Starting phenix.real_space_refine (version: dev) on Mon Feb 20 20:01:02 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gni_0044/02_2023/6gni_0044_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gni_0044/02_2023/6gni_0044.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gni_0044/02_2023/6gni_0044.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gni_0044/02_2023/6gni_0044.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gni_0044/02_2023/6gni_0044_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gni_0044/02_2023/6gni_0044_updated.pdb" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.078 sd= 2.069 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 12937 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 733, 5780 Classifications: {'peptide': 733} Link IDs: {'PCIS': 2, 'PTRANS': 40, 'TRANS': 690} Chain breaks: 2 Chain: "E" Number of atoms: 5823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5823 Classifications: {'peptide': 735} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 48, 'TRANS': 686} Chain breaks: 5 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 1299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1299 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 7, 'TRANS': 156} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 437 SG CYS A 56 25.283 95.993 40.196 1.00 36.61 S ATOM 470 SG CYS A 61 28.219 97.443 38.030 1.00 44.87 S ATOM 621 SG CYS A 80 25.933 99.722 40.589 1.00 40.87 S ATOM 642 SG CYS A 83 24.701 97.819 37.045 1.00 42.31 S ATOM 6560 SG CYS E 231 127.821 59.329 21.872 1.00 36.48 S ATOM 6588 SG CYS E 234 124.733 57.052 21.914 1.00 38.71 S ATOM 6759 SG CYS E 253 127.572 55.707 22.811 1.00 39.41 S ATOM 6784 SG CYS E 256 127.744 57.088 18.866 1.00 35.91 S Time building chain proxies: 7.19, per 1000 atoms: 0.56 Number of scatterers: 12937 At special positions: 0 Unit cell: (155.259, 156.586, 82.274, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 65 16.00 P 3 15.00 Mg 1 11.99 O 2445 8.00 N 2194 7.00 C 8227 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.38 Conformation dependent library (CDL) restraints added in 1.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 56 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 61 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 80 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 83 " pdb=" ZN E1001 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 253 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 256 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 231 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 234 " Number of angles added : 12 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3118 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 56 helices and 15 sheets defined 32.5% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'A' and resid 3 through 10 removed outlier: 3.759A pdb=" N GLU A 7 " --> pdb=" O PHE A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 28 Processing helix chain 'A' and resid 103 through 106 No H-bonds generated for 'chain 'A' and resid 103 through 106' Processing helix chain 'A' and resid 134 through 150 removed outlier: 3.687A pdb=" N LEU A 150 " --> pdb=" O THR A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 198 Processing helix chain 'A' and resid 224 through 227 Processing helix chain 'A' and resid 231 through 244 removed outlier: 6.324A pdb=" N PHE A 236 " --> pdb=" O GLU A 232 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N LYS A 237 " --> pdb=" O GLN A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 276 Processing helix chain 'A' and resid 311 through 315 Processing helix chain 'A' and resid 322 through 339 Processing helix chain 'A' and resid 355 through 363 removed outlier: 5.548A pdb=" N GLN A 360 " --> pdb=" O SER A 356 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N LEU A 361 " --> pdb=" O GLU A 357 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N THR A 362 " --> pdb=" O MET A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 388 removed outlier: 4.205A pdb=" N PHE A 388 " --> pdb=" O TYR A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 522 Processing helix chain 'A' and resid 525 through 540 Processing helix chain 'A' and resid 545 through 563 Processing helix chain 'A' and resid 571 through 573 No H-bonds generated for 'chain 'A' and resid 571 through 573' Processing helix chain 'A' and resid 583 through 591 Processing helix chain 'A' and resid 603 through 615 removed outlier: 3.810A pdb=" N