 % Favored : 97.69 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.15), residues: 3294 helix: 1.83 (0.12), residues: 1820 sheet: 0.68 (0.25), residues: 434 loop : 0.01 (0.20), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP w 64 HIS 0.007 0.001 HIS n 116 PHE 0.024 0.001 PHE j 39 TYR 0.020 0.001 TYR f 100 ARG 0.013 0.000 ARG u 92 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 3163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 3.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 195 MET cc_start: 0.6198 (mpp) cc_final: 0.5831 (mmt) REVERT: n 510 MET cc_start: 0.1558 (tpt) cc_final: -0.0367 (mmt) REVERT: n 767 MET cc_start: -0.0306 (mpp) cc_final: -0.2667 (mpp) REVERT: v 1 MET cc_start: 0.7234 (ppp) cc_final: 0.7002 (ppp) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.4097 time to fit residues: 78.9526 Evaluate side-chains 103 residues out of total 3163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 3.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 208 optimal weight: 6.9990 chunk 279 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 chunk 242 optimal weight: 7.9990 chunk 38 optimal weight: 20.0000 chunk 72 optimal weight: 0.0970 chunk 263 optimal weight: 5.9990 chunk 110 optimal weight: 10.0000 chunk 270 optimal weight: 40.0000 chunk 33 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 overall best weight: 4.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 82 ASN ** j 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.042854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.032420 restraints weight = 460007.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.032676 restraints weight = 378932.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.032455 restraints weight = 294723.274| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3127 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3126 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.5119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 28039 Z= 0.212 Angle : 0.598 10.651 37837 Z= 0.314 Chirality : 0.041 0.193 4341 Planarity : 0.004 0.055 4801 Dihedral : 4.145 25.366 3628 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 17.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.61 % Favored : 97.36 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.15), residues: 3294 helix: 1.66 (0.12), residues: 1826 sheet: 0.55 (0.25), residues: 433 loop : -0.07 (0.20), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP h 62 HIS 0.007 0.001 HIS n 116 PHE 0.023 0.002 PHE j 39 TYR 0.022 0.001 TYR z 17 ARG 0.010 0.001 ARG u 92 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4162.77 seconds wall clock time: 78 minutes 8.65 seconds (4688.65 seconds total)