Starting phenix.real_space_refine on Wed Mar 20 05:19:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfn_33794/03_2024/7yfn_33794_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfn_33794/03_2024/7yfn_33794.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfn_33794/03_2024/7yfn_33794.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfn_33794/03_2024/7yfn_33794.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfn_33794/03_2024/7yfn_33794_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfn_33794/03_2024/7yfn_33794_updated.pdb" } resolution = 3.8 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 31 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 100 5.16 5 C 16894 2.51 5 N 4503 2.21 5 O 4897 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 107": "OE1" <-> "OE2" Residue "A GLU 117": "OE1" <-> "OE2" Residue "A GLU 195": "OE1" <-> "OE2" Residue "B GLU 126": "OE1" <-> "OE2" Residue "B ARG 236": "NH1" <-> "NH2" Residue "D ARG 76": "NH1" <-> "NH2" Residue "D ARG 305": "NH1" <-> "NH2" Residue "D GLU 332": "OE1" <-> "OE2" Residue "D ARG 343": "NH1" <-> "NH2" Residue "D GLU 551": "OE1" <-> "OE2" Residue "D GLU 609": "OE1" <-> "OE2" Residue "D ARG 618": "NH1" <-> "NH2" Residue "D GLU 653": "OE1" <-> "OE2" Residue "D ARG 753": "NH1" <-> "NH2" Residue "D ARG 756": "NH1" <-> "NH2" Residue "E ARG 189": "NH1" <-> "NH2" Residue "E ARG 270": "NH1" <-> "NH2" Residue "E GLU 274": "OE1" <-> "OE2" Residue "E ARG 275": "NH1" <-> "NH2" Residue "T GLU 971": "OE1" <-> "OE2" Residue "T ARG 1054": "NH1" <-> "NH2" Residue "T GLU 1058": "OE1" <-> "OE2" Residue "T ARG 1123": "NH1" <-> "NH2" Residue "T ARG 1170": "NH1" <-> "NH2" Residue "T GLU 1192": "OE1" <-> "OE2" Residue "T ARG 2432": "NH1" <-> "NH2" Residue "T ARG 2445": "NH1" <-> "NH2" Residue "T ARG 2456": "NH1" <-> "NH2" Residue "T ARG 2482": "NH1" <-> "NH2" Residue "T TYR 2492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 2575": "OE1" <-> "OE2" Residue "T GLU 2659": "OE1" <-> "OE2" Residue "T ARG 2681": "NH1" <-> "NH2" Residue "T ARG 2715": "NH1" <-> "NH2" Residue "T ARG 2807": "NH1" <-> "NH2" Residue "T GLU 2819": "OE1" <-> "OE2" Residue "T ARG 2887": "NH1" <-> "NH2" Residue "T ARG 2938": "NH1" <-> "NH2" Residue "T ARG 2969": "NH1" <-> "NH2" Residue "T ARG 3034": "NH1" <-> "NH2" Residue "T GLU 3070": "OE1" <-> "OE2" Residue "T GLU 3127": "OE1" <-> "OE2" Residue "T ARG 3172": "NH1" <-> "NH2" Residue "T GLU 3243": "OE1" <-> "OE2" Residue "T ARG 3313": "NH1" <-> "NH2" Residue "T ARG 3320": "NH1" <-> "NH2" Residue "T GLU 3353": "OE1" <-> "OE2" Residue "T ARG 3373": "NH1" <-> "NH2" Residue "T ARG 3382": "NH1" <-> "NH2" Residue "T ARG 3424": "NH1" <-> "NH2" Residue "T GLU 3435": "OE1" <-> "OE2" Residue "T ARG 3438": "NH1" <-> "NH2" Residue "T GLU 3473": "OE1" <-> "OE2" Residue "T PHE 3521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 3545": "NH1" <-> "NH2" Residue "T ARG 3689": "NH1" <-> "NH2" Residue "F GLU 522": "OE1" <-> "OE2" Residue "F GLU 530": "OE1" <-> "OE2" Residue "F PHE 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 593": "NH1" <-> "NH2" Residue "F ARG 641": "NH1" <-> "NH2" 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: 26397 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2904 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Chain: "B" Number of atoms: 3172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3172 Classifications: {'peptide': 402} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 382} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 3777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3777 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 22, 'TRANS': 431} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1668 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 193} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "T" Number of atoms: 13822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1688, 13822 Classifications: {'peptide': 1688} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 13} Link IDs: {'CIS': 1, 'PTRANS': 79, 'TRANS': 1607} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 2, 'PHE:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 53 Chain: "F" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1023 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 115} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 12.80, per 1000 atoms: 0.48 Number of scatterers: 26397 At special positions: 0 Unit cell: (137.28, 164.34, 172.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 100 16.00 P 3 15.00 O 4897 8.00 N 4503 7.00 C 16894 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.27 Conformation dependent library (CDL) restraints added in 4.4 seconds 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6236 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 140 helices and 17 sheets defined 50.6% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.47 Creating SS restraints... Processing helix chain 'A' and resid 55 through 60 Processing helix chain 'A' and resid 79 through 91 Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 113 through 127 removed outlier: 4.016A pdb=" N THR A 120 " --> pdb=" O ARG A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 182 through 196 removed outlier: 4.844A pdb=" N ASP A 187 " --> pdb=" O ARG A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 215 Processing helix chain 'A' and resid 223 through 232 Processing helix chain 'A' and resid 252 through 262 removed outlier: 4.766A pdb=" N ALA A 257 " --> pdb=" O ARG A 254 " (cutoff:3.500A) Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 274 through 284 Processing helix chain 'A' and resid 288 through 296 removed outlier: 4.412A pdb=" N GLU A 292 " --> pdb=" O ASP A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 320 Processing helix chain 'A' and resid 338 through 348 Processing helix chain 'A' and resid 351 through 354 Processing helix chain 'A' and resid 359 through 364 Processing helix chain 'A' and resid 367 through 373 Processing helix chain 'B' and resid 83 through 96 removed outlier: 4.680A pdb=" N GLU B 88 " --> pdb=" O ASP B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 130 Processing helix chain 'B' and resid 142 through 150 Processing helix chain 'B' and resid 187 through 197 removed outlier: 4.675A pdb=" N HIS B 192 " --> pdb=" O LYS B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 243 removed outlier: 4.500A pdb=" N PHE B 239 " --> pdb=" O ASN B 235 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLN B 240 " --> pdb=" O ARG B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 257 No H-bonds generated for 'chain 'B' and resid 255 through 257' Processing helix chain 'B' and resid 259 through 262 No H-bonds generated for 'chain 'B' and resid 259 through 262' Processing helix chain 'B' and resid 282 through 293 removed outlier: 4.432A pdb=" N ALA B 289 " --> pdb=" O ARG B 285 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LEU B 292 " --> pdb=" O PHE B 288 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE B 293 " --> pdb=" O ALA B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 395 Processing helix chain 'B' and resid 401 through 406 Processing helix chain 'B' and resid 414 through 416 No H-bonds generated for 'chain 'B' and resid 414 through 416' Processing helix chain 'B' and resid 420 through 431 removed outlier: 4.278A pdb=" N MET B 425 " --> pdb=" O SER B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 449 No H-bonds generated for 'chain 'B' and resid 447 through 449' Processing helix chain 'B' and resid 451 through 461 Processing helix chain 'B' and resid 472 through 478 Processing helix chain 'B' and resid 480 through 486 Processing helix chain 'D' and resid 26 through 47 Processing helix chain 'D' and resid 70 through 73 No H-bonds generated for 'chain 'D' and resid 70 through 73' Processing helix chain 'D' and resid 287 through 296 Processing helix chain 'D' and resid 300 through 305 Proline residue: D 304 - end of helix No H-bonds generated for 'chain 'D' and resid 300 through 305' Processing helix chain 'D' and resid 312 through 335 Processing helix chain 'D' and resid 358 through 397 Processing helix chain 'D' and resid 563 through 565 No H-bonds generated for 'chain 'D' and resid 563 through 565' Processing helix chain 'D' and resid 639 through 641 No H-bonds generated for 'chain 'D' and resid 639 through 641' Processing helix chain 'D' and resid 652 through 665 removed outlier: 3.567A pdb=" N LYS D 660 " --> pdb=" O GLN D 656 " (cutoff:3.500A) Processing helix chain 'D' and resid 669 through 676 Processing helix chain 'D' and resid 693 through 703 Processing helix chain 'D' and resid 709 through 711 No H-bonds generated for 'chain 'D' and resid 709 through 711' Processing helix chain 'D' and resid 715 through 733 removed outlier: 4.208A pdb=" N HIS D 718 " --> pdb=" O PRO D 715 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG D 733 " --> pdb=" O PHE D 730 " (cutoff:3.500A) Processing helix chain 'D' and resid 753 through 771 removed outlier: 4.409A pdb=" N TRP D 757 " --> pdb=" O ARG D 753 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N PHE D 761 " --> pdb=" O TRP D 757 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N GLU D 762 " --> pdb=" O ALA D 758 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LYS D 766 " --> pdb=" O GLU D 762 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS D 770 " --> pdb=" O LYS D 766 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 102 No H-bonds generated for 'chain 'E' and resid 99 through 102' Processing helix chain 'E' and resid 166 through 176 removed outlier: 4.232A pdb=" N ASN E 174 " --> pdb=" O GLU E 170 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N LEU E 175 " --> pdb=" O TYR E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 181 No H-bonds generated for 'chain 'E' and resid 179 through 181' Processing helix chain 'E' and resid 185 through 189 Processing helix chain 'E' and resid 198 through 216 Processing helix chain 'E' and resid 221 through 225 Processing helix chain 'E' and resid 230 through 245 Processing helix chain 'E' and resid 248 through 265 Processing helix chain 'E' and resid 271 through 278 Processing helix chain 'E' and resid 280 through 283 removed outlier: 3.678A pdb=" N ASP E 283 " --> pdb=" O ARG E 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 280 through 283' Processing helix chain 'E' and resid 300 through 307 Processing helix chain 'T' and resid 837 through 845 removed outlier: 4.517A pdb=" N GLN T 844 " --> pdb=" O GLN T 840 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N MET T 845 " --> pdb=" O SER T 841 " (cutoff:3.500A) Processing helix chain 'T' and resid 856 through 865 Processing helix chain 'T' and resid 880 through 889 Processing helix chain 'T' and resid 892 through 904 removed outlier: 4.046A pdb=" N SER T 895 " --> pdb=" O ASP T 892 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG T 899 " --> pdb=" O GLN T 896 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU T 902 " --> pdb=" O ARG T 899 " (cutoff:3.500A) Processing helix chain 'T' and resid 913 through 931 Proline residue: T 919 - end of helix removed outlier: 4.681A pdb=" N ASP T 922 " --> pdb=" O GLU T 918 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ASP T 923 " --> pdb=" O PRO T 919 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS T 926 " --> pdb=" O ASP T 922 " (cutoff:3.500A) Processing helix chain 'T' and resid 939 through 951 Processing helix chain 'T' and resid 971 through 973 No H-bonds generated for 'chain 'T' and resid 971 through 973' Processing helix chain 'T' and resid 997 through 1005 removed outlier: 4.006A pdb=" N ASN T1002 " --> pdb=" O GLN T 998 " (cutoff:3.500A) Processing helix chain 'T' and resid 1011 through 1033 removed outlier: 4.638A pdb=" N SER T1031 " --> pdb=" O LEU T1027 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N SER T1032 " --> pdb=" O MET T1028 " (cutoff:3.500A) Processing helix chain 'T' and resid 1039 through 1051 removed outlier: 4.158A pdb=" N LYS T1051 " --> pdb=" O VAL T1047 " (cutoff:3.500A) Processing helix chain 'T' and resid 1069 through 1091 removed outlier: 3.951A pdb=" N SER T1091 " --> pdb=" O PHE T1087 " (cutoff:3.500A) Processing helix chain 'T' and resid 1096 through 1124 removed outlier: 4.058A pdb=" N ASN T1116 " --> pdb=" O LEU T1112 " (cutoff:3.500A) Processing helix chain 'T' and resid 1144 through 1154 Proline residue: T1150 - end of helix Processing helix chain 'T' and resid 1158 through 1179 Processing helix chain 'T' and resid 1182 through 1187 Processing helix chain 'T' and resid 1190 through 1202 Processing helix chain 'T' and resid 1206 through 1223 Processing helix chain 'T' and resid 1229 through 1232 No H-bonds generated for 'chain 'T' and resid 1229 through 1232' Processing helix chain 'T' and resid 1235 through 1246 Processing helix chain 'T' and resid 2417 through 2425 removed outlier: 3.503A pdb=" N THR T2424 " --> pdb=" O PHE T2420 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ARG T2425 " --> pdb=" O LEU T2421 " (cutoff:3.500A) Processing helix chain 'T' and resid 2429 through 2442 removed outlier: 3.790A pdb=" N ARG T2434 " --> pdb=" O GLY T2430 " (cutoff:3.500A) Processing helix chain 'T' and resid 2447 through 2456 Processing helix chain 'T' and resid 2469 through 2479 Processing helix chain 'T' and resid 2497 through 2502 removed outlier: 3.741A pdb=" N GLU T2502 " --> pdb=" O SER T2498 " (cutoff:3.500A) Processing helix chain 'T' and resid 2505 through 2507 No H-bonds generated for 'chain 'T' and