ARG A 615 " --> pdb=" O HIS A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 625 Processing helix chain 'A' and resid 668 through 676 Processing helix chain 'A' and resid 678 through 680 No H-bonds generated for 'chain 'A' and resid 678 through 680' Processing helix chain 'A' and resid 686 through 702 Proline residue: A 694 - end of helix removed outlier: 3.681A pdb=" N ALA A 699 " --> pdb=" O LYS A 695 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU A 700 " --> pdb=" O LEU A 696 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU A 702 " --> pdb=" O ALA A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 725 removed outlier: 3.559A pdb=" N LEU A 725 " --> pdb=" O ARG A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 765 removed outlier: 3.703A pdb=" N SER A 765 " --> pdb=" O GLN A 761 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 155 No H-bonds generated for 'chain 'E' and resid 153 through 155' Processing helix chain 'E' and resid 165 through 167 No H-bonds generated for 'chain 'E' and resid 165 through 167' Processing helix chain 'E' and resid 193 through 199 Processing helix chain 'E' and resid 264 through 266 No H-bonds generated for 'chain 'E' and resid 264 through 266' Processing helix chain 'E' and resid 268 through 270 No H-bonds generated for 'chain 'E' and resid 268 through 270' Processing helix chain 'E' and resid 274 through 279 removed outlier: 4.043A pdb=" N ARG E 277 " --> pdb=" O PRO E 274 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N TYR E 278 " --> pdb=" O LYS E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 284 No H-bonds generated for 'chain 'E' and resid 281 through 284' Processing helix chain 'E' and resid 294 through 296 No H-bonds generated for 'chain 'E' and resid 294 through 296' Processing helix chain 'E' and resid 314 through 318 Processing helix chain 'E' and resid 321 through 331 Processing helix chain 'E' and resid 400 through 413 Proline residue: E 411 - end of helix Processing helix chain 'E' and resid 424 through 435 Processing helix chain 'E' and resid 471 through 475 Processing helix chain 'E' and resid 481 through 493 removed outlier: 4.369A pdb=" N PHE E 486 " --> pdb=" O TYR E 483 " (cutoff:3.500A) Processing helix chain 'E' and resid 509 through 517 removed outlier: 4.465A pdb=" N ASN E 514 " --> pdb=" O ALA E 510 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N LEU E 515 " --> pdb=" O SER E 511 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N SER E 516 " --> pdb=" O LEU E 512 " (cutoff:3.500A) Processing helix chain 'E' and resid 534 through 549 removed outlier: 3.763A pdb=" N VAL E 538 " --> pdb=" O PRO E 534 " (cutoff:3.500A) Processing helix chain 'E' and resid 639 through 645 Processing helix chain 'E' and resid 648 through 665 Processing helix chain 'E' and resid 669 through 689 removed outlier: 3.523A pdb=" N VAL E 679 " --> pdb=" O ILE E 675 " (cutoff:3.500A) Processing helix chain 'E' and resid 705 through 707 No H-bonds generated for 'chain 'E' and resid 705 through 707' Processing helix chain 'E' and resid 710 through 719 Processing helix chain 'E' and resid 730 through 742 Processing helix chain 'E' and resid 745 through 752 removed outlier: 3.919A pdb=" N LYS E 750 " --> pdb=" O LYS E 746 " (cutoff:3.500A) Processing helix chain 'E' and resid 819 through 821 No H-bonds generated for 'chain 'E' and resid 819 through 821' Processing helix chain 'E' and resid 849 through 858 Processing helix chain 'E' and resid 890 through 901 removed outlier: 3.502A pdb=" N THR E 901 " --> pdb=" O TRP E 897 " (cutoff:3.500A) Processing helix chain 'E' and resid 913 through 924 Processing helix chain 'B' and resid 36 through 45 Processing helix chain 'B' and resid 78 through 87 removed outlier: 4.115A pdb=" N ARG B 82 " --> pdb=" O GLN B 79 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LYS B 85 " --> pdb=" O ARG B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 117 removed outlier: 5.070A pdb=" N ASP B 107 " --> pdb=" O GLU B 104 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG B 110 " --> pdb=" O ASP B 107 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL B 111 " --> pdb=" O GLU B 108 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP B 114 " --> pdb=" O VAL B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 149 Processing helix chain 'B' and resid 179 through 188 removed outlier: 3.817A pdb=" N GLN B 188 " --> pdb=" O GLN B 184 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 12 through 14 removed outlier: 4.268A pdb=" N VAL A 33 " --> pdb=" O PHE A 460 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY A 416 " --> pdb=" O PHE A 459 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N GLU A 461 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N VAL A 414 " --> pdb=" O GLU A 461 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 18 through 20 removed outlier: 8.220A pdb=" N PHE A 19 " --> pdb=" O ALA A 508 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLN A 510 " --> pdb=" O PHE A 19 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 77 through 79 Processing sheet with id= D, first strand: chain 'A' and resid 109 through 113 Processing sheet with id= E, first strand: chain 'A' and resid 369 through 372 removed outlier: 8.367A pdb=" N LEU A 370 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE A 345 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N THR A 372 " --> pdb=" O ILE A 345 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N ALA A 347 " --> pdb=" O THR A 372 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ALA A 282 " --> pdb=" O THR A 342 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ASP A 344 " --> pdb=" O ALA A 282 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE A 284 " --> pdb=" O ASP A 344 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N PHE A 346 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU A 286 " --> pdb=" O PHE A 346 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N GLY A 348 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ALA A 288 " --> pdb=" O GLY A 348 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE A 123 " --> pdb=" O ARG A 283 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ILE A 285 " --> pdb=" O ILE A 123 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N PHE A 125 " --> pdb=" O ILE A 285 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N PHE A 287 " --> pdb=" O PHE A 125 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL A 127 " --> pdb=" O PHE A 287 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU A 156 " --> pdb=" O PHE A 124 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N PHE A 126 " --> pdb=" O LEU A 156 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N GLY A 158 " --> pdb=" O PHE A 126 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N VAL A 128 " --> pdb=" O GLY A 158 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE A 160 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N LEU A 159 " --> pdb=" O HIS A 169 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG A 178 " --> pdb=" O ASP A 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 628 through 632 removed outlier: 6.162A pdb=" N ARG A 710 " --> pdb=" O ILE A 662 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ILE A 664 " --> pdb=" O ARG A 710 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE A 712 " --> pdb=" O ILE A 664 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N HIS A 666 " --> pdb=" O ILE A 712 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N THR A 714 " --> pdb=" O HIS A 666 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 140 through 142 Processing sheet with id= H, first strand: chain 'E' and resid 182 through 184 removed outlier: 3.760A pdb=" N ARG E 570 " --> pdb=" O GLU E 597 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ASN E 599 " --> pdb=" O MET E 568 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N MET E 568 " --> pdb=" O ASN E 599 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 188 through 190 removed outlier: 8.347A pdb=" N VAL E 189 " --> pdb=" O ALA E 632 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN E 623 " --> pdb=" O LEU E 619 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 221 through 223 Processing sheet with id= K, first strand: chain 'E' and resid 243 through 245 Processing sheet with id= L, first strand: chain 'E' and resid 347 through 350 removed outlier: 8.079A pdb=" N LEU E 348 " --> pdb=" O TYR E 306 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N PHE E 308 " --> pdb=" O LEU E 348 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N VAL E 350 " --> pdb=" O PHE E 308 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE E 310 " --> pdb=" O VAL E 350 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LYS E 441 " --> pdb=" O CYS E 307 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N LEU E 309 " --> pdb=" O LYS E 441 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE E 443 " --> pdb=" O LEU E 309 