resid 2505 through 2507' Processing helix chain 'T' and resid 2519 through 2534 Processing helix chain 'T' and resid 2538 through 2551 removed outlier: 3.609A pdb=" N GLU T2547 " --> pdb=" O ASP T2543 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE T2548 " --> pdb=" O SER T2544 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N TYR T2550 " --> pdb=" O ILE T2546 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN T2551 " --> pdb=" O GLU T2547 " (cutoff:3.500A) Processing helix chain 'T' and resid 2553 through 2561 removed outlier: 3.632A pdb=" N HIS T2557 " --> pdb=" O PRO T2553 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG T2558 " --> pdb=" O LYS T2554 " (cutoff:3.500A) Processing helix chain 'T' and resid 2564 through 2568 Processing helix chain 'T' and resid 2576 through 2587 Processing helix chain 'T' and resid 2604 through 2613 Processing helix chain 'T' and resid 2624 through 2629 removed outlier: 4.011A pdb=" N ILE T2628 " --> pdb=" O TYR T2625 " (cutoff:3.500A) Processing helix chain 'T' and resid 2633 through 2646 removed outlier: 3.561A pdb=" N LEU T2640 " --> pdb=" O SER T2636 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLN T2644 " --> pdb=" O LEU T2640 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N SER T2645 " --> pdb=" O GLU T2641 " (cutoff:3.500A) Processing helix chain 'T' and resid 2653 through 2669 removed outlier: 3.802A pdb=" N ASP T2660 " --> pdb=" O GLU T2656 " (cutoff:3.500A) Processing helix chain 'T' and resid 2672 through 2682 removed outlier: 3.706A pdb=" N TYR T2676 " --> pdb=" O GLU T2672 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N GLY T2677 " --> pdb=" O ASP T2673 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TRP T2679 " --> pdb=" O PHE T2675 " (cutoff:3.500A) Processing helix chain 'T' and resid 2686 through 2697 Processing helix chain 'T' and resid 2700 through 2713 removed outlier: 3.538A pdb=" N GLN T2705 " --> pdb=" O ASP T2701 " (cutoff:3.500A) Processing helix chain 'T' and resid 2725 through 2740 Processing helix chain 'T' and resid 2747 through 2752 removed outlier: 3.771A pdb=" N HIS T2752 " --> pdb=" O GLU T2748 " (cutoff:3.500A) Processing helix chain 'T' and resid 2755 through 2760 Processing helix chain 'T' and resid 2773 through 2782 removed outlier: 3.502A pdb=" N SER T2779 " --> pdb=" O ALA T2775 " (cutoff:3.500A) Processing helix chain 'T' and resid 2789 through 2805 removed outlier: 3.905A pdb=" N PHE T2794 " --> pdb=" O ARG T2790 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS T2795 " --> pdb=" O ARG T2791 " (cutoff:3.500A) Processing helix chain 'T' and resid 2813 through 2830 Processing helix chain 'T' and resid 2837 through 2864 removed outlier: 4.069A pdb=" N TRP T2841 " --> pdb=" O PRO T2837 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU T2842 " --> pdb=" O ALA T2838 " (cutoff:3.500A) Processing helix chain 'T' and resid 2874 through 2886 Processing helix chain 'T' and resid 2896 through 2919 Proline residue: T2918 - end of helix Processing helix chain 'T' and resid 2942 through 2957 removed outlier: 3.515A pdb=" N HIS T2957 " --> pdb=" O VAL T2953 " (cutoff:3.500A) Processing helix chain 'T' and resid 2960 through 2968 Processing helix chain 'T' and resid 2980 through 2993 Processing helix chain 'T' and resid 2996 through 2998 No H-bonds generated for 'chain 'T' and resid 2996 through 2998' Processing helix chain 'T' and resid 3019 through 3032 Processing helix chain 'T' and resid 3037 through 3050 removed outlier: 3.844A pdb=" N ASP T3050 " --> pdb=" O ALA T3046 " (cutoff:3.500A) Processing helix chain 'T' and resid 3054 through 3070 Processing helix chain 'T' and resid 3079 through 3091 Processing helix chain 'T' and resid 3098 through 3108 removed outlier: 3.587A pdb=" N ILE T3104 " --> pdb=" O LEU T3100 " (cutoff:3.500A) Processing helix chain 'T' and resid 3116 through 3123 Processing helix chain 'T' and resid 3130 through 3145 removed outlier: 3.812A pdb=" N THR T3135 " --> pdb=" O TYR T3132 " (cutoff:3.500A) Proline residue: T3138 - end of helix Processing helix chain 'T' and resid 3152 through 3162 Processing helix chain 'T' and resid 3164 through 3181 removed outlier: 4.325A pdb=" N PHE T3169 " --> pdb=" O GLN T3165 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N GLN T3170 " --> pdb=" O ALA T3166 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR T3173 " --> pdb=" O PHE T3169 " (cutoff:3.500A) Processing helix chain 'T' and resid 3204 through 3217 removed outlier: 3.539A pdb=" N LEU T3208 " --> pdb=" O PRO T3204 " (cutoff:3.500A) Processing helix chain 'T' and resid 3220 through 3236 Processing helix chain 'T' and resid 3241 through 3262 Processing helix chain 'T' and resid 3274 through 3284 removed outlier: 3.504A pdb=" N VAL T3281 " --> pdb=" O GLU T3277 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER T3284 " --> pdb=" O LEU T3280 " (cutoff:3.500A) Processing helix chain 'T' and resid 3289 through 3299 removed outlier: 4.135A pdb=" N ARG T3293 " --> pdb=" O ALA T3289 " (cutoff:3.500A) Proline residue: T3294 - end of helix removed outlier: 3.784A pdb=" N ASP T3299 " --> pdb=" O LYS T3295 " (cutoff:3.500A) Processing helix chain 'T' and resid 3309 through 3327 Processing helix chain 'T' and resid 3334 through 3337 No H-bonds generated for 'chain 'T' and resid 3334 through 3337' Processing helix chain 'T' and resid 3339 through 3342 No H-bonds generated for 'chain 'T' and resid 3339 through 3342' Processing helix chain 'T' and resid 3411 through 3432 removed outlier: 3.878A pdb=" N ARG T3414 " --> pdb=" O ARG T3411 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR T3423 " --> pdb=" O PHE T3420 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS T3428 " --> pdb=" O LEU T3425 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS T3432 " --> pdb=" O SER T3429 " (cutoff:3.500A) Processing helix chain 'T' and resid 3467 through 3477 Processing helix chain 'T' and resid 3482 through 3497 removed outlier: 4.272A pdb=" N GLN T3486 " --> pdb=" O PRO T3482 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N HIS T3497 " --> pdb=" O LEU T3493 " (cutoff:3.500A) Processing helix chain 'T' and resid 3506 through 3520 Processing helix chain 'T' and resid 3526 through 3534 Processing helix chain 'T' and resid 3538 through 3560 Processing helix chain 'T' and resid 3569 through 3571 No H-bonds generated for 'chain 'T' and resid 3569 through 3571' Processing helix chain 'T' and resid 3626 through 3632 Processing helix chain 'T' and resid 3634 through 3639 removed outlier: 3.611A pdb=" N GLU T3638 " --> pdb=" O ASP T3634 " (cutoff:3.500A) Processing helix chain 'T' and resid 3641 through 3653 Processing helix chain 'T' and resid 3659 through 3677 removed outlier: 3.684A pdb=" N LEU T3665 " --> pdb=" O THR T3661 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE T3666 " --> pdb=" O TYR T3662 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU T3670 " --> pdb=" O PHE T3666 " (cutoff:3.500A) Processing helix chain 'T' and resid 3686 through 3705 removed outlier: 3.788A pdb=" N GLU T3690 " --> pdb=" O PRO T3686 " (cutoff:3.500A) Processing helix chain 'T' and resid 3718 through 3728 Processing helix chain 'T' and resid 3730 through 3735 Processing helix chain 'T' and resid 3738 through 3740 No H-bonds generated for 'chain 'T' and resid 3738 through 3740' Processing helix chain 'F' and resid 521 through 534 removed outlier: 3.891A pdb=" N GLU F 525 " --> pdb=" O GLN F 521 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 8 through 12 removed outlier: 3.817A pdb=" N VAL A 9 " --> pdb=" O GLY A 20 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY A 20 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA A 19 " --> pdb=" O ALA A 29 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA A 29 " --> pdb=" O ALA A 19 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 153 through 155 Processing sheet with id= C, first strand: chain 'A' and resid 160 through 162 Processing sheet with id= D, first strand: chain 'A' and resid 238 through 242 Processing sheet with id= E, first strand: chain 'B' and resid 17 through 21 Processing sheet with id= F, first strand: chain 'B' and resid 45 through 47 Processing sheet with id= G, first strand: chain 'B' and resid 107 through 112 removed outlier: 6.537A pdb=" N ALA B 136 " --> pdb=" O ALA B 108 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N LEU B 110 " --> pdb=" O ALA B 136 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N TYR B 138 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N GLU B 112 " --> pdb=" O TYR B 138 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ALA B 140 " --> pdb=" O GLU B 112 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'B' and resid 165 through 170 Processing sheet with id= I, first strand: chain 'B' and resid 209 through 212 removed outlier: 6.082A pdb=" N ILE B 217 " --> pdb=" O LYS B 210 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 268 through 270 Processing sheet with id= K, first strand: chain 'E' and resid 78 through 83 Processing sheet with id= L, first strand: chain 'T' and resid 977 through 980 Processing sheet with id= M, first strand: chain 'T' and resid 3379 through 3381 removed outlier: 3.886A pdb=" N ARG T3389 " --> pdb=" O VAL T3405 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'T' and resid 3464 through 3466 Processing sheet with id= O, first strand: chain 'T' and resid 3371 through 3374 removed outlier: 7.216A pdb=" N ARG T3394 " --> pdb=" O ALA T3372 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 546 through 548 removed outlier: 3.739A pdb=" N GLN F 571 " --> pdb=" O VAL F 546 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASP F 548 " --> pdb=" O LYS F 569 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LYS F 569 " --> pdb=" O ASP F 548 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 636 through 643 removed outlier: 3.810A pdb=" N ARG F 639 " --> pdb=" O ASP F 651 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE F 647 " --> pdb=" O GLY F 643 " (cutoff:3.500A) 1076 hydrogen bonds defined for protein. 3015 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: 9.96 Time building geometry restraints manager: 10.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4764 1.32 - 1.45: 6871 1.45 - 1.57: 15197 1.57 - 1.69: 6 1.69 - 1.81: 165 Bond restraints: 27003 Sorted by residual: bond pdb=" N PRO T2620 " pdb=" CA PRO T2620 " ideal model delta sigma weight residual 1.469 1.666 -0.197 1.28e-02 6.10e+03 2.37e+02 bond pdb=" C4 ATP B 501 " pdb=" C5 ATP B 501 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.96e+01 bond pdb=" C5 ATP B 501 " pdb=" C6 ATP B 501 " ideal model delta sigma weight residual 1.409 1.476 -0.067 1.00e-02 1.00e+04 4.56e+01 bond pdb=" C PRO T2619 " pdb=" N PRO T2620 " ideal model delta sigma weight residual 1.334 1.453 -0.119 2.34e-02 1.83e+03 2.60e+01 bond pdb=" N MET T2959 " pdb=" CA MET T2959 " ideal model delta sigma weight residual 1.458 1.494 -0.037 7.40e-03 1.83e+04 2.46e+01 ... (remaining 26998 not shown) Histogram of bond angle deviations from ideal: 91.91 - 101.46: 68 101.46 - 111.01: 9866 111.01 - 120.55: 16743 120.55 - 130.10: 9711 130.10 - 139.65: 197 Bond angle restraints: 36585 Sorted by residual: angle pdb=" PB ATP B 501 " pdb=" O3B ATP B 501 " pdb=" PG ATP B 501 " ideal model delta sigma weight residual 139.87 121.22 18.65 1.00e+00 1.00e+00 3.48e+02 angle pdb=" PA ATP B 501 " pdb=" O3A ATP B 501 " pdb=" PB ATP B 501 " ideal model delta sigma weight residual 136.83 119.92 16.91 1.00e+00 1.00e+00 2.86e+02 angle pdb=" C PRO T2619 " pdb=" N PRO T2620 " pdb=" CA PRO T2620 " ideal model delta sigma weight residual 119.84 139.65 -19.81 1.25e+00 6.40e-01 2.51e+02 angle pdb=" CA PRO T2620 " pdb=" N PRO T2620 " pdb=" CD PRO T2620 " ideal model delta sigma weight residual 112.00 91.91 20.09 1.40e+00 5.10e-01 2.06e+02 angle pdb=" N PRO T2619 " pdb=" CA PRO T2619 " pdb=" C PRO T2619 " ideal model delta sigma weight residual 110.70 122.44 -11.74 1.22e+00 6.72e-01 9.27e+01 ... (remaining 36580 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.31: 15395 25.31 - 50.63: 904 50.63 - 75.94: 68 75.94 - 101.26: 6 101.26 - 126.57: 1 Dihedral angle restraints: 16374 sinusoidal: 6782 harmonic: 9592 Sorted by residual: dihedral pdb=" CA ASP T3112 " pdb=" C ASP T3112 " pdb=" N ALA T3113 " pdb=" CA ALA T3113 " ideal model delta harmonic sigma weight residual -180.00 -53.43 -126.57 0 5.00e+00 4.00e-02 6.41e+02 dihedral pdb=" CA ALA D 540 " pdb=" C ALA D 540 " pdb=" N PRO D 541 " pdb=" CA PRO D 541 " ideal model delta harmonic sigma weight residual -180.00 -122.30 -57.70 0 5.00e+00 4.00e-02 1.33e+02 dihedral pdb=" CA LEU T 847 " pdb=" C LEU T 847 " pdb=" N THR T 848 " pdb=" CA THR T 848 " ideal model delta harmonic sigma weight residual 0.00 -33.59 33.59 0 5.00e+00 4.00e-02 4.51e+01 ... (remaining 16371 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 3399 0.094 - 0.189: 554 0.189 - 0.283: 79 0.283 - 0.377: 5 0.377 - 0.472: 1 Chirality restraints: 4038 Sorted by residual: chirality pdb=" CA TYR T2721 " pdb=" N TYR T2721 " pdb=" C TYR T2721 " pdb=" CB TYR T2721 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.56e+00 chirality pdb=" CA PRO T2620 " pdb=" N PRO T2620 " pdb=" C PRO T2620 " pdb=" CB PRO T2620 " both_signs ideal model delta sigma weight residual False 2.72 3.08 -0.36 2.00e-01 2.50e+01 3.26e+00 chirality pdb=" CA ASN T3710 " pdb=" N ASN T3710 " pdb=" C ASN T3710 " pdb=" CB ASN T3710 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.36 2.00e-01 2.50e+01 3.15e+00 ... (remaining 4035 not shown) Planarity restraints: 4692 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO D 541 " 0.102 5.00e-02 4.00e+02 1.54e-01 3.81e+01 pdb=" N PRO D 542 " -0.267 5.00e-02 4.00e+02 pdb=" CA PRO D 542 " 0.086 5.00e-02 4.00e+02 pdb=" CD PRO D 542 " 0.079 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN T3442 " -0.028 2.00e-02 2.50e+03 5.73e-02 3.29e+01 pdb=" C GLN T3442 " 0.099 2.00e-02 2.50e+03 pdb=" O GLN T3442 " -0.036 2.00e-02 2.50e+03 pdb=" N PHE T3443 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE T2697 " 0.027 2.00e-02 2.50e+03 5.66e-02 3.20e+01 pdb=" C ILE T2697 " -0.098 2.00e-02 2.50e+03 pdb=" O ILE T2697 " 0.037 2.00e-02 2.50e+03 pdb=" N GLY T2698 " 0.034 2.00e-02 2.50e+03 ... (remaining 4689 not shown) Histogram of nonbonded interaction distances: 1.13 - 1.88: 6 1.88 - 2.64: 581 2.64 - 3.39: 39003 3.39 - 4.15: 59189 4.15 - 4.90: 106019 Nonbonded interactions: 204798 Sorted by model distance: nonbonded pdb=" CD2 TYR T1013 " pdb=" OE1 GLN T2551 " model vdw 1.130 3.340 nonbonded pdb=" CD1 ILE D 277 " pdb=" OH TYR F 577 " model vdw 1.552 3.460 nonbonded pdb=" CE2 TYR T1013 " pdb=" OE1 GLN T2551 " model vdw 1.610 3.340 nonbonded pdb=" NE ARG T3315 " pdb=" OD2 ASP T3483 " model vdw 1.750 2.520 nonbonded pdb=" CG PRO F 582 " pdb=" CE1 TYR F 584 " model vdw 1.752 3.740 ... (remaining 204793 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 6.