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N ASP E 311 " --> pdb=" O ILE E 443 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N VAL E 445 " --> pdb=" O ASP E 311 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 354 through 358 Processing sheet with id= N, first strand: chain 'E' and resid 755 through 758 removed outlier: 6.123A pdb=" N SER E 870 " --> pdb=" O LEU E 808 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N LEU E 810 " --> pdb=" O SER E 870 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N TYR E 872 " --> pdb=" O LEU E 810 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N MET E 812 " --> pdb=" O TYR E 872 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL E 874 " --> pdb=" O MET E 812 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 166 through 171 removed outlier: 6.701A pdb=" N PHE B 127 " --> pdb=" O GLU B 167 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N PHE B 169 " --> pdb=" O PHE B 127 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ILE B 129 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N CYS B 171 " --> pdb=" O ILE B 129 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N GLY B 131 " --> pdb=" O CYS B 171 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY B 93 " --> pdb=" O LYS B 25 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N THR B 70 " --> pdb=" O LEU B 26 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N PHE B 28 " --> pdb=" O THR B 70 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N PHE B 72 " --> pdb=" O PHE B 28 " (cutoff:3.500A) 427 hydrogen bonds defined for protein. 1158 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: 4.26 Time building geometry restraints manager: 5.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4209 1.34 - 1.47: 3134 1.47 - 1.60: 5767 1.60 - 1.73: 6 1.73 - 1.86: 103 Bond restraints: 13219 Sorted by residual: bond pdb=" N3B GNP B 201 " pdb=" PG GNP B 201 " ideal model delta sigma weight residual 1.801 1.609 0.192 2.00e-02 2.50e+03 9.26e+01 bond pdb=" O1G GNP B 201 " pdb=" PG GNP B 201 " ideal model delta sigma weight residual 1.531 1.442 0.089 2.00e-02 2.50e+03 1.98e+01 bond pdb=" CA THR A 131 " pdb=" CB THR A 131 " ideal model delta sigma weight residual 1.524 1.574 -0.051 1.31e-02 5.83e+03 1.49e+01 bond pdb=" CA ILE E 435 " pdb=" CB ILE E 435 " ideal model delta sigma weight residual 1.542 1.583 -0.041 1.08e-02 8.57e+03 1.42e+01 bond pdb=" O3A GNP B 201 " pdb=" PB GNP B 201 " ideal model delta sigma weight residual 1.687 1.617 0.070 2.00e-02 2.50e+03 1.24e+01 ... (remaining 13214 not shown) Histogram of bond angle deviations from ideal: 97.60 - 104.89: 492 104.89 - 112.19: 6158 112.19 - 119.48: 4370 119.48 - 126.78: 6819 126.78 - 134.07: 131 Bond angle restraints: 17970 Sorted by residual: angle pdb=" N VAL E 189 " pdb=" CA VAL E 189 " pdb=" C VAL E 189 " ideal model delta sigma weight residual 108.63 116.49 -7.86 8.60e-01 1.35e+00 8.34e+01 angle pdb=" N ILE B 78 " pdb=" CA ILE B 78 " pdb=" C ILE B 78 " ideal model delta sigma weight residual 110.36 119.18 -8.82 1.05e+00 9.07e-01 7.05e+01 angle pdb=" N ALA A 685 " pdb=" CA ALA A 685 " pdb=" C ALA A 685 " ideal model delta sigma weight residual 113.97 104.27 9.70 1.28e+00 6.10e-01 5.75e+01 angle pdb=" N ILE E 454 " pdb=" CA ILE E 454 " pdb=" C ILE E 454 " ideal model delta sigma weight residual 110.36 118.26 -7.90 1.05e+00 9.07e-01 5.67e+01 angle pdb=" N VAL E 394 " pdb=" CA VAL E 394 " pdb=" C VAL E 394 " ideal model delta sigma weight residual 109.17 120.69 -11.52 1.54e+00 4.22e-01 5.60e+01 ... (remaining 17965 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 7309 17.63 - 35.26: 459 35.26 - 52.89: 152 52.89 - 70.51: 69 70.51 - 88.14: 21 Dihedral angle restraints: 8010 sinusoidal: 3211 harmonic: 4799 Sorted by residual: dihedral pdb=" CG ARG E 459 " pdb=" CD ARG E 459 " pdb=" NE ARG E 459 " pdb=" CZ ARG E 459 " ideal model delta sinusoidal sigma weight residual -90.00 -43.70 -46.30 2 1.50e+01 4.44e-03 1.12e+01 dihedral pdb=" CA ASN A 601 " pdb=" CB ASN A 601 " pdb=" CG ASN A 601 " pdb=" OD1 ASN A 601 " ideal model delta sinusoidal sigma weight residual 120.00 -166.44 -73.56 2 2.00e+01 2.50e-03 1.10e+01 dihedral pdb=" N MET E 291 " pdb=" C MET E 291 " pdb=" CA MET E 291 " pdb=" CB MET E 291 " ideal model delta harmonic sigma weight residual 122.80 114.54 8.26 0 2.50e+00 1.60e-01 1.09e+01 ... (remaining 8007 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1087 0.072 - 0.143: 659 0.143 - 0.215: 216 0.215 - 0.287: 66 0.287 - 0.359: 13 Chirality restraints: 2041 Sorted by residual: chirality pdb=" CA MET E 291 " pdb=" N MET E 291 " pdb=" C MET E 291 " pdb=" CB MET E 291 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.22e+00 chirality pdb=" CA VAL E 393 " pdb=" N VAL E 393 " pdb=" C VAL E 393 " pdb=" CB VAL E 393 " both_signs ideal model delta sigma weight residual False 2.44 2.79 -0.35 2.00e-01 2.50e+01 3.06e+00 chirality pdb=" CA VAL E 206 " pdb=" N VAL E 206 " pdb=" C VAL E 206 " pdb=" CB VAL E 206 " both_signs ideal model delta sigma weight residual False 2.44 2.77 -0.33 2.00e-01 2.50e+01 2.71e+00 ... (remaining 2038 not shown) Planarity restraints: 2328 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 290 " -0.093 2.00e-02 2.50e+03 4.72e-02 4.45e+01 pdb=" CG TYR E 290 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR E 290 " 0.041 2.00e-02 2.50e+03 pdb=" CD2 TYR E 290 " 0.042 2.00e-02 2.50e+03 pdb=" CE1 TYR E 290 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 TYR E 290 " 0.013 2.00e-02 2.50e+03 pdb=" CZ TYR E 290 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR E 290 " -0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 453 " -0.090 2.00e-02 2.50e+03 4.70e-02 4.41e+01 pdb=" CG TYR A 453 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR A 453 " 0.039 2.00e-02 2.50e+03 pdb=" CD2 TYR A 453 " 0.037 2.00e-02 2.50e+03 pdb=" CE1 TYR A 453 " 0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR A 453 " 0.018 2.00e-02 2.50e+03 pdb=" CZ TYR A 453 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 453 " -0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 583 " 0.084 2.00e-02 2.50e+03 4.44e-02 3.95e+01 pdb=" CG TYR A 583 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR A 583 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 TYR A 583 " -0.035 2.00e-02 2.50e+03 pdb=" CE1 TYR A 583 " -0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR A 583 " -0.019 2.00e-02 2.50e+03 pdb=" CZ TYR A 583 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR A 583 " 0.065 2.00e-02 2.50e+03 ... (remaining 2325 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 91 2.53 - 3.13: 10905 3.13 - 3.72: 19972 3.72 - 4.31: 30816 4.31 - 4.90: 48932 Nonbonded interactions: 110716 Sorted by model distance: nonbonded pdb=" O1B GNP B 201 " pdb="MG MG B 202 " model vdw 1.943 2.170 nonbonded pdb=" O1G GNP B 201 " pdb="MG MG B 202 " model vdw 1.979 2.170 nonbonded pdb=" O TYR E 296 " pdb=" NH1 ARG E 624 " model vdw 2.186 2.520 nonbonded pdb=" O LEU E 147 " pdb=" C PRO E 148 " model vdw 2.216 3.270 nonbonded pdb=" OG1 THR B 54 " pdb="MG MG B 202 " model vdw 2.221 2.170 ... (remaining 110711 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 Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 3 5.49 5 Mg 1 5.21 5 S 65 5.16 5 C 8227 2.51 5 N 2194 2.21 5 O 2445 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.300 Check model and map are aligned: 0.170 Process input model: 37.110 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.120 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6275 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 0.192 13219 Z= 0.536 Angle : 1.475 14.413 17970 Z= 0.966 Chirality : 0.101 0.359 2041 Planarity : 0.008 0.154 2328 Dihedral : 15.174 88.143 4892 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 21.32 Ramachandran Plot: Outliers : 2.36 % Allowed : 6.34 % Favored : 91.30 % Rotamer Outliers : 3.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.39 (0.18), residues: 1610 helix: -2.80 (0.16), residues: 548 sheet: -0.94 (0.28), residues: 285 loop : -2.28 (0.20), residues: 777 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 197 time to evaluate : 1.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 6 residues processed: 245 average time/residue: 0.2682 time to fit residues: 93.8518 Evaluate side-chains 104 residues out of total 1443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 98 time to evaluate : 1.672 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1359 time to fit residues: 3.6714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 9.9990 chunk 122 optimal weight: 6.9990 chunk 68 optimal weight: 8.9990 chunk 41 optimal weight: 20.0000 chunk 82 optimal weight: 30.0000 chunk 65 optimal weight: 0.6980 chunk 126 optimal weight: 20.0000 chunk 49 optimal weight: 9.9990 chunk 77 optimal weight: 0.9990 chunk 94 optimal weight: 6.9990 chunk 147 optimal weight: 7.