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.160 Construct map_model_manager: 0.020 Extract box with map and model: 26.770 Check model and map are aligned: 0.380 Set scattering table: 0.220 Process input model: 65.550 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 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 : 0.008 0.197 27003 Z= 0.551 Angle : 1.322 20.088 36585 Z= 0.962 Chirality : 0.069 0.472 4038 Planarity : 0.007 0.154 4692 Dihedral : 14.717 126.570 10138 Min Nonbonded Distance : 1.130 Molprobity Statistics. All-atom Clashscore : 19.45 Ramachandran Plot: Outliers : 0.56 % Allowed : 9.23 % Favored : 90.21 % Rotamer: Outliers : 3.57 % Allowed : 8.86 % Favored : 87.56 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.14), residues: 3207 helix: -0.19 (0.12), residues: 1636 sheet: -2.79 (0.33), residues: 193 loop : -3.65 (0.14), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 469 HIS 0.010 0.001 HIS T2621 PHE 0.056 0.002 PHE T3464 TYR 0.044 0.002 TYR T3092 ARG 0.014 0.001 ARG T2599 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 2938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 590 time to evaluate : 2.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 TYR cc_start: 0.8714 (m-10) cc_final: 0.8422 (m-80) REVERT: A 148 THR cc_start: 0.8522 (p) cc_final: 0.8166 (p) REVERT: A 190 MET cc_start: 0.8908 (ttm) cc_final: 0.8452 (tpt) REVERT: A 293 LEU cc_start: 0.8215 (tp) cc_final: 0.8013 (tp) REVERT: A 296 ASN cc_start: 0.8587 (m-40) cc_final: 0.8081 (m110) REVERT: B 399 ASP cc_start: 0.8593 (p0) cc_final: 0.8353 (p0) REVERT: B 427 GLU cc_start: 0.8157 (tp30) cc_final: 0.7916 (tt0) REVERT: D 292 TYR cc_start: 0.7631 (t80) cc_final: 0.7359 (t80) REVERT: D 339 LEU cc_start: 0.7888 (mt) cc_final: 0.7149 (pp) REVERT: D 602 GLU cc_start: 0.7967 (tt0) cc_final: 0.7402 (tt0) REVERT: D 640 ARG cc_start: 0.8700 (mtt180) cc_final: 0.8494 (tmt170) REVERT: D 644 ASN cc_start: 0.8831 (m110) cc_final: 0.8052 (t0) REVERT: D 657 GLU cc_start: 0.8755 (tt0) cc_final: 0.8363 (tt0) REVERT: D 676 MET cc_start: 0.8277 (mmm) cc_final: 0.7999 (mmt) REVERT: D 691 ARG cc_start: 0.8311 (mmt-90) cc_final: 0.7187 (mmt90) REVERT: D 726 GLU cc_start: 0.7798 (tp30) cc_final: 0.7318 (tp30) REVERT: E 181 LEU cc_start: 0.8936 (tp) cc_final: 0.8473 (tt) REVERT: E 208 THR cc_start: 0.9330 (p) cc_final: 0.9129 (p) REVERT: E 271 THR cc_start: 0.8581 (m) cc_final: 0.8326 (p) REVERT: T 1147 ASP cc_start: 0.8389 (t0) cc_final: 0.8127 (t0) REVERT: T 1206 TYR cc_start: 0.8018 (p90) cc_final: 0.6044 (p90) REVERT: T 1231 LYS cc_start: 0.7827 (mtpt) cc_final: 0.7464 (tttp) REVERT: T 2443 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8145 (tt) REVERT: T 2643 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8357 (mt) REVERT: T 2656 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7803 (tp30) REVERT: T 2684 LYS cc_start: 0.8238 (tttp) cc_final: 0.7721 (ttpt) REVERT: T 2715 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7454 (ptp90) REVERT: T 2721 TYR cc_start: 0.7354 (OUTLIER) cc_final: 0.6961 (p90) REVERT: T 2723 GLN cc_start: 0.7440 (tp40) cc_final: 0.7190 (tp-100) REVERT: T 2904 TRP cc_start: 0.3682 (m100) cc_final: 0.2610 (m100) REVERT: T 3080 ASN cc_start: 0.7898 (OUTLIER) cc_final: 0.7427 (p0) REVERT: T 3086 LEU cc_start: 0.9420 (mt) cc_final: 0.9208 (mt) REVERT: T 3134 ILE cc_start: 0.9254 (mt) cc_final: 0.9048 (mm) REVERT: T 3205 TRP cc_start: 0.6842 (p-90) cc_final: 0.6371 (p-90) REVERT: T 3209 GLN cc_start: 0.8893 (mt0) cc_final: 0.8673 (mt0) REVERT: T 3232 GLN cc_start: 0.8275 (mm-40) cc_final: 0.7620 (mm-40) REVERT: T 3436 THR cc_start: 0.9262 (OUTLIER) cc_final: 0.8999 (m) REVERT: T 3534 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8970 (tp) REVERT: T 3661 THR cc_start: 0.8472 (m) cc_final: 0.8166 (t) REVERT: T 3721 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8785 (mm) outliers start: 104 outliers final: 44 residues processed: 664 average time/residue: 0.4003 time to fit residues: 413.1639 Evaluate side-chains 460 residues out of total 2938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 408 time to evaluate : 3.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 2424 THR Chi-restraints excluded: chain T residue 2443 LEU Chi-restraints excluded: chain T residue 2455 ILE Chi-restraints excluded: chain T residue 2459 ASN Chi-restraints excluded: chain T residue 2545 LEU Chi-restraints excluded: chain T residue 2556 ILE Chi-restraints excluded: chain T residue 2600 THR Chi-restraints excluded: chain T residue 2602 VAL Chi-restraints excluded: chain T residue 2621 HIS Chi-restraints excluded: chain T residue 2626 LEU Chi-restraints excluded: chain T residue 2643 ILE Chi-restraints excluded: chain T residue 2715 ARG Chi-restraints excluded: chain T residue 2721 TYR Chi-restraints excluded: chain T residue 2788 THR Chi-restraints excluded: chain T residue 2962 VAL Chi-restraints excluded: chain T residue 2970 ILE Chi-restraints excluded: chain T residue 2975 ASN Chi-restraints excluded: chain T residue 2978 ILE Chi-restraints excluded: chain T residue 2997 ASN Chi-restraints excluded: chain T residue 3006 ILE Chi-restraints excluded: chain T residue 3012 VAL Chi-restraints excluded: chain T residue 3053 LEU Chi-restraints excluded: chain T residue 3059 GLN Chi-restraints excluded: chain T residue 3074 ASN Chi-restraints excluded: chain T residue 3080 ASN Chi-restraints excluded: chain T residue 3167 LEU Chi-restraints excluded: chain T residue 3338 CYS Chi-restraints excluded: chain T residue 3349 PHE Chi-restraints excluded: chain T residue 3361 ASN Chi-restraints excluded: chain T residue 3365 ASN Chi-restraints excluded: chain T residue 3369 ILE Chi-restraints excluded: chain T residue 3410 VAL Chi-restraints excluded: chain T residue 3434 VAL Chi-restraints excluded: chain T residue 3436 THR Chi-restraints excluded: chain T residue 3449 ILE Chi-restraints excluded: chain T residue 3457 ILE Chi-restraints excluded: chain T residue 3494 ASN Chi-restraints excluded: chain T residue 3505 ASP Chi-restraints excluded: chain T residue 3511 VAL Chi-restraints excluded: chain T residue 3534 LEU Chi-restraints excluded: chain T residue 3564 ILE Chi-restraints excluded: chain T residue 3572 ILE Chi-restraints excluded: chain T residue 3624 LEU Chi-restraints excluded: chain T residue 3625 THR Chi-restraints excluded: chain T residue 3682 ILE Chi-restraints excluded: chain T residue 3709 LEU Chi-restraints excluded: chain T residue 3721 LEU Chi-restraints excluded: chain F residue 572 ILE Chi-restraints excluded: chain F residue 577 TYR Chi-restraints excluded: chain F residue 588 ILE Chi-restraints excluded: chain F residue 591 ASP Chi-restraints excluded: chain F residue 593 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 271 optimal weight: 1.9990 chunk 244 optimal weight: 8.9990 chunk 135 optimal weight: 0.9990 chunk 83 optimal weight: 10.0000 chunk 164 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 252 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 153 optimal weight: 5.9990 chunk 187 optimal weight: 0.6980 chunk 292 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN B 37 GLN ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 GLN ** B 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 752 HIS E 241 GLN E 298 GLN ** T 956 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T1239 ASN T2470 ASN T2515 ASN T2638 ASN T2741 GLN T2792 GLN T2811 GLN ** T2847 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T2899 ASN T2992 HIS ** T3261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T3695 ASN T3732 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 27003 Z= 0.234 Angle : 0.740 12.127 36585 Z= 0.378 Chirality : 0.045 0.213 4038 Planarity : 0.006 0.145 4692 Dihedral : 7.287 78.430 3671 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.41 % Allowed : 8.04 % Favored : 91.55 % Rotamer: Outliers : 3.19 % Allowed : 14.15 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.31 % Twisted General : 0.10 % 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: -1.58 (0.14), residues: 3207 helix: 0.63 (0.12), residues: 1627 sheet: -2.33 (0.35), residues: 179 loop : -3.05 (0.15), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 340 HIS 0.014 0.001 HIS D 675 PHE 0.024 0.002 PHE T3464 TYR 0.029 0.002 TYR T2721 ARG 0.008 0.001 ARG T3315 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 2938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 471 time to evaluate : 3.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 TYR cc_start: 0.8868 (m-10) cc_final: 0.8485 (m-80) REVERT: A 190 MET cc_start: 0.9008 (ttm) cc_final: 0.8563 (tpt) REVERT: A 296 ASN cc_start: 0.8490 (m-40) cc_final: 0.8006 (m-40) REVERT: A 364 GLU cc_start: 0.9046 (tm-30) cc_final: 0.8599 (tm-30) REVERT: B 399 ASP cc_start: 0.8492 (p0) cc_final: 0.8227 (p0) REVERT: B 427 GLU cc_start: 0.8330 (tp30) cc_final: 0.8015 (tt0) REVERT: D 273 MET cc_start: 0.8217 (mtp) cc_final: 0.6902 (mtp) REVERT: D 332 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7798 (tm-30) REVERT: D 339 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.6945 (pp) REVERT: D 553 ASN cc_start: 0.7744 (OUTLIER) cc_final: 0.7124 (p0) REVERT: D 602 GLU cc_start: 0.7849 (tt0) cc_final: 0.7307 (tt0) REVERT: D 640 ARG cc_start: 0.8665 (mtt180) cc_final: 0.8331 (tmt170) REVERT: D 650 TRP cc_start: 0.9290 (m100) cc_final: 0.8878 (m100) REVERT: D 676 MET cc_start: 0.8679 (mmm) cc_final: 0.8146 (mmt) REVERT: D 726 GLU cc_start: 0.7840 (tp30) cc_final: 0.7545 (tp30) REVERT: D 752 HIS cc_start: 0.7906 (OUTLIER) cc_final: 0.7446 (m-70) REVERT: E 181 LEU cc_start: 0.9089 (tp) cc_final: 0.8610 (tt) REVERT: E 210 ARG cc_start: 0.8583 (ttm110) cc_final: 0.8069 (mtm110) REVERT: E 266 MET cc_start: 0.8591 (mtt) cc_final: 0.8316 (mtt) REVERT: E 271 THR cc_start: 0.8629 (m) cc_final: 0.8386 (m) REVERT: E 300 MET cc_start: 0.7603 (mmt) cc_final: 0.7077 (mmt) REVERT: T 845 MET cc_start: 0.8049 (ttp) cc_final: 0.7715 (ttt) REVERT: T 1206 TYR cc_start: 0.7621 (p90) cc_final: 0.7070 (p90) REVERT: T 1231 LYS cc_start: 0.7812 (mtpt) cc_final: 0.7501 (pttt) REVERT: T 1233 TYR cc_start: 0.6603 (m-80) cc_final: 0.6040 (m-80) REVERT: T 2443 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8126 (tt) REVERT: T 2575 GLU cc_start: 0.8317 (mp0) cc_final: 0.8073 (mp0) REVERT: T 2643 ILE cc_start: 0.8414 (tp) cc_final: 0.8100 (tt) REVERT: T 2695 GLU cc_start: 0.8756 (tp30) cc_final: 0.8455 (tp30) REVERT: T 2721 TYR cc_start: 0.7869 (p90) cc_final: 0.7516 (p90) REVERT: T 2778 GLN cc_start: 0.7859 (pp30) cc_final: 0.6883 (tm-30) REVERT: T 2948 ASN cc_start: 0.8881 (t0) cc_final: 0.8212 (t0) REVERT: T 3086 LEU cc_start: 0.9364 (mt) cc_final: 0.9158 (mt) REVERT: T 3093 LYS cc_start: 0.8346 (ptmt) cc_final: 0.8145 (mtmm) REVERT: T 3232 GLN cc_start: 0.8306 (mm-40) cc_final: 0.8083 (mm-40) REVERT: T 3283 PHE cc_start: 0.7487 (m-80) cc_final: 0.7244 (m-80) REVERT: T 3680 ARG cc_start: 0.7669 (mtm180) cc_final: 0.7396 (mtp-110) REVERT: T 3721 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8906 (mm) REVERT: F 649 TYR cc_start: 0.8819 (m-10) cc_final: 0.8569 (m-10) outliers start: 93 outliers final: 50 residues processed: 528 average time/residue: 0.3761 time to fit residues: 316.5084 Evaluate side-chains 439 residues out of total 2938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 384 time to evaluate : 3.