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 66 ASN A 189 GLN A 233 GLN A 339 ASN A 464 ASN A 510 GLN ** A 611 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 666 HIS A 735 GLN A 760 GLN ** E 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 372 GLN E 421 ASN E 533 ASN E 535 ASN E 599 ASN E 732 HIS E 751 ASN E 806 ASN E 857 ASN B 23 HIS B 66 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6467 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.111 13219 Z= 0.218 Angle : 0.680 8.732 17970 Z= 0.346 Chirality : 0.045 0.188 2041 Planarity : 0.006 0.143 2328 Dihedral : 4.708 35.932 1766 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.54 % Favored : 96.21 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.09 (0.20), residues: 1610 helix: -0.33 (0.21), residues: 566 sheet: -0.45 (0.28), residues: 301 loop : -1.05 (0.22), residues: 743 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 117 time to evaluate : 1.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 120 average time/residue: 0.2639 time to fit residues: 47.6612 Evaluate side-chains 75 residues out of total 1443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 74 time to evaluate : 1.750 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1270 time to fit residues: 2.4770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 81 optimal weight: 0.0040 chunk 45 optimal weight: 20.0000 chunk 122 optimal weight: 8.9990 chunk 100 optimal weight: 10.0000 chunk 40 optimal weight: 50.0000 chunk 147 optimal weight: 30.0000 chunk 159 optimal weight: 50.0000 chunk 131 optimal weight: 40.0000 chunk 146 optimal weight: 7.9990 chunk 50 optimal weight: 7.9990 chunk 118 optimal weight: 30.0000 overall best weight: 7.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS A 75 ASN A 87 ASN A 312 HIS ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 GLN A 585 GLN A 611 HIS A 626 GLN E 187 ASN E 211 GLN ** E 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6627 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.104 13219 Z= 0.224 Angle : 0.627 9.248 17970 Z= 0.317 Chirality : 0.043 0.170 2041 Planarity : 0.006 0.142 2328 Dihedral : 4.595 34.681 1766 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.25 % Allowed : 2.98 % Favored : 96.77 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 1.03 % 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: -0.13 (0.21), residues: 1610 helix: 0.33 (0.23), residues: 564 sheet: 0.07 (0.28), residues: 299 loop : -0.35 (0.23), residues: 747 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 1.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.2592 time to fit residues: 40.5620 Evaluate side-chains 68 residues out of total 1443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 1.610 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 145 optimal weight: 30.0000 chunk 110 optimal weight: 40.0000 chunk 76 optimal weight: 0.9980 chunk 16 optimal weight: 20.0000 chunk 70 optimal weight: 0.2980 chunk 98 optimal weight: 50.0000 chunk 147 optimal weight: 30.0000 chunk 156 optimal weight: 30.0000 chunk 77 optimal weight: 0.0000 chunk 140 optimal weight: 10.0000 chunk 42 optimal weight: 20.0000 overall best weight: 6.2592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 601 ASN E 187 ASN E 314 GLN E 599 ASN E 806 ASN ** B 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6652 moved from start: 0.4605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.097 13219 Z= 0.199 Angle : 0.579 8.471 17970 Z= 0.291 Chirality : 0.042 0.155 2041 Planarity : 0.006 0.139 2328 Dihedral : 4.524 37.668 1766 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.25 % Allowed : 2.86 % Favored : 96.89 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 1.03 % 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: 0.23 (0.21), residues: 1610 helix: 0.64 (0.23), residues: 561 sheet: 0.15 (0.28), residues: 309 loop : -0.08 (0.23), residues: 740 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 1.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.2511 time to fit residues: 32.9326 Evaluate side-chains 66 residues out of total 1443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.598 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 130 optimal weight: 6.9990 chunk 88 optimal weight: 20.0000 chunk 2 optimal weight: 9.9990 chunk 116 optimal weight: 40.0000 chunk 64 optimal weight: 0.0970 chunk 133 optimal weight: 3.9990 chunk 108 optimal weight: 9.9990 chunk 0 optimal weight: 60.0000 chunk 79 optimal weight: 40.0000 chunk 140 optimal weight: 30.0000 chunk 39 optimal weight: 5.9990 overall best weight: 5.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 GLN A 415 GLN ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 594 GLN ** E 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 676 ASN ** B 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 moved from start: 0.5022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.095 13219 Z= 0.185 Angle : 0.557 7.968 17970 Z= 0.278 Chirality : 0.041 0.145 2041 Planarity : 0.005 0.137 2328 Dihedral : 4.390 38.674 1766 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.25 % Allowed : 2.92 % Favored : 96.83 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 1.03 % 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: 0.50 (0.21), residues: 1610 helix: 0.93 (0.23), residues: 545 sheet: 0.23 (0.28), residues: 316 loop : 0.06 (0.23), residues: 749 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 1.762 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.2838 time to fit residues: 35.0571 Evaluate side-chains 63 residues out of total 1443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 1.564 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 52 optimal weight: 30.0000 chunk 141 optimal weight: 8.9990 chunk 30 optimal weight: 50.0000 chunk 91 optimal weight: 20.0000 chunk 38 optimal weight: 6.9990 chunk 156 optimal weight: 40.0000 chunk 130 optimal weight: 10.0000 chunk 72 optimal weight: 6.9990 chunk 13 optimal weight: 40.0000 chunk 51 optimal weight: 7.9990 chunk 82 optimal weight: 40.0000 overall best weight: 8.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 200 GLN ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 594 GLN A 620 ASN A 720 GLN ** E 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 moved from start: 0.5595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.096 13219 Z= 0.236 Angle : 0.593 7.434 17970 Z= 0.300 Chirality : 0.042 0.158 2041 Planarity : 0.006 0.136 2328 Dihedral : 4.682 42.864 1766 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.17 % Favored : 96.65 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 1.03 % 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: 0.52 (0.21), residues: 1610 helix: 1.00 (0.23), residues: 534 sheet: 0.29 (0.29), residues: 307 loop : 0.03 (0.23), residues: 769 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 1.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.2516 time to fit residues: 29.4537 Evaluate side-chains 60 residues out of total 1443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.601 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 151 optimal weight: 30.0000 chunk 17 optimal weight: 0.0170 chunk 89 optimal weight: 9.9990 chunk 114 optimal weight: 9.9990 chunk 88 optimal weight: 10.0000 chunk 131 optimal weight: 50.0000 chunk 87 optimal weight: 50.0000 chunk 156 optimal weight: 20.0000 chunk 97 optimal weight: 4.9990 chunk 95 optimal weight: 20.0000 chunk 72 optimal weight: 10.0000 overall best weight: 7.0028 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 488 GLN ** E 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 moved from start: 0.5833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.097 13219 Z= 0.208 Angle : 0.556 7.267 17970 Z= 0.281 Chirality : 0.042 0.189 2041 Planarity : 0.006 0.135 2328 Dihedral : 4.571 41.252 1766 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.35 % Favored : 96.46 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.21), residues: 1610 helix: 1.12 (0.23), residues: 534 sheet: 0.23 (0.29), residues: 321 loop : 0.09 (0.23), residues: 755 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.2650 time to fit residues: 29.5235 Evaluate side-chains 58 residues out of total 1443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 1.491 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 96 optimal weight: 40.0000 chunk 62 optimal weight: 2.9990 chunk 93 optimal weight: 0.0970 chunk 47 optimal weight: 20.0000 chunk 30 optimal weight: 8.9990 chunk 99 optimal weight: 7.9990 chunk 106 optimal weight: 30.0000 chunk 77 optimal weight: 20.0000 chunk 14 optimal weight: 8.9990 chunk 122 optimal weight: 20.0000 chunk 142 optimal weight: 50.0000 overall best weight: 5.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 moved from start: 0.6035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.097 13219 Z= 0.191 Angle : 0.546 7.190 17970 Z= 0.277 Chirality : 0.042 0.209 2041 Planarity : 0.005 0.134 2328 Dihedral : 4.517 42.355 1766 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.29 % Favored : 96.52 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.21), residues: 1610 helix: 1.17 (0.23), residues: 534 sheet: 0.25 (0.29), residues: 320 loop : 0.13 (0.23), residues: 756 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 1.