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 415 SER Chi-restraints excluded: chain B residue 469 TRP Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 283 GLN Chi-restraints excluded: chain D residue 289 GLU Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 553 ASN Chi-restraints excluded: chain D residue 663 ASN Chi-restraints excluded: chain D residue 678 HIS Chi-restraints excluded: chain D residue 735 ASN Chi-restraints excluded: chain D residue 752 HIS Chi-restraints excluded: chain T residue 914 ASP Chi-restraints excluded: chain T residue 939 HIS Chi-restraints excluded: chain T residue 992 SER Chi-restraints excluded: chain T residue 2424 THR Chi-restraints excluded: chain T residue 2426 VAL Chi-restraints excluded: chain T residue 2443 LEU Chi-restraints excluded: chain T residue 2455 ILE Chi-restraints excluded: chain T residue 2459 ASN Chi-restraints excluded: chain T residue 2556 ILE Chi-restraints excluded: chain T residue 2600 THR Chi-restraints excluded: chain T residue 2621 HIS Chi-restraints excluded: chain T residue 2689 ASN Chi-restraints excluded: chain T residue 2870 LEU Chi-restraints excluded: chain T residue 2890 ASN Chi-restraints excluded: chain T residue 2963 CYS Chi-restraints excluded: chain T residue 3012 VAL Chi-restraints excluded: chain T residue 3074 ASN Chi-restraints excluded: chain T residue 3127 GLU Chi-restraints excluded: chain T residue 3167 LEU Chi-restraints excluded: chain T residue 3208 LEU Chi-restraints excluded: chain T residue 3349 PHE Chi-restraints excluded: chain T residue 3365 ASN Chi-restraints excluded: chain T residue 3375 LEU Chi-restraints excluded: chain T residue 3410 VAL Chi-restraints excluded: chain T residue 3457 ILE Chi-restraints excluded: chain T residue 3494 ASN Chi-restraints excluded: chain T residue 3505 ASP Chi-restraints excluded: chain T residue 3564 ILE Chi-restraints excluded: chain T residue 3586 MET Chi-restraints excluded: chain T residue 3624 LEU Chi-restraints excluded: chain T residue 3709 LEU Chi-restraints excluded: chain T residue 3721 LEU Chi-restraints excluded: chain F residue 550 SER Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 572 ILE Chi-restraints excluded: chain F residue 591 ASP Chi-restraints excluded: chain F residue 627 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 162 optimal weight: 8.9990 chunk 90 optimal weight: 0.7980 chunk 243 optimal weight: 8.9990 chunk 199 optimal weight: 0.0010 chunk 80 optimal weight: 7.9990 chunk 292 optimal weight: 0.9980 chunk 316 optimal weight: 0.3980 chunk 260 optimal weight: 5.9990 chunk 290 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 235 optimal weight: 2.9990 overall best weight: 1.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 GLN B 234 ASN ** B 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 752 HIS ** T 956 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T1239 ASN ** T2847 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T2869 ASN T2992 HIS ** T3261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T3367 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27003 Z= 0.205 Angle : 0.663 11.535 36585 Z= 0.338 Chirality : 0.043 0.206 4038 Planarity : 0.005 0.140 4692 Dihedral : 6.523 79.776 3614 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.01 % Favored : 91.80 % Rotamer: Outliers : 3.09 % Allowed : 17.35 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 1.31 % Twisted General : 0.07 % 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: -1.08 (0.15), residues: 3207 helix: 1.06 (0.13), residues: 1606 sheet: -1.89 (0.34), residues: 204 loop : -2.80 (0.16), residues: 1397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 469 HIS 0.024 0.001 HIS D 752 PHE 0.020 0.001 PHE T3464 TYR 0.028 0.002 TYR T1013 ARG 0.010 0.000 ARG T3327 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 2938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 444 time to evaluate : 3.438 Fit side-chains revert: symmetry clash REVERT: A 190 MET cc_start: 0.9013 (ttm) cc_final: 0.8589 (tpt) REVERT: A 296 ASN cc_start: 0.8365 (m-40) cc_final: 0.7962 (m-40) REVERT: A 364 GLU cc_start: 0.9031 (tm-30) cc_final: 0.8607 (tm-30) REVERT: B 37 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.8451 (tm-30) REVERT: B 399 ASP cc_start: 0.8429 (p0) cc_final: 0.8156 (p0) REVERT: B 427 GLU cc_start: 0.8467 (tp30) cc_final: 0.8050 (tt0) REVERT: D 36 ARG cc_start: 0.7386 (OUTLIER) cc_final: 0.7169 (pmt-80) REVERT: D 332 GLU cc_start: 0.8069 (tm-30) cc_final: 0.7773 (tm-30) REVERT: D 339 LEU cc_start: 0.7921 (mt) cc_final: 0.6896 (pp) REVERT: D 375 GLU cc_start: 0.7859 (tp30) cc_final: 0.7114 (mm-30) REVERT: D 553 ASN cc_start: 0.7691 (OUTLIER) cc_final: 0.7118 (p0) REVERT: D 602 GLU cc_start: 0.8009 (tt0) cc_final: 0.7401 (tt0) REVERT: D 640 ARG cc_start: 0.8611 (mtt180) cc_final: 0.8282 (tmt170) REVERT: D 650 TRP cc_start: 0.9078 (m100) cc_final: 0.8779 (m100) REVERT: D 676 MET cc_start: 0.9030 (mmm) cc_final: 0.8581 (mmt) REVERT: D 726 GLU cc_start: 0.7891 (tp30) cc_final: 0.7533 (tp30) REVERT: E 92 ARG cc_start: 0.8092 (mtp180) cc_final: 0.7740 (mtp85) REVERT: E 181 LEU cc_start: 0.9180 (tp) cc_final: 0.8649 (tt) REVERT: E 266 MET cc_start: 0.8713 (mtt) cc_final: 0.8442 (mtt) REVERT: E 271 THR cc_start: 0.8740 (m) cc_final: 0.8395 (m) REVERT: E 300 MET cc_start: 0.7292 (mmt) cc_final: 0.6972 (mmt) REVERT: T 1138 PHE cc_start: 0.8351 (m-80) cc_final: 0.7914 (m-80) REVERT: T 1147 ASP cc_start: 0.8272 (t0) cc_final: 0.7926 (t0) REVERT: T 1231 LYS cc_start: 0.7785 (mtpt) cc_final: 0.7316 (tttm) REVERT: T 2443 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8091 (tt) REVERT: T 2643 ILE cc_start: 0.8385 (tp) cc_final: 0.8161 (tt) REVERT: T 2778 GLN cc_start: 0.7821 (pp30) cc_final: 0.6863 (tm-30) REVERT: T 2948 ASN cc_start: 0.8954 (t0) cc_final: 0.8749 (t0) REVERT: T 3041 GLN cc_start: 0.7283 (tp-100) cc_final: 0.6728 (tm-30) REVERT: T 3086 LEU cc_start: 0.9425 (mt) cc_final: 0.9207 (mt) REVERT: T 3093 LYS cc_start: 0.8381 (ptmt) cc_final: 0.8123 (ttpt) REVERT: T 3721 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8881 (mm) REVERT: F 649 TYR cc_start: 0.8833 (m-10) cc_final: 0.8614 (m-10) outliers start: 90 outliers final: 55 residues processed: 497 average time/residue: 0.3868 time to fit residues: 307.5295 Evaluate side-chains 440 residues out of total 2938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 380 time to evaluate : 2.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain B residue 37 GLN Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 415 SER Chi-restraints excluded: chain B residue 469 TRP Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 36 ARG Chi-restraints excluded: chain D residue 283 GLN Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 553 ASN Chi-restraints excluded: chain D residue 678 HIS Chi-restraints excluded: chain D residue 701 VAL Chi-restraints excluded: chain D residue 735 ASN Chi-restraints excluded: chain T residue 878 PHE Chi-restraints excluded: chain T residue 914 ASP Chi-restraints excluded: chain T residue 939 HIS Chi-restraints excluded: chain T residue 992 SER Chi-restraints excluded: chain T residue 1166 LEU Chi-restraints excluded: chain T residue 1200 LEU Chi-restraints excluded: chain T residue 1242 LEU Chi-restraints excluded: chain T residue 2416 MET Chi-restraints excluded: chain T residue 2424 THR Chi-restraints excluded: chain T residue 2426 VAL Chi-restraints excluded: chain T residue 2443 LEU Chi-restraints excluded: chain T residue 2455 ILE Chi-restraints excluded: chain T residue 2517 LEU Chi-restraints excluded: chain T residue 2679 TRP Chi-restraints excluded: chain T residue 2706 LEU Chi-restraints excluded: chain T residue 2709 VAL Chi-restraints excluded: chain T residue 2719 LEU Chi-restraints excluded: chain T residue 2870 LEU Chi-restraints excluded: chain T residue 2962 VAL Chi-restraints excluded: chain T residue 2963 CYS Chi-restraints excluded: chain T residue 3009 THR Chi-restraints excluded: chain T residue 3012 VAL Chi-restraints excluded: chain T residue 3101 LEU Chi-restraints excluded: chain T residue 3105 LEU Chi-restraints excluded: chain T residue 3112 ASP Chi-restraints excluded: chain T residue 3167 LEU Chi-restraints excluded: chain T residue 3208 LEU Chi-restraints excluded: chain T residue 3349 PHE Chi-restraints excluded: chain T residue 3359 LEU Chi-restraints excluded: chain T residue 3410 VAL Chi-restraints excluded: chain T residue 3457 ILE Chi-restraints excluded: chain T residue 3505 ASP Chi-restraints excluded: chain T residue 3586 MET Chi-restraints excluded: chain T residue 3624 LEU Chi-restraints excluded: chain T residue 3682 ILE Chi-restraints excluded: chain T residue 3709 LEU Chi-restraints excluded: chain T residue 3710 ASN Chi-restraints excluded: chain T residue 3712 THR Chi-restraints excluded: chain T residue 3721 LEU Chi-restraints excluded: chain F residue 550 SER Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 572 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 289 optimal weight: 3.9990 chunk 220 optimal weight: 0.8980 chunk 152 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 196 optimal weight: 3.9990 chunk 293 optimal weight: 2.9990 chunk 311 optimal weight: 6.9990 chunk 153 optimal weight: 3.9990 chunk 278 optimal weight: 7.9990 chunk 83 optimal weight: 8.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 389 GLN ** D 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 656 GLN ** T1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T1239 ASN T2458 GLN T2551 GLN ** T2847 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T2992 HIS ** T3010 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T3064 ASN T3094 ASN ** T3261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T3365 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 27003 Z= 0.337 Angle : 0.697 9.672 36585 Z= 0.359 Chirality : 0.045 0.245 4038 Planarity : 0.005 0.138 4692 Dihedral : 6.548 87.426 3597 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.35 % Favored : 90.46 % Rotamer: Outliers : 4.64 % Allowed : 17.35 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.31 % Twisted General : 0.10 % 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: -1.13 (0.15), residues: 3207 helix: 0.96 (0.13), residues: 1642 sheet: -1.78 (0.36), residues: 191 loop : -2.86 (0.16), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 469 HIS 0.009 0.001 HIS T2592 PHE 0.025 0.002 PHE A 255 TYR 0.025 0.002 TYR T2492 ARG 0.018 0.001 ARG D 75 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 2938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 412 time to evaluate : 3.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 ASN cc_start: 0.8622 (m110) cc_final: 0.8415 (m-40) REVERT: A 143 TYR cc_start: 0.8988 (m-10) cc_final: 0.8549 (m-80) REVERT: A 190 MET cc_start: 0.9020 (ttm) cc_final: 0.8613 (tpt) REVERT: A 296 ASN cc_start: 0.8460 (m-40) cc_final: 0.8126 (m110) REVERT: B 89 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.8207 (tm-30) REVERT: B 399 ASP cc_start: 0.8465 (p0) cc_final: 0.8171 (p0) REVERT: D 30 ASP cc_start: 0.8380 (t70) cc_final: 0.7840 (t0) REVERT: D 36 ARG cc_start: 0.7498 (OUTLIER) cc_final: 0.7274 (pmt-80) REVERT: D 332 GLU cc_start: 0.8165 (tm-30) cc_final: 0.7870 (tm-30) REVERT: D 339 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7059 (pp) REVERT: D 375 GLU cc_start: 0.8312 (tp30) cc_final: 0.6912 (mm-30) REVERT: D 553 ASN cc_start: 0.7765 (OUTLIER) cc_final: 0.7025 (p0) REVERT: D 602 GLU cc_start: 0.8122 (tt0) cc_final: 0.7343 (tt0) REVERT: D 640 ARG cc_start: 0.8638 (mtt180) cc_final: 0.8386 (tmt170) REVERT: D 650 TRP cc_start: 0.9142 (m100) cc_final: 0.8940 (m100) REVERT: D 656 GLN cc_start: 0.8305 (tp40) cc_final: 0.7977 (tp-100) REVERT: D 752 HIS cc_start: 0.8038 (OUTLIER) cc_final: 0.7312 (m-70) REVERT: D 767 CYS cc_start: 0.8385 (t) cc_final: 0.7863 (t) REVERT: E 92 ARG cc_start: 0.8045 (mtp180) cc_final: 0.7696 (mtp85) REVERT: E 181 LEU cc_start: 0.9182 (tp) cc_final: 0.8592 (tt) REVERT: E 271 THR cc_start: 0.8894 (m) cc_final: 0.8616 (m) REVERT: T 1147 ASP cc_start: 0.8321 (t0) cc_final: 0.7962 (t0) REVERT: T 1231 LYS cc_start: 0.7949 (mtpt) cc_final: 0.7516 (tttp) REVERT: T 2443 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8113 (tt) REVERT: T 2662 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.9041 (tt) REVERT: T 2721 TYR cc_start: 0.8166 (p90) cc_final: 0.7485 (p90) REVERT: T 2723 GLN cc_start: 0.8304 (tp-100) cc_final: 0.8043 (tp-100) REVERT: T 2778 GLN cc_start: 0.8048 (pp30) cc_final: 0.6995 (tm-30) REVERT: T 3041 GLN cc_start: 0.7353 (tp-100) cc_final: 0.6800 (tm-30) REVERT: T 3093 LYS cc_start: 0.8437 (ptmt) cc_final: 0.8191 (ttpt) REVERT: T 3131 TRP cc_start: 0.8851 (t60) cc_final: 0.8609 (t60) REVERT: T 3232 GLN cc_start: 0.8280 (mm-40) cc_final: 0.8035 (mm-40) REVERT: T 3326 ASP cc_start: 0.8772 (t0) cc_final: 0.8565 (t0) REVERT: T 3419 MET cc_start: 0.9186 (tpp) cc_final: 0.8948 (tpp) REVERT: T 3721 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8893 (mm) outliers start: 135 outliers final: 94 residues processed: 507 average time/residue: 0.3683 time to fit residues: 299.7558 Evaluate side-chains 481 residues out of total 2938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 379 time to evaluate : 2.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 415 SER Chi-restraints excluded: chain B residue 434 SER Chi-restraints excluded: chain B residue 469 TRP Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 36 ARG Chi-restraints excluded: chain D residue 283 GLN Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 531 GLU Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 553 ASN Chi-restraints excluded: chain D residue 593 ASP Chi-restraints excluded: chain D residue 594 ASP Chi-restraints excluded: chain D residue 659 VAL Chi-restraints excluded: chain D residue 663 ASN Chi-restraints excluded: chain D residue 678 HIS Chi-restraints excluded: chain D residue 701 VAL Chi-restraints excluded: chain D residue 735 ASN Chi-restraints excluded: chain D residue 744 ASN Chi-restraints excluded: chain D residue 752 HIS Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain T residue 878 PHE Chi-restraints excluded: chain T residue 914 ASP Chi-restraints excluded: chain T residue 939 HIS Chi-restraints excluded: chain T residue 967 THR Chi-restraints excluded: chain T residue 992 SER Chi-restraints excluded: chain T residue 1117 THR Chi-restraints excluded: chain T residue 1132 ASP Chi-restraints excluded: chain T residue 1177 LEU Chi-restraints excluded: chain T residue 1242 LEU Chi-restraints excluded: chain T residue 2415 ARG Chi-restraints excluded: chain T residue 2424 THR Chi-restraints excluded: chain T residue 2426 VAL Chi-restraints excluded: chain T residue 2443 LEU Chi-restraints excluded: chain T residue 2455 ILE Chi-restraints excluded: chain T residue 2516 ASP Chi-restraints excluded: chain T residue 2517 LEU Chi-restraints excluded: chain T residue 2537 ILE Chi-restraints excluded: chain T residue 2551 GLN Chi-restraints excluded: chain T residue 2574 ASN Chi-restraints excluded: chain T residue 2600 THR Chi-restraints excluded: chain T residue 2609 SER Chi-restraints excluded: chain T residue 2613 ILE Chi-restraints excluded: chain T residue 2662 LEU Chi-restraints excluded: chain T residue 2663 LEU Chi-restraints excluded: chain T residue 2679 TRP Chi-restraints excluded: chain T residue 2689 ASN Chi-restraints excluded: chain T residue 2706 LEU Chi-restraints excluded: chain T residue 2709 VAL Chi-restraints excluded: chain T residue 2719 LEU Chi-restraints excluded: chain T residue 2793 MET Chi-restraints excluded: chain T residue 2870 LEU Chi-restraints excluded: chain T residue 2962 VAL Chi-restraints excluded: chain T residue 2963 CYS Chi-restraints excluded: chain T residue 2978 ILE Chi-restraints excluded: chain T residue 3009 THR Chi-restraints excluded: chain T residue 3012 VAL Chi-restraints excluded: chain T residue 3101 LEU Chi-restraints excluded: chain T residue 3112 ASP Chi-restraints excluded: chain T residue 3127 GLU Chi-restraints excluded: chain T residue 3167 LEU Chi-restraints excluded: chain T residue 3208 LEU Chi-restraints excluded: chain T residue 3219 TYR Chi-restraints excluded: chain T residue 3338 CYS Chi-restraints excluded: chain T residue 3349 PHE Chi-restraints excluded: chain T residue 3352 ILE Chi-restraints excluded: chain T residue 3359 LEU Chi-restraints excluded: chain T residue 3410 VAL Chi-restraints excluded: chain T residue 3457 ILE Chi-restraints excluded: chain T residue 3460 ASP Chi-restraints excluded: chain T residue 3505 ASP Chi-restraints excluded: chain T residue 3511 VAL Chi-restraints excluded: chain T residue 3525 ASN Chi-restraints excluded: chain T residue 3563 MET Chi-restraints excluded: chain T residue 3564 ILE Chi-restraints excluded: chain T residue 3568 THR Chi-restraints excluded: chain T residue 3581 VAL Chi-restraints excluded: chain T residue 3586 MET Chi-restraints excluded: chain T residue 3624 LEU Chi-restraints excluded: chain T residue 3703 VAL Chi-restraints excluded: chain T residue 3709 LEU Chi-restraints excluded: chain T residue 3710 ASN Chi-restraints excluded: chain T residue 3712 THR Chi-restraints excluded: chain T residue 3721 LEU Chi-restraints excluded: chain F residue 550 SER Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 572 ILE Chi-restraints excluded: chain F residue 573 ASP Chi-restraints excluded: chain F residue 591 ASP Chi-restraints excluded: chain F residue 627 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 259 optimal weight: 0.7980 chunk 176 optimal weight: 1.9990 chunk 4 optimal weight: 8.9990 chunk 231 optimal weight: 0.8980 chunk 128 optimal weight: 0.0010 chunk 265 optimal weight: 0.2980 chunk 215 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 158 optimal weight: 6.9990 chunk 279 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T1239 ASN ** T2847 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T2992 HIS ** T3010 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T3261 ASN ** T3357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T3365 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27003 Z= 0.177 Angle : 0.640 11.147 36585 Z= 0.325 Chirality : 0.042 0.202 4038 Planarity : 0.005 0.136 4692 Dihedral : 6.288 86.692 3597 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.64 % Favored : 92.20 % Rotamer: Outliers : 3.61 % Allowed : 19.68 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.65 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.15), residues: 3207 helix: 1.18 (0.13), residues: 1621 sheet: -1.57 (0.37), residues: 190 loop : -2.66 (0.16), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 469 HIS 0.006 0.001 HIS D 728 PHE 0.024 0.001 PHE T1151 TYR 0.022 0.001 TYR T2492 ARG 0.008 0.000 ARG T2879 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 2938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 438 time to evaluate : 3.437 Fit side-chains revert: symmetry clash REVERT: A 92 ASN cc_start: 0.8594 (m110) cc_final: 0.8387 (m-40) REVERT: A 143 TYR cc_start: 0.8909 (m-10) cc_final: 0.8508 (m-80) REVERT: A 190 MET cc_start: 0.9029 (ttm) cc_final: 0.8609 (tpt) REVERT: A 296 ASN cc_start: 0.8321 (m-40) cc_final: 0.8003 (m-40) REVERT: B 37 GLN cc_start: 0.8930 (OUTLIER) cc_final: 0.8464 (tm-30) REVERT: B 89 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.8206 (tm-30) REVERT: B 394 MET cc_start: 0.9155 (mmm) cc_final: 0.8946 (mmt) REVERT: B 399 ASP cc_start: 0.8362 (p0) cc_final: 0.8089 (p0) REVERT: D 30 ASP cc_start: 0.8313 (t70) cc_final: 0.7744 (t0) REVERT: D 36 ARG cc_start: 0.7310 (OUTLIER) cc_final: 0.7038 (pmt-80) REVERT: D 332 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7798 (tm-30) REVERT: D 339 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7001 (pp) REVERT: D 375 GLU cc_start: 0.8092 (tp30) cc_final: 0.6954 (mm-30) REVERT: D 553 ASN cc_start: 0.7656 (OUTLIER) cc_final: 0.7099 (p0) REVERT: D 602 GLU cc_start: 0.8070 (tt0) cc_final: 0.7295 (tt0) REVERT: D 640 ARG cc_start: 0.8591 (mtt180) cc_final: 0.8289 (tmt170) REVERT: D 752 HIS cc_start: 0.7795 (OUTLIER) cc_final: 0.7207 (m-70) REVERT: D 767 CYS cc_start: 0.8086 (t) cc_final: 0.7655 (t) REVERT: E 92 ARG cc_start: 0.7968 (mtp180) cc_final: 0.7604 (mtp85) REVERT: E 181 LEU cc_start: 0.9160 (tp) cc_final: 0.8559 (tt) REVERT: E 271 THR cc_start: 0.8950 (m) cc_final: 0.8696 (m) REVERT: T 1080 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8603 (mt) REVERT: T 1147 ASP cc_start: 0.8196 (t0) cc_final: 0.7820 (t0) REVERT: T 1220 ILE cc_start: 0.9248 (pt) cc_final: 0.8981 (mt) REVERT: T 1231 LYS cc_start: 0.7789 (mtpt) cc_final: 0.7364 (tttp) REVERT: T 2443 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8099 (tt) REVERT: T 2551 GLN cc_start: 0.7734 (OUTLIER) cc_final: 0.7409 (mm110) REVERT: T 2662 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.8995 (tt) REVERT: T 2755 PHE cc_start: 0.7010 (m-10) cc_final: 0.6646 (m-10) REVERT: T 2778 GLN cc_start: 0.7883 (pp30) cc_final: 0.6831 (tm-30) REVERT: T 2879 ARG cc_start: 0.8113 (ttp-110) cc_final: 0.7908 (ttp80) REVERT: T 3029 PHE cc_start: 0.8914 (m-80) cc_final: 0.8695 (m-10) REVERT: T 3041 GLN cc_start: 0.7189 (tp-100) cc_final: 0.6658 (tm-30) REVERT: T 3721 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8821 (mm) outliers start: 105 outliers final: 69 residues processed: 510 average time/residue: 0.3729 time to fit residues: 307.6118 Evaluate side-chains 479 residues out of total 2938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 399 time to evaluate : 3.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain B residue 37 GLN Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain B residue 434 SER Chi-restraints excluded: chain B residue 469 TRP Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 36 ARG Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 531 GLU Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 553 ASN Chi-restraints excluded: chain D residue 554 THR Chi-restraints excluded: chain D residue 663 ASN Chi-restraints excluded: chain D residue 678 HIS Chi-restraints excluded: chain D residue 701 VAL Chi-restraints excluded: chain D residue 735 ASN Chi-restraints excluded: chain D residue 744 ASN Chi-restraints excluded: chain D residue 752 HIS Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain T residue 878 PHE Chi-restraints excluded: chain T residue 890 TYR Chi-restraints excluded: chain T residue 914 ASP Chi-restraints excluded: chain T residue 939 HIS Chi-restraints excluded: chain T residue 970 THR Chi-restraints excluded: chain T residue 992 SER Chi-restraints excluded: chain T residue 1042 LEU Chi-restraints excluded: chain T residue 1043 LEU Chi-restraints excluded: chain T residue 1080 LEU Chi-restraints excluded: chain T residue 1132 ASP Chi-restraints excluded: chain T residue 2424 THR Chi-restraints excluded: chain T residue 2426 VAL Chi-restraints excluded: chain T residue 2443 LEU Chi-restraints excluded: chain T residue 2455 ILE Chi-restraints excluded: chain T residue 2551 GLN Chi-restraints excluded: chain T residue 2571 ILE Chi-restraints excluded: chain T residue 2600 THR Chi-restraints excluded: chain T residue 2604 ASN Chi-restraints excluded: chain T residue 2609 SER Chi-restraints excluded: chain T residue 2621 HIS Chi-restraints excluded: chain T residue 2626 LEU Chi-restraints excluded: chain T residue 2654 ILE Chi-restraints excluded: chain T residue 2662 LEU Chi-restraints excluded: chain T residue 2679 TRP Chi-restraints excluded: chain T residue 2689 ASN Chi-restraints excluded: chain T residue 2706 LEU Chi-restraints excluded: chain T residue 2709 VAL Chi-restraints excluded: chain T residue 2719 LEU Chi-restraints excluded: chain T residue 2734 ILE Chi-restraints excluded: chain T residue 2870 LEU Chi-restraints excluded: chain T residue 2963 CYS Chi-restraints excluded: chain T residue 2978 ILE Chi-restraints excluded: chain T residue 3009 THR Chi-restraints excluded: chain T residue 3012 VAL Chi-restraints excluded: chain T residue 3101 LEU Chi-restraints excluded: chain T residue 3112 ASP Chi-restraints excluded: chain T residue 3167 LEU Chi-restraints excluded: chain T residue 3208 LEU Chi-restraints excluded: chain T residue 3219 TYR Chi-restraints excluded: chain T residue 3338 CYS Chi-restraints excluded: chain T residue 3359 LEU Chi-restraints excluded: chain T residue 3410 VAL Chi-restraints excluded: chain T residue 3457 ILE Chi-restraints excluded: chain T residue 3505 ASP Chi-restraints excluded: chain T residue 3581 VAL Chi-restraints excluded: chain T residue 3586 MET Chi-restraints excluded: chain T residue 3709 LEU Chi-restraints excluded: chain T residue 3712 THR Chi-restraints excluded: chain T residue 3721 LEU Chi-restraints excluded: chain F residue 540 ASP Chi-restraints excluded: chain F residue 550 SER Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 568 SER Chi-restraints excluded: chain F residue 572 ILE Chi-restraints excluded: chain F residue 591 ASP Chi-restraints excluded: chain F residue 627 LEU Chi-restraints excluded: chain F residue 653 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 104 optimal weight: 0.2980 chunk 280 optimal weight: 0.9980 chunk 61 optimal weight: 0.4980 chunk 182 optimal weight: 4.9990 chunk 76 optimal weight: 8.9990 chunk 311 optimal weight: 5.9990 chunk 258 optimal weight: 0.7980 chunk 144 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 163 optimal weight: 4.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 317 ASN T1239 ASN T2668 ASN T2792 GLN ** T2847 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T2992 HIS ** T3010 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T3357 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 27003 Z= 0.182 Angle : 0.631 10.943 36585 Z= 0.319 Chirality : 0.041 0.201 4038 Planarity : 0.005 0.106 4692 Dihedral : 6.051 86.133 3593 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.20 % Favored : 91.64 % Rotamer: Outliers : 3.68 % Allowed : 20.71 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.15), residues: 3207 helix: 1.24 (0.13), residues: 1631 sheet: -1.38 (0.36), residues: 202 loop : -2.61 (0.16), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 469 HIS 0.005 0.001 HIS D 728 PHE 0.022 0.001 PHE T3464 TYR 0.021 0.001 TYR T2492 ARG 0.006 0.000 ARG T2879 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 2938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 422 time to evaluate : 3.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ASN cc_start: 0.8593 (m110) cc_final: 0.8387 (m-40) REVERT: A 143 TYR cc_start: 0.8835 (m-10) cc_final: 0.8523 (m-80) REVERT: A 190 MET cc_start: 0.8957 (ttm) cc_final: 0.8756 (tpt) REVERT: A 250 ILE cc_start: 0.8682 (mm) cc_final: 0.8346 (pt) REVERT: A 296 ASN cc_start: 0.8348 (m-40) cc_final: 0.8002 (m-40) REVERT: B 37 GLN cc_start: 0.8919 (OUTLIER) cc_final: 0.8458 (tm-30) REVERT: B 399 ASP cc_start: 0.8375 (p0) cc_final: 0.8090 (p0) REVERT: D 30 ASP cc_start: 0.8303 (t70) cc_final: 0.7708 (t0) REVERT: D 36 ARG cc_start: 0.7306 (OUTLIER) cc_final: 0.7057 (pmt-80) REVERT: D 332 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7791 (tm-30) REVERT: D 339 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7004 (pp) REVERT: D 375 GLU cc_start: 0.7807 (tp30) cc_final: 0.6780 (mm-30) REVERT: D 553 ASN cc_start: 0.7633 (OUTLIER) cc_final: 0.7142 (p0) REVERT: D 573 ARG cc_start: 0.6680 (OUTLIER) cc_final: 0.6236 (ptt180) REVERT: D 602 GLU cc_start: 0.8087 (tt0) cc_final: 0.7330 (tt0) REVERT: D 640 ARG cc_start: 0.8591 (mtt180) cc_final: 0.8296 (tmt170) REVERT: D 752 HIS cc_start: 0.7885 (OUTLIER) cc_final: 0.7314 (m-70) REVERT: D 767 CYS cc_start: 0.8114 (t) cc_final: 0.7627 (t) REVERT: E 92 ARG cc_start: 0.7981 (mtp180) cc_final: 0.7592 (mtp85) REVERT: E 181 LEU cc_start: 0.9151 (tp) cc_final: 0.8558 (tt) REVERT: E 271 THR cc_start: 0.8989 (m) cc_final: 0.8486 (m) REVERT: T 885 PHE cc_start: 0.8103 (m-80) cc_final: 0.7559 (t80) REVERT: T 1080 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8634 (mt) REVERT: T 1147 ASP cc_start: 0.8179 (t0) cc_final: 0.7815 (t0) REVERT: T 1220 ILE cc_start: 0.9228 (pt) cc_final: 0.8997 (mt) REVERT: T 1231 LYS cc_start: 0.7709 (mtpt) cc_final: 0.7303 (pttt) REVERT: T 1233 TYR cc_start: 0.6141 (m-80) cc_final: 0.5912 (m-80) REVERT: T 2443 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8073 (tt) REVERT: T 2471 GLN cc_start: 0.5235 (OUTLIER) cc_final: 0.4527 (mm-40) REVERT: T 2575 GLU cc_start: 0.8386 (mp0) cc_final: 0.7913 (mp0) REVERT: T 2662 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.8996 (tt) REVERT: T 2755 PHE cc_start: 0.7046 (m-10) cc_final: 0.6685 (m-10) REVERT: T 2778 GLN cc_start: 0.7877 (pp30) cc_final: 0.6836 (tm-30) REVERT: T 2959 MET cc_start: 0.8715 (ptp) cc_final: 0.8410 (ptp) REVERT: T 3041 GLN cc_start: 0.7126 (tp-100) cc_final: 0.6597 (tm-30) REVERT: T 3638 GLU cc_start: 0.8661 (tm-30) cc_final: 0.8419 (tm-30) outliers start: 107 outliers final: 72 residues processed: 491 average time/residue: 0.3701 time to fit residues: 292.6352 Evaluate side-chains 483 residues out of total 2938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 401 time to evaluate : 3.