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.2565 time to fit residues: 29.0318 Evaluate side-chains 60 residues out of total 1443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.583 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 149 optimal weight: 0.5980 chunk 136 optimal weight: 0.0020 chunk 145 optimal weight: 40.0000 chunk 87 optimal weight: 50.0000 chunk 63 optimal weight: 7.9990 chunk 114 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 131 optimal weight: 0.9990 chunk 137 optimal weight: 6.9990 chunk 144 optimal weight: 0.2980 chunk 95 optimal weight: 30.0000 overall best weight: 1.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 509 ASN ** E 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 45 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6698 moved from start: 0.6087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.098 13219 Z= 0.146 Angle : 0.516 7.026 17970 Z= 0.260 Chirality : 0.041 0.202 2041 Planarity : 0.005 0.133 2328 Dihedral : 4.306 39.282 1766 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.86 % Favored : 96.96 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 1.03 % 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: 0.82 (0.21), residues: 1610 helix: 1.27 (0.24), residues: 534 sheet: 0.36 (0.29), residues: 309 loop : 0.24 (0.23), residues: 767 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 1.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.2599 time to fit residues: 30.1059 Evaluate side-chains 61 residues out of total 1443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 1.517 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 153 optimal weight: 20.0000 chunk 93 optimal weight: 40.0000 chunk 72 optimal weight: 50.0000 chunk 106 optimal weight: 20.0000 chunk 161 optimal weight: 6.9990 chunk 148 optimal weight: 7.9990 chunk 128 optimal weight: 0.1980 chunk 13 optimal weight: 40.0000 chunk 99 optimal weight: 20.0000 chunk 78 optimal weight: 10.0000 chunk 102 optimal weight: 0.0370 overall best weight: 5.0466 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6739 moved from start: 0.6243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.097 13219 Z= 0.174 Angle : 0.529 6.900 17970 Z= 0.267 Chirality : 0.041 0.196 2041 Planarity : 0.005 0.132 2328 Dihedral : 4.368 41.090 1766 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.11 % Favored : 96.71 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 1.03 % 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: 0.74 (0.21), residues: 1610 helix: 1.29 (0.23), residues: 534 sheet: 0.18 (0.29), residues: 316 loop : 0.18 (0.23), residues: 760 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 1.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.2698 time to fit residues: 29.6667 Evaluate side-chains 60 residues out of total 1443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.628 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 0.9980 chunk 39 optimal weight: 0.0070 chunk 118 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 128 optimal weight: 30.0000 chunk 53 optimal weight: 9.9990 chunk 132 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 23 optimal weight: 40.0000 chunk 113 optimal weight: 9.9990 overall best weight: 2.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.051445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.040252 restraints weight = 86233.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.041808 restraints weight = 59266.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.043160 restraints weight = 39857.732| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.6321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.098 13219 Z= 0.149 Angle : 0.509 6.891 17970 Z= 0.258 Chirality : 0.041 0.197 2041 Planarity : 0.005 0.131 2328 Dihedral : 4.220 38.881 1766 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.92 % Favored : 96.89 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 1.03 % 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: 0.82 (0.21), residues: 1610 helix: 1.34 (0.24), residues: 533 sheet: 0.22 (0.29), residues: 312 loop : 0.24 (0.23), residues: 765 =============================================================================== Job complete usr+sys time: 1918.94 seconds wall clock time: 36 minutes 23.73 seconds (2183.73 seconds total)