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain B residue 37 GLN Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 280 PHE Chi-restraints excluded: chain B residue 415 SER Chi-restraints excluded: chain B residue 434 SER Chi-restraints excluded: chain B residue 469 TRP Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 36 ARG Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 531 GLU Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 553 ASN Chi-restraints excluded: chain D residue 573 ARG Chi-restraints excluded: chain D residue 663 ASN Chi-restraints excluded: chain D residue 678 HIS Chi-restraints excluded: chain D residue 701 VAL Chi-restraints excluded: chain D residue 735 ASN Chi-restraints excluded: chain D residue 744 ASN Chi-restraints excluded: chain D residue 752 HIS Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain T residue 878 PHE Chi-restraints excluded: chain T residue 890 TYR Chi-restraints excluded: chain T residue 914 ASP Chi-restraints excluded: chain T residue 952 LEU Chi-restraints excluded: chain T residue 970 THR Chi-restraints excluded: chain T residue 992 SER Chi-restraints excluded: chain T residue 1023 CYS Chi-restraints excluded: chain T residue 1042 LEU Chi-restraints excluded: chain T residue 1043 LEU Chi-restraints excluded: chain T residue 1080 LEU Chi-restraints excluded: chain T residue 1132 ASP Chi-restraints excluded: chain T residue 1242 LEU Chi-restraints excluded: chain T residue 2424 THR Chi-restraints excluded: chain T residue 2426 VAL Chi-restraints excluded: chain T residue 2443 LEU Chi-restraints excluded: chain T residue 2455 ILE Chi-restraints excluded: chain T residue 2471 GLN Chi-restraints excluded: chain T residue 2517 LEU Chi-restraints excluded: chain T residue 2571 ILE Chi-restraints excluded: chain T residue 2596 ILE Chi-restraints excluded: chain T residue 2600 THR Chi-restraints excluded: chain T residue 2626 LEU Chi-restraints excluded: chain T residue 2662 LEU Chi-restraints excluded: chain T residue 2679 TRP Chi-restraints excluded: chain T residue 2689 ASN Chi-restraints excluded: chain T residue 2706 LEU Chi-restraints excluded: chain T residue 2719 LEU Chi-restraints excluded: chain T residue 2734 ILE Chi-restraints excluded: chain T residue 2836 THR Chi-restraints excluded: chain T residue 2870 LEU Chi-restraints excluded: chain T residue 2963 CYS Chi-restraints excluded: chain T residue 2978 ILE Chi-restraints excluded: chain T residue 3009 THR Chi-restraints excluded: chain T residue 3012 VAL Chi-restraints excluded: chain T residue 3101 LEU Chi-restraints excluded: chain T residue 3105 LEU Chi-restraints excluded: chain T residue 3127 GLU Chi-restraints excluded: chain T residue 3167 LEU Chi-restraints excluded: chain T residue 3208 LEU Chi-restraints excluded: chain T residue 3219 TYR Chi-restraints excluded: chain T residue 3338 CYS Chi-restraints excluded: chain T residue 3352 ILE Chi-restraints excluded: chain T residue 3359 LEU Chi-restraints excluded: chain T residue 3410 VAL Chi-restraints excluded: chain T residue 3505 ASP Chi-restraints excluded: chain T residue 3581 VAL Chi-restraints excluded: chain T residue 3624 LEU Chi-restraints excluded: chain T residue 3682 ILE Chi-restraints excluded: chain T residue 3709 LEU Chi-restraints excluded: chain T residue 3712 THR Chi-restraints excluded: chain T residue 3721 LEU Chi-restraints excluded: chain F residue 540 ASP Chi-restraints excluded: chain F residue 550 SER Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 572 ILE Chi-restraints excluded: chain F residue 591 ASP Chi-restraints excluded: chain F residue 627 LEU Chi-restraints excluded: chain F residue 634 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 300 optimal weight: 0.5980 chunk 35 optimal weight: 8.9990 chunk 177 optimal weight: 1.9990 chunk 227 optimal weight: 7.9990 chunk 176 optimal weight: 0.6980 chunk 262 optimal weight: 5.9990 chunk 173 optimal weight: 0.4980 chunk 310 optimal weight: 20.0000 chunk 194 optimal weight: 6.9990 chunk 189 optimal weight: 0.9990 chunk 143 optimal weight: 6.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 ASN D 644 ASN T1239 ASN T2792 GLN ** T2847 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T2992 HIS ** T3010 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T3365 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.3815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27003 Z= 0.189 Angle : 0.630 10.771 36585 Z= 0.318 Chirality : 0.041 0.230 4038 Planarity : 0.004 0.050 4692 Dihedral : 5.953 86.416 3591 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.29 % Favored : 91.58 % Rotamer: Outliers : 3.54 % Allowed : 21.68 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.15), residues: 3207 helix: 1.31 (0.13), residues: 1630 sheet: -1.26 (0.37), residues: 202 loop : -2.54 (0.16), residues: 1375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP T2468 HIS 0.005 0.001 HIS T2957 PHE 0.027 0.001 PHE T1151 TYR 0.021 0.001 TYR T2492 ARG 0.014 0.000 ARG E 210 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 2938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 432 time to evaluate : 3.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ASN cc_start: 0.8581 (m110) cc_final: 0.8373 (m-40) REVERT: A 143 TYR cc_start: 0.8834 (m-10) cc_final: 0.8529 (m-80) REVERT: A 155 SER cc_start: 0.9004 (m) cc_final: 0.7867 (p) REVERT: A 180 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8522 (tp) REVERT: A 250 ILE cc_start: 0.8722 (mm) cc_final: 0.8393 (pt) REVERT: A 296 ASN cc_start: 0.8343 (m-40) cc_final: 0.7995 (m110) REVERT: B 37 GLN cc_start: 0.8915 (OUTLIER) cc_final: 0.8464 (tm-30) REVERT: B 280 PHE cc_start: 0.7660 (OUTLIER) cc_final: 0.7194 (t80) REVERT: B 394 MET cc_start: 0.9113 (mmm) cc_final: 0.8857 (mmt) REVERT: B 399 ASP cc_start: 0.8372 (p0) cc_final: 0.8102 (p0) REVERT: B 468 LEU cc_start: 0.8488 (tt) cc_final: 0.8240 (tt) REVERT: D 30 ASP cc_start: 0.8315 (t70) cc_final: 0.7697 (t0) REVERT: D 36 ARG cc_start: 0.7329 (OUTLIER) cc_final: 0.7051 (pmt-80) REVERT: D 332 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7796 (tm-30) REVERT: D 339 LEU cc_start: 0.8070 (mt) cc_final: 0.6988 (pp) REVERT: D 375 GLU cc_start: 0.7878 (tp30) cc_final: 0.6752 (mm-30) REVERT: D 395 TRP cc_start: 0.8433 (t-100) cc_final: 0.7871 (m-90) REVERT: D 553 ASN cc_start: 0.7579 (OUTLIER) cc_final: 0.7135 (p0) REVERT: D 573 ARG cc_start: 0.6718 (OUTLIER) cc_final: 0.6249 (ptt180) REVERT: D 602 GLU cc_start: 0.8123 (tt0) cc_final: 0.7346 (tt0) REVERT: D 640 ARG cc_start: 0.8598 (mtt180) cc_final: 0.8292 (tmt170) REVERT: D 656 GLN cc_start: 0.8916 (tt0) cc_final: 0.8240 (tm-30) REVERT: D 752 HIS cc_start: 0.7824 (OUTLIER) cc_final: 0.7248 (m-70) REVERT: D 767 CYS cc_start: 0.8091 (t) cc_final: 0.7618 (t) REVERT: E 92 ARG cc_start: 0.7944 (mtp180) cc_final: 0.7547 (mtp85) REVERT: E 181 LEU cc_start: 0.9146 (tp) cc_final: 0.8568 (tt) REVERT: E 271 THR cc_start: 0.8948 (m) cc_final: 0.8707 (m) REVERT: T 885 PHE cc_start: 0.7905 (m-80) cc_final: 0.7481 (t80) REVERT: T 1080 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8637 (mt) REVERT: T 1147 ASP cc_start: 0.8132 (t0) cc_final: 0.7794 (t0) REVERT: T 1220 ILE cc_start: 0.9233 (pt) cc_final: 0.9023 (mt) REVERT: T 1231 LYS cc_start: 0.7734 (mtpt) cc_final: 0.7386 (pttt) REVERT: T 1233 TYR cc_start: 0.6180 (m-80) cc_final: 0.5909 (m-80) REVERT: T 2443 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8065 (tt) REVERT: T 2471 GLN cc_start: 0.5294 (OUTLIER) cc_final: 0.4509 (mm-40) REVERT: T 2575 GLU cc_start: 0.8392 (mp0) cc_final: 0.8051 (mp0) REVERT: T 2662 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.9000 (tt) REVERT: T 2755 PHE cc_start: 0.7044 (m-10) cc_final: 0.6700 (m-10) REVERT: T 2778 GLN cc_start: 0.7887 (pp30) cc_final: 0.6848 (tm-30) REVERT: T 3041 GLN cc_start: 0.7063 (tp-100) cc_final: 0.6656 (tm-30) REVERT: T 3638 GLU cc_start: 0.8710 (tm-30) cc_final: 0.8378 (tm-30) outliers start: 103 outliers final: 73 residues processed: 498 average time/residue: 0.3790 time to fit residues: 307.6109 Evaluate side-chains 486 residues out of total 2938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 402 time to evaluate : 3.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain B residue 37 GLN Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 280 PHE Chi-restraints excluded: chain B residue 415 SER Chi-restraints excluded: chain B residue 434 SER Chi-restraints excluded: chain B residue 469 TRP Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 36 ARG Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 531 GLU Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 553 ASN Chi-restraints excluded: chain D residue 567 ASN Chi-restraints excluded: chain D residue 573 ARG Chi-restraints excluded: chain D residue 678 HIS Chi-restraints excluded: chain D residue 701 VAL Chi-restraints excluded: chain D residue 735 ASN Chi-restraints excluded: chain D residue 744 ASN Chi-restraints excluded: chain D residue 752 HIS Chi-restraints excluded: chain T residue 878 PHE Chi-restraints excluded: chain T residue 914 ASP Chi-restraints excluded: chain T residue 952 LEU Chi-restraints excluded: chain T residue 970 THR Chi-restraints excluded: chain T residue 992 SER Chi-restraints excluded: chain T residue 1023 CYS Chi-restraints excluded: chain T residue 1042 LEU Chi-restraints excluded: chain T residue 1043 LEU Chi-restraints excluded: chain T residue 1080 LEU Chi-restraints excluded: chain T residue 1132 ASP Chi-restraints excluded: chain T residue 1242 LEU Chi-restraints excluded: chain T residue 2424 THR Chi-restraints excluded: chain T residue 2443 LEU Chi-restraints excluded: chain T residue 2455 ILE Chi-restraints excluded: chain T residue 2471 GLN Chi-restraints excluded: chain T residue 2517 LEU Chi-restraints excluded: chain T residue 2537 ILE Chi-restraints excluded: chain T residue 2574 ASN Chi-restraints excluded: chain T residue 2596 ILE Chi-restraints excluded: chain T residue 2600 THR Chi-restraints excluded: chain T residue 2604 ASN Chi-restraints excluded: chain T residue 2662 LEU Chi-restraints excluded: chain T residue 2679 TRP Chi-restraints excluded: chain T residue 2695 GLU Chi-restraints excluded: chain T residue 2706 LEU Chi-restraints excluded: chain T residue 2719 LEU Chi-restraints excluded: chain T residue 2734 ILE Chi-restraints excluded: chain T residue 2759 LEU Chi-restraints excluded: chain T residue 2788 THR Chi-restraints excluded: chain T residue 2836 THR Chi-restraints excluded: chain T residue 2870 LEU Chi-restraints excluded: chain T residue 2963 CYS Chi-restraints excluded: chain T residue 2978 ILE Chi-restraints excluded: chain T residue 3009 THR Chi-restraints excluded: chain T residue 3012 VAL Chi-restraints excluded: chain T residue 3101 LEU Chi-restraints excluded: chain T residue 3167 LEU Chi-restraints excluded: chain T residue 3208 LEU Chi-restraints excluded: chain T residue 3219 TYR Chi-restraints excluded: chain T residue 3338 CYS Chi-restraints excluded: chain T residue 3352 ILE Chi-restraints excluded: chain T residue 3359 LEU Chi-restraints excluded: chain T residue 3410 VAL Chi-restraints excluded: chain T residue 3505 ASP Chi-restraints excluded: chain T residue 3581 VAL Chi-restraints excluded: chain T residue 3624 LEU Chi-restraints excluded: chain T residue 3682 ILE Chi-restraints excluded: chain T residue 3709 LEU Chi-restraints excluded: chain T residue 3712 THR Chi-restraints excluded: chain T residue 3721 LEU Chi-restraints excluded: chain F residue 540 ASP Chi-restraints excluded: chain F residue 550 SER Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 572 ILE Chi-restraints excluded: chain F residue 591 ASP Chi-restraints excluded: chain F residue 627 LEU Chi-restraints excluded: chain F residue 634 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 192 optimal weight: 9.9990 chunk 123 optimal weight: 9.9990 chunk 185 optimal weight: 2.9990 chunk 93 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 chunk 197 optimal weight: 0.9990 chunk 211 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 243 optimal weight: 2.9990 chunk 282 optimal weight: 0.0020 overall best weight: 1.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN ** B 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 889 GLN T1239 ASN T2792 GLN ** T2847 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T2992 HIS ** T3010 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T3365 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 27003 Z= 0.232 Angle : 0.648 14.525 36585 Z= 0.326 Chirality : 0.042 0.255 4038 Planarity : 0.004 0.048 4692 Dihedral : 6.015 88.793 3591 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.86 % Favored : 91.05 % Rotamer: Outliers : 3.78 % Allowed : 21.81 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.15), residues: 3207 helix: 1.33 (0.13), residues: 1625 sheet: -1.24 (0.37), residues: 201 loop : -2.50 (0.16), residues: 1381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 757 HIS 0.006 0.001 HIS T2621 PHE 0.028 0.001 PHE T1189 TYR 0.022 0.001 TYR E 111 ARG 0.007 0.000 ARG E 210 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 2938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 417 time to evaluate : 3.167 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 ASN cc_start: 0.8578 (m110) cc_final: 0.8370 (m-40) REVERT: A 143 TYR cc_start: 0.8854 (m-10) cc_final: 0.8564 (m-80) REVERT: A 155 SER cc_start: 0.9027 (m) cc_final: 0.7881 (p) REVERT: A 180 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8579 (tp) REVERT: A 250 ILE cc_start: 0.8706 (mm) cc_final: 0.8382 (pt) REVERT: A 296 ASN cc_start: 0.8342 (m-40) cc_final: 0.7986 (m110) REVERT: A 305 MET cc_start: 0.7142 (mtm) cc_final: 0.6471 (ptt) REVERT: B 37 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.8477 (tm-30) REVERT: B 280 PHE cc_start: 0.7703 (OUTLIER) cc_final: 0.7250 (t80) REVERT: B 399 ASP cc_start: 0.8407 (p0) cc_final: 0.8108 (p0) REVERT: B 468 LEU cc_start: 0.8558 (tt) cc_final: 0.8331 (tt) REVERT: D 30 ASP cc_start: 0.8378 (t70) cc_final: 0.7756 (t0) REVERT: D 36 ARG cc_start: 0.7349 (OUTLIER) cc_final: 0.7076 (pmt-80) REVERT: D 332 GLU cc_start: 0.8143 (tm-30) cc_final: 0.7845 (tm-30) REVERT: D 339 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7042 (pp) REVERT: D 375 GLU cc_start: 0.8012 (tp30) cc_final: 0.6666 (mm-30) REVERT: D 553 ASN cc_start: 0.7634 (OUTLIER) cc_final: 0.7117 (p0) REVERT: D 573 ARG cc_start: 0.6754 (OUTLIER) cc_final: 0.6291 (ptt180) REVERT: D 602 GLU cc_start: 0.8171 (tt0) cc_final: 0.7383 (tt0) REVERT: D 640 ARG cc_start: 0.8598 (mtt180) cc_final: 0.8303 (tmt170) REVERT: D 656 GLN cc_start: 0.8975 (tt0) cc_final: 0.8309 (tm-30) REVERT: D 752 HIS cc_start: 0.7925 (OUTLIER) cc_final: 0.7315 (m-70) REVERT: D 767 CYS cc_start: 0.8167 (t) cc_final: 0.7700 (t) REVERT: E 92 ARG cc_start: 0.7946 (mtp180) cc_final: 0.7543 (mtp85) REVERT: E 181 LEU cc_start: 0.9102 (tp) cc_final: 0.8522 (tt) REVERT: E 271 THR cc_start: 0.9059 (m) cc_final: 0.8843 (m) REVERT: T 885 PHE cc_start: 0.7970 (m-80) cc_final: 0.7579 (t80) REVERT: T 1080 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8700 (mt) REVERT: T 1147 ASP cc_start: 0.8172 (t0) cc_final: 0.7826 (t0) REVERT: T 1220 ILE cc_start: 0.9268 (pt) cc_final: 0.9036 (mt) REVERT: T 1231 LYS cc_start: 0.7780 (mtpt) cc_final: 0.7457 (pttt) REVERT: T 1233 TYR cc_start: 0.6152 (m-80) cc_final: 0.5858 (m-80) REVERT: T 2443 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8019 (tt) REVERT: T 2471 GLN cc_start: 0.5586 (OUTLIER) cc_final: 0.4560 (mm-40) REVERT: T 2662 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.9008 (tt) REVERT: T 2755 PHE cc_start: 0.7127 (m-10) cc_final: 0.6826 (m-10) REVERT: T 2778 GLN cc_start: 0.7931 (pp30) cc_final: 0.6861 (tm-30) REVERT: T 2792 GLN cc_start: 0.9220 (OUTLIER) cc_final: 0.8877 (tp40) REVERT: T 2847 GLN cc_start: 0.9061 (OUTLIER) cc_final: 0.7921 (tt0) REVERT: T 2901 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8494 (tt) REVERT: T 3041 GLN cc_start: 0.7061 (tp-100) cc_final: 0.6642 (tm-30) REVERT: T 3232 GLN cc_start: 0.8272 (mm-40) cc_final: 0.8049 (mm-40) REVERT: T 3288 LEU cc_start: 0.6368 (OUTLIER) cc_final: 0.6094 (tp) outliers start: 110 outliers final: 77 residues processed: 486 average time/residue: 0.3804 time to fit residues: 297.9581 Evaluate side-chains 496 residues out of total 2938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 403 time to evaluate : 3.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain B residue 37 GLN Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 280 PHE Chi-restraints excluded: chain B residue 415 SER Chi-restraints excluded: chain B residue 434 SER Chi-restraints excluded: chain B residue 469 TRP Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 36 ARG Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 531 GLU Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 553 ASN Chi-restraints excluded: chain D residue 554 THR Chi-restraints excluded: chain D residue 565 LEU Chi-restraints excluded: chain D residue 567 ASN Chi-restraints excluded: chain D residue 573 ARG Chi-restraints excluded: chain D residue 682 TYR Chi-restraints excluded: chain D residue 701 VAL Chi-restraints excluded: chain D residue 735 ASN Chi-restraints excluded: chain D residue 744 ASN Chi-restraints excluded: chain D residue 752 HIS Chi-restraints excluded: chain T residue 878 PHE Chi-restraints excluded: chain T residue 914 ASP Chi-restraints excluded: chain T residue 952 LEU Chi-restraints excluded: chain T residue 967 THR Chi-restraints excluded: chain T residue 970 THR Chi-restraints excluded: chain T residue 992 SER Chi-restraints excluded: chain T residue 994 THR Chi-restraints excluded: chain T residue 1023 CYS Chi-restraints excluded: chain T residue 1042 LEU Chi-restraints excluded: chain T residue 1043 LEU Chi-restraints excluded: chain T residue 1080 LEU Chi-restraints excluded: chain T residue 1132 ASP Chi-restraints excluded: chain T residue 1242 LEU Chi-restraints excluded: chain T residue 2424 THR Chi-restraints excluded: chain T residue 2443 LEU Chi-restraints excluded: chain T residue 2471 GLN Chi-restraints excluded: chain T residue 2517 LEU Chi-restraints excluded: chain T residue 2537 ILE Chi-restraints excluded: chain T residue 2574 ASN Chi-restraints excluded: chain T residue 2596 ILE Chi-restraints excluded: chain T residue 2600 THR Chi-restraints excluded: chain T residue 2604 ASN Chi-restraints excluded: chain T residue 2662 LEU Chi-restraints excluded: chain T residue 2679 TRP Chi-restraints excluded: chain T residue 2706 LEU Chi-restraints excluded: chain T residue 2719 LEU Chi-restraints excluded: chain T residue 2734 ILE Chi-restraints excluded: chain T residue 2759 LEU Chi-restraints excluded: chain T residue 2788 THR Chi-restraints excluded: chain T residue 2792 GLN Chi-restraints excluded: chain T residue 2836 THR Chi-restraints excluded: chain T residue 2847 GLN Chi-restraints excluded: chain T residue 2870 LEU Chi-restraints excluded: chain T residue 2901 LEU Chi-restraints excluded: chain T residue 2963 CYS Chi-restraints excluded: chain T residue 2978 ILE Chi-restraints excluded: chain T residue 3009 THR Chi-restraints excluded: chain T residue 3012 VAL Chi-restraints excluded: chain T residue 3101 LEU Chi-restraints excluded: chain T residue 3117 LEU Chi-restraints excluded: chain T residue 3167 LEU Chi-restraints excluded: chain T residue 3208 LEU Chi-restraints excluded: chain T residue 3219 TYR Chi-restraints excluded: chain T residue 3287 LEU Chi-restraints excluded: chain T residue 3288 LEU Chi-restraints excluded: chain T residue 3352 ILE Chi-restraints excluded: chain T residue 3359 LEU Chi-restraints excluded: chain T residue 3410 VAL Chi-restraints excluded: chain T residue 3505 ASP Chi-restraints excluded: chain T residue 3568 THR Chi-restraints excluded: chain T residue 3581 VAL Chi-restraints excluded: chain T residue 3586 MET Chi-restraints excluded: chain T residue 3624 LEU Chi-restraints excluded: chain T residue 3682 ILE Chi-restraints excluded: chain T residue 3703 VAL Chi-restraints excluded: chain T residue 3709 LEU Chi-restraints excluded: chain T residue 3712 THR Chi-restraints excluded: chain T residue 3721 LEU Chi-restraints excluded: chain F residue 540 ASP Chi-restraints excluded: chain F residue 550 SER Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 572 ILE Chi-restraints excluded: chain F residue 573 ASP Chi-restraints excluded: chain F residue 591 ASP Chi-restraints excluded: chain F residue 627 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 297 optimal weight: 0.6980 chunk 271 optimal weight: 1.9990 chunk 289 optimal weight: 3.9990 chunk 174 optimal weight: 0.8980 chunk 125 optimal weight: 0.9980 chunk 227 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 261 optimal weight: 10.0000 chunk 273 optimal weight: 4.9990 chunk 288 optimal weight: 0.9990 chunk 189 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T1239 ASN T2792 GLN ** T2847 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T2875 GLN ** T2948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T2992 HIS ** T3010 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T3573 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.4077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 27003 Z= 0.198 Angle : 0.644 12.628 36585 Z= 0.323 Chirality : 0.042 0.303 4038 Planarity : 0.004 0.048 4692 Dihedral : 5.923 89.362 3589 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.29 % Favored : 91.61 % Rotamer: Outliers : 3.50 % Allowed : 22.43 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.15), residues: 3207 helix: 1.33 (0.13), residues: 1625 sheet: -1.14 (0.37), residues: 201 loop : -2.48 (0.16), residues: 1381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 757 HIS 0.006 0.001 HIS T2621 PHE 0.029 0.001 PHE E 173 TYR 0.021 0.001 TYR T2492 ARG 0.006 0.000 ARG E 210 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 2938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 428 time to evaluate : 3.263 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 ASN cc_start: 0.8563 (m110) cc_final: 0.8358 (m-40) REVERT: A 143 TYR cc_start: 0.8829 (m-10) cc_final: 0.8537 (m-80) REVERT: A 155 SER cc_start: 0.9014 (m) cc_final: 0.7880 (p) REVERT: A 180 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8594 (tp) REVERT: A 227 MET cc_start: 0.7710 (mmm) cc_final: 0.7185 (mmt) REVERT: A 250 ILE cc_start: 0.8696 (mm) cc_final: 0.8383 (pt) REVERT: A 296 ASN cc_start: 0.8257 (m-40) cc_final: 0.7884 (m110) REVERT: A 305 MET cc_start: 0.7162 (mtm) cc_final: 0.6502 (ptt) REVERT: A 362 TYR cc_start: 0.8954 (t80) cc_final: 0.8679 (t80) REVERT: B 37 GLN cc_start: 0.8918 (OUTLIER) cc_final: 0.8475 (tm-30) REVERT: B 159 ASP cc_start: 0.8054 (t70) cc_final: 0.7615 (t0) REVERT: B 280 PHE cc_start: 0.7698 (OUTLIER) cc_final: 0.7297 (t80) REVERT: B 394 MET cc_start: 0.9108 (mmm) cc_final: 0.8894 (mmt) REVERT: B 399 ASP cc_start: 0.8395 (p0) cc_final: 0.8123 (p0) REVERT: B 468 LEU cc_start: 0.8561 (tt) cc_final: 0.8351 (tt) REVERT: D 30 ASP cc_start: 0.8366 (t70) cc_final: 0.7731 (t0) REVERT: D 36 ARG cc_start: 0.7314 (OUTLIER) cc_final: 0.7018 (pmt-80) REVERT: D 332 GLU cc_start: 0.8133 (tm-30) cc_final: 0.7839 (tm-30) REVERT: D 339 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7050 (pp) REVERT: D 375 GLU cc_start: 0.7803 (tp30) cc_final: 0.6906 (mm-30) REVERT: D 553 ASN cc_start: 0.7561 (OUTLIER) cc_final: 0.7113 (p0) REVERT: D 573 ARG cc_start: 0.6808 (OUTLIER) cc_final: 0.6351 (ptt180) REVERT: D 602 GLU cc_start: 0.8172 (tt0) cc_final: 0.7402 (tt0) REVERT: D 640 ARG cc_start: 0.8580 (mtt180) cc_final: 0.8293 (tmt170) REVERT: D 656 GLN cc_start: 0.8952 (tt0) cc_final: 0.8308 (tm-30) REVERT: D 752 HIS cc_start: 0.7861 (OUTLIER) cc_final: 0.7284 (m-70) REVERT: D 767 CYS cc_start: 0.8079 (t) cc_final: 0.7630 (t) REVERT: E 181 LEU cc_start: 0.9097 (tp) cc_final: 0.8515 (tt) REVERT: E 271 THR cc_start: 0.9053 (m) cc_final: 0.8843 (m) REVERT: T 885 PHE cc_start: 0.7946 (m-80) cc_final: 0.7562 (t80) REVERT: T 1080 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8682 (mt) REVERT: T 1147 ASP cc_start: 0.8168 (t0) cc_final: 0.7810 (t0) REVERT: T 1220 ILE cc_start: 0.9239 (pt) cc_final: 0.9010 (mt) REVERT: T 1231 LYS cc_start: 0.7750 (mtpt) cc_final: 0.7449 (pttt) REVERT: T 1233 TYR cc_start: 0.6209 (m-80) cc_final: 0.5908 (m-80) REVERT: T 2443 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8043 (tt) REVERT: T 2471 GLN cc_start: 0.5391 (OUTLIER) cc_final: 0.4488 (mm-40) REVERT: T 2662 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.8978 (tt) REVERT: T 2684 LYS cc_start: 0.8785 (tptm) cc_final: 0.8582 (tptp) REVERT: T 2755 PHE cc_start: 0.7089 (m-10) cc_final: 0.6771 (m-10) REVERT: T 2778 GLN cc_start: 0.7888 (pp30) cc_final: 0.6816 (tm-30) REVERT: T 2808 LYS cc_start: 0.8835 (tptp) cc_final: 0.8490 (pttt) REVERT: T 2847 GLN cc_start: 0.9053 (OUTLIER) cc_final: 0.7879 (tt0) REVERT: T 2901 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8468 (tt) REVERT: T 3041 GLN cc_start: 0.7030 (tp-100) cc_final: 0.6602 (tm-30) REVERT: T 3288 LEU cc_start: 0.6410 (OUTLIER) cc_final: 0.6154 (tp) REVERT: T 3638 GLU cc_start: 0.8689 (tm-30) cc_final: 0.8291 (tm-30) REVERT: F 649 TYR cc_start: 0.8743 (m-10) cc_final: 0.8446 (m-10) outliers start: 102 outliers final: 73 residues processed: 495 average time/residue: 0.3742 time to fit residues: 299.0735 Evaluate side-chains 494 residues out of total 2938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 406 time to evaluate : 3.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain B residue 37 GLN Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 280 PHE Chi-restraints excluded: chain B residue 415 SER Chi-restraints excluded: chain B residue 434 SER Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 469 TRP Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 36 ARG Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 531 GLU Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 553 ASN Chi-restraints excluded: chain D residue 554 THR Chi-restraints excluded: chain D residue 565 LEU Chi-restraints excluded: chain D residue 567 ASN Chi-restraints excluded: chain D residue 573 ARG Chi-restraints excluded: chain D residue 678 HIS Chi-restraints excluded: chain D residue 701 VAL Chi-restraints excluded: chain D residue 735 ASN Chi-restraints excluded: chain D residue 744 ASN Chi-restraints excluded: chain D residue 752 HIS Chi-restraints excluded: chain T residue 878 PHE Chi-restraints excluded: chain T residue 914 ASP Chi-restraints excluded: chain T residue 952 LEU Chi-restraints excluded: chain T residue 970 THR Chi-restraints excluded: chain T residue 992 SER Chi-restraints excluded: chain T residue 994 THR Chi-restraints excluded: chain T residue 1042 LEU Chi-restraints excluded: chain T residue 1043 LEU Chi-restraints excluded: chain T residue 1080 LEU Chi-restraints excluded: chain T residue 1132 ASP Chi-restraints excluded: chain T residue 1189 PHE Chi-restraints excluded: chain T residue 2424 THR Chi-restraints excluded: chain T residue 2443 LEU Chi-restraints excluded: chain T residue 2471 GLN Chi-restraints excluded: chain T residue 2517 LEU Chi-restraints excluded: chain T residue 2537 ILE Chi-restraints excluded: chain T residue 2574 ASN Chi-restraints excluded: chain T residue 2596 ILE Chi-restraints excluded: chain T residue 2600 THR Chi-restraints excluded: chain T residue 2604 ASN Chi-restraints excluded: chain T residue 2662 LEU Chi-restraints excluded: chain T residue 2679 TRP Chi-restraints excluded: chain T residue 2706 LEU Chi-restraints excluded: chain T residue 2719 LEU Chi-restraints excluded: chain T residue 2734 ILE Chi-restraints excluded: chain T residue 2788 THR Chi-restraints excluded: chain T residue 2836 THR Chi-restraints excluded: chain T residue 2847 GLN Chi-restraints excluded: chain T residue 2870 LEU Chi-restraints excluded: chain T residue 2901 LEU Chi-restraints excluded: chain T residue 2963 CYS Chi-restraints excluded: chain T residue 2978 ILE Chi-restraints excluded: chain T residue 3009 THR Chi-restraints excluded: chain T residue 3012 VAL Chi-restraints excluded: chain T residue 3101 LEU Chi-restraints excluded: chain T residue 3167 LEU Chi-restraints excluded: chain T residue 3208 LEU Chi-restraints excluded: chain T residue 3219 TYR Chi-restraints excluded: chain T residue 3287 LEU Chi-restraints excluded: chain T residue 3288 LEU Chi-restraints excluded: chain T residue 3352 ILE Chi-restraints excluded: chain T residue 3359 LEU Chi-restraints excluded: chain T residue 3410 VAL Chi-restraints excluded: chain T residue 3505 ASP Chi-restraints excluded: chain T residue 3581 VAL Chi-restraints excluded: chain T residue 3586 MET Chi-restraints excluded: chain T residue 3682 ILE Chi-restraints excluded: chain T residue 3703 VAL Chi-restraints excluded: chain T residue 3709 LEU Chi-restraints excluded: chain T residue 3712 THR Chi-restraints excluded: chain T residue 3721 LEU Chi-restraints excluded: chain F residue 540 ASP Chi-restraints excluded: chain F residue 550 SER Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 572 ILE Chi-restraints excluded: chain F residue 573 ASP Chi-restraints excluded: chain F residue 591 ASP Chi-restraints excluded: chain F residue 627 LEU Chi-restraints excluded: chain F residue 634 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 305 optimal weight: 2.9990 chunk 186 optimal weight: 0.5980 chunk 145 optimal weight: 0.3980 chunk 212 optimal weight: 10.0000 chunk 320 optimal weight: 0.9980 chunk 295 optimal weight: 5.9990 chunk 255 optimal weight: 0.0670 chunk 26 optimal weight: 8.9990 chunk 197 optimal weight: 0.0040 chunk 156 optimal weight: 0.3980 chunk 202 optimal weight: 0.5980 overall best weight: 0.2930 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T1239 ASN T2723 GLN T2792 GLN ** T2847 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T2958 ASN T2992 HIS ** T3010 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T3365 ASN F 624 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.4291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 27003 Z= 0.177 Angle : 0.654 16.065 36585 Z= 0.326 Chirality : 0.042 0.283 4038 Planarity : 0.004 0.048 4692 Dihedral : 5.765 87.691 3589 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.01 % Favored : 91.89 % Rotamer: Outliers : 3.06 % Allowed : 23.12 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.15), residues: 3207 helix: 1.34 (0.13), residues: 1633 sheet: -0.98 (0.37), residues: 199 loop : -2.44 (0.16), residues: 1375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP T3131 HIS 0.005 0.001 HIS T3396 PHE 0.023 0.001 PHE A 255 TYR 0.021 0.001 TYR E 190 ARG 0.009 0.000 ARG T2879 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 2938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 468 time to evaluate : 3.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ASN cc_start: 0.8545 (m110) cc_final: 0.8340 (m-40) REVERT: A 143 TYR cc_start: 0.8786 (m-10) cc_final: 0.8534 (m-80) REVERT: A 155 SER cc_start: 0.8986 (m) cc_final: 0.7873 (p) REVERT: A 227 MET cc_start: 0.7425 (mmm) cc_final: 0.7109 (mmt) REVERT: A 250 ILE cc_start: 0.8711 (mm) cc_final: 0.8416 (pt) REVERT: A 283 MET cc_start: 0.7944 (mmm) cc_final: 0.7702 (mmm) REVERT: A 296 ASN cc_start: 0.8240 (m-40) cc_final: 0.7852 (m110) REVERT: A 305 MET cc_start: 0.7168 (mtm) cc_final: 0.6551 (ptt) REVERT: A 362 TYR cc_start: 0.8914 (t80) cc_final: 0.8619 (t80) REVERT: B 37 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.8419 (tm-30) REVERT: B 159 ASP cc_start: 0.7954 (t70) cc_final: 0.7524 (t0) REVERT: B 280 PHE cc_start: 0.7641 (OUTLIER) cc_final: 0.7307 (t80) REVERT: B 394 MET cc_start: 0.9050 (mmm) cc_final: 0.8840 (mmt) REVERT: B 399 ASP cc_start: 0.8397 (p0) cc_final: 0.8105 (p0) REVERT: D 30 ASP cc_start: 0.8311 (t70) cc_final: 0.7655 (t0) REVERT: D 36 ARG cc_start: 0.7230 (OUTLIER) cc_final: 0.6936 (pmt-80) REVERT: D 310 LEU cc_start: 0.8693 (mt) cc_final: 0.7931 (mp) REVERT: D 332 GLU cc_start: 0.8114 (tm-30) cc_final: 0.7835 (tm-30) REVERT: D 339 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7084 (pp) REVERT: D 375 GLU cc_start: 0.7797 (tp30) cc_final: 0.6762 (mm-30) REVERT: D 553 ASN cc_start: 0.7489 (OUTLIER) cc_final: 0.6861 (p0) REVERT: D 555 PHE cc_start: 0.7706 (m-80) cc_final: 0.6937 (m-80) REVERT: D 602 GLU cc_start: 0.8089 (tt0) cc_final: 0.7296 (tt0) REVERT: D 640 ARG cc_start: 0.8518 (mtt180) cc_final: 0.8248 (tmt170) REVERT: D 656 GLN cc_start: 0.8963 (tt0) cc_final: 0.8282 (tm-30) REVERT: D 752 HIS cc_start: 0.7824 (OUTLIER) cc_final: 0.7368 (m-70) REVERT: D 767 CYS cc_start: 0.7990 (t) cc_final: 0.7555 (t) REVERT: E 181 LEU cc_start: 0.9076 (tp) cc_final: 0.8488 (tt) REVERT: E 271 THR cc_start: 0.9028 (m) cc_final: 0.8815 (m) REVERT: T 845 MET cc_start: 0.8304 (ttp) cc_final: 0.8097 (tmm) REVERT: T 889 GLN cc_start: 0.8242 (mm110) cc_final: 0.7779 (mt0) REVERT: T 1080 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8698 (mt) REVERT: T 1147 ASP cc_start: 0.8062 (t0) cc_final: 0.7781 (t0) REVERT: T 1166 LEU cc_start: 0.9120 (tt) cc_final: 0.8692 (mm) REVERT: T 1220 ILE cc_start: 0.9158 (pt) cc_final: 0.8957 (mt) REVERT: T 1231 LYS cc_start: 0.7630 (mtpt) cc_final: 0.7371 (pttt) REVERT: T 2443 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7989 (tt) REVERT: T 2601 ASN cc_start: 0.7933 (m-40) cc_final: 0.7666 (m110) REVERT: T 2662 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8944 (tt) REVERT: T 2694 TYR cc_start: 0.8844 (m-80) cc_final: 0.8619 (m-80) REVERT: T 2755 PHE cc_start: 0.7023 (m-10) cc_final: 0.6651 (m-10) REVERT: T 2778 GLN cc_start: 0.7786 (pp30) cc_final: 0.6729 (tm-30) REVERT: T 2847 GLN cc_start: 0.8973 (OUTLIER) cc_final: 0.7782 (tt0) REVERT: T 2901 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8467 (tt) REVERT: T 3029 PHE cc_start: 0.8951 (m-10) cc_final: 0.8727 (m-80) REVERT: T 3232 GLN cc_start: 0.7929 (mm-40) cc_final: 0.7609 (tp-100) REVERT: T 3638 GLU cc_start: 0.8659 (tm-30) cc_final: 0.8344 (tm-30) REVERT: F 577 TYR cc_start: 0.5099 (p90) cc_final: 0.4808 (p90) outliers start: 89 outliers final: 61 residues processed: 523 average time/residue: 0.3824 time to fit residues: 325.8458 Evaluate side-chains 503 residues out of total 2938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 431 time to evaluate : 3.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain B residue 37 GLN Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 280 PHE Chi-restraints excluded: chain B residue 415 SER Chi-restraints excluded: chain B residue 434 SER Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 469 TRP Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 36 ARG Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 531 GLU Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 553 ASN Chi-restraints excluded: chain D residue 554 THR Chi-restraints excluded: chain D residue 565 LEU Chi-restraints excluded: chain D residue 701 VAL Chi-restraints excluded: chain D residue 744 ASN Chi-restraints excluded: chain D residue 752 HIS Chi-restraints excluded: chain T residue 846 ILE Chi-restraints excluded: chain T residue 878 PHE Chi-restraints excluded: chain T residue 914 ASP Chi-restraints excluded: chain T residue 952 LEU Chi-restraints excluded: chain T residue 967 THR Chi-restraints excluded: chain T residue 970 THR Chi-restraints excluded: chain T residue 992 SER Chi-restraints excluded: chain T residue 994 THR Chi-restraints excluded: chain T residue 1023 CYS Chi-restraints excluded: chain T residue 1042 LEU Chi-restraints excluded: chain T residue 1043 LEU Chi-restraints excluded: chain T residue 1080 LEU Chi-restraints excluded: chain T residue 2443 LEU Chi-restraints excluded: chain T residue 2517 LEU Chi-restraints excluded: chain T residue 2537 ILE Chi-restraints excluded: chain T residue 2596 ILE Chi-restraints excluded: chain T residue 2600 THR Chi-restraints excluded: chain T residue 2604 ASN Chi-restraints excluded: chain T residue 2662 LEU Chi-restraints excluded: chain T residue 2679 TRP Chi-restraints excluded: chain T residue 2695 GLU Chi-restraints excluded: chain T residue 2706 LEU Chi-restraints excluded: chain T residue 2719 LEU Chi-restraints excluded: chain T residue 2734 ILE Chi-restraints excluded: chain T residue 2788 THR Chi-restraints excluded: chain T residue 2829 VAL Chi-restraints excluded: chain T residue 2847 GLN Chi-restraints excluded: chain T residue 2870 LEU Chi-restraints excluded: chain T residue 2901 LEU Chi-restraints excluded: chain T residue 2958 ASN Chi-restraints excluded: chain T residue 2963 CYS Chi-restraints excluded: chain T residue 2978 ILE Chi-restraints excluded: chain T residue 3009 THR Chi-restraints excluded: chain T residue 3012 VAL Chi-restraints excluded: chain T residue 3101 LEU Chi-restraints excluded: chain T residue 3167 LEU Chi-restraints excluded: chain T residue 3208 LEU Chi-restraints excluded: chain T residue 3410 VAL Chi-restraints excluded: chain T residue 3505 ASP Chi-restraints excluded: chain T residue 3568 THR Chi-restraints excluded: chain T residue 3586 MET Chi-restraints excluded: chain T residue 3682 ILE Chi-restraints excluded: chain T residue 3709 LEU Chi-restraints excluded: chain T residue 3712 THR Chi-restraints excluded: chain T residue 3721 LEU Chi-restraints excluded: chain F residue 540 ASP Chi-restraints excluded: chain F residue 550 SER Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 591 ASP Chi-restraints excluded: chain F residue 627 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 272 optimal weight: 10.0000 chunk 78 optimal weight: 4.9990 chunk 235 optimal weight: 0.8980 chunk 37 optimal weight: 10.0000 chunk 70 optimal weight: 0.6980 chunk 255 optimal weight: 0.6980 chunk 107 optimal weight: 10.0000 chunk 262 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 47 optimal weight: 0.0030 chunk 224 optimal weight: 4.9990 overall best weight: 1.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 678 HIS T1239 ASN T2670 GLN ** T2847 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T2958 ASN T2992 HIS ** T3010 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.122738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.098851 restraints weight = 64731.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.101829 restraints weight = 34074.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.103742 restraints weight = 22547.019| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.4329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 27003 Z= 0.229 Angle : 0.680 15.764 36585 Z= 0.337 Chirality : 0.043 0.332 4038 Planarity : 0.004 0.046 4692 Dihedral : 5.792 88.457 3586 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.33 % Favored : 91.58 % Rotamer: Outliers : 3.09 % Allowed : 23.50 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.15), residues: 3207 helix: 1.42 (0.13), residues: 1628 sheet: -0.94 (0.37), residues: 205 loop : -2.45 (0.17), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP A 340 HIS 0.015 0.001 HIS T2957 PHE 0.027 0.001 PHE T1138 TYR 0.034 0.001 TYR F 649 ARG 0.011 0.000 ARG T2879 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6415.43 seconds wall clock time: 116 minutes 23.97 seconds (6983.97 seconds total)