Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 00:23:27 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wiv_32537/04_2023/7wiv_32537_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wiv_32537/04_2023/7wiv_32537.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wiv_32537/04_2023/7wiv_32537.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wiv_32537/04_2023/7wiv_32537.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wiv_32537/04_2023/7wiv_32537_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wiv_32537/04_2023/7wiv_32537_updated.pdb" } resolution = 2.88 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= -0.001 sd= 0.049 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 14 5.16 5 C 5511 2.51 5 N 1553 2.21 5 O 1565 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 278": "NH1" <-> "NH2" Residue "A PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A ARG 361": "NH1" <-> "NH2" Residue "A ARG 364": "NH1" <-> "NH2" Residue "A PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 458": "NH1" <-> "NH2" Residue "A ARG 464": "NH1" <-> "NH2" Residue "A TYR 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 509": "NH1" <-> "NH2" Residue "A ASP 519": "OD1" <-> "OD2" Residue "A ARG 523": "NH1" <-> "NH2" Residue "A PHE 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 591": "OE1" <-> "OE2" Residue "A PHE 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 628": "OD1" <-> "OD2" Residue "A ARG 658": "NH1" <-> "NH2" Residue "A ASP 673": "OD1" <-> "OD2" Residue "A PHE 688": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 702": "OE1" <-> "OE2" Residue "A ARG 721": "NH1" <-> "NH2" Residue "A ARG 728": "NH1" <-> "NH2" Residue "A ASP 734": "OD1" <-> "OD2" Residue "A TYR 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 758": "NH1" <-> "NH2" Residue "A PHE 775": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 803": "NH1" <-> "NH2" Residue "A ARG 809": "NH1" <-> "NH2" Residue "A ASP 817": "OD1" <-> "OD2" Residue "A ARG 820": "NH1" <-> "NH2" Residue "A GLU 829": "OE1" <-> "OE2" Residue "B ARG 14": "NH1" <-> "NH2" Residue "B ARG 16": "NH1" <-> "NH2" Residue "B PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 52": "NH1" <-> "NH2" Residue "B ARG 76": "NH1" <-> "NH2" Residue "B PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 282": "NH1" <-> "NH2" Residue "B GLU 285": "OE1" <-> "OE2" Residue "B ARG 324": "NH1" <-> "NH2" Residue "B ASP 336": "OD1" <-> "OD2" Residue "B ASP 350": "OD1" <-> "OD2" Residue "B ARG 387": "NH1" <-> "NH2" Residue "B ASP 393": "OD1" <-> "OD2" Residue "B PHE 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 424": "NH1" <-> "NH2" Residue "B PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 436": "OD1" <-> "OD2" Residue "B PHE 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 447": "NH1" <-> "NH2" Residue "B ARG 454": "NH1" <-> "NH2" Residue "B ARG 482": "NH1" <-> "NH2" Residue "B GLU 503": "OE1" <-> "OE2" Residue "B GLU 505": "OE1" <-> "OE2" Residue "B ARG 532": "NH1" <-> "NH2" Residue "B ASP 541": "OD1" <-> "OD2" Residue "B ARG 544": "NH1" <-> "NH2" Residue "B PHE 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 8646 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4344 Classifications: {'peptide': 571} Link IDs: {'PTRANS': 25, 'TRANS': 545} Chain: "B" Number of atoms: 4271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4271 Classifications: {'peptide': 576} Link IDs: {'PTRANS': 25, 'TRANS': 550} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.89, per 1000 atoms: 0.57 Number of scatterers: 8646 At special positions: 0 Unit cell: (71.34, 95.94, 132.84, 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 14 16.00 P 3 15.00 O 1565 8.00 N 1553 7.00 C 5511 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: 3.47 Conformation dependent library (CDL) restraints added in 1.5 seconds 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2102 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 57 helices and 5 sheets defined 55.4% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 281 through 287 removed outlier: 4.098A pdb=" N ALA A 287 " --> pdb=" O SER A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 305 Processing helix chain 'A' and resid 309 through 322 removed outlier: 3.559A pdb=" N VAL A 315 " --> pdb=" O PHE A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 374 removed outlier: 3.811A pdb=" N HIS A 356 " --> pdb=" O THR A 352 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASP A 359 " --> pdb=" O LEU A 355 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG A 361 " --> pdb=" O VAL A 357 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE A 362 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 384 removed outlier: 3.883A pdb=" N THR A 383 " --> pdb=" O LEU A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 394 removed outlier: 3.969A pdb=" N LEU A 393 " --> pdb=" O SER A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 406 removed outlier: 3.564A pdb=" N LEU A 401 " --> pdb=" O ASP A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 429 removed outlier: 3.720A pdb=" N VAL A 416 " --> pdb=" O ALA A 412 " (cutoff:3.500A) Proline residue: A 419 - end of helix Processing helix chain 'A' and resid 431 through 452 removed outlier: 3.837A pdb=" N VAL A 436 " --> pdb=" O ARG A 432 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU A 437 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N PHE A 438 " --> pdb=" O ALA A 434 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLY A 439 " --> pdb=" O LEU A 435 " (cutoff:3.500A) Proline residue: A 440 - end of helix removed outlier: 3.512A pdb=" N TYR A 444 " --> pdb=" O PRO A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 478 removed outlier: 4.076A pdb=" N GLN A 463 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASN A 470 " --> pdb=" O ALA A 466 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY A 471 " --> pdb=" O GLU A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 485 Processing helix chain 'A' and resid 487 through 489 No H-bonds generated for 'chain 'A' and resid 487 through 489' Processing helix chain 'A' and resid 491 through 508 removed outlier: 3.665A pdb=" N ASP A 498 " --> pdb=" O ARG A 494 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N VAL A 505 " --> pdb=" O ILE A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 512 No H-bonds generated for 'chain 'A' and resid 510 through 512' Processing helix chain 'A' and resid 517 through 520 No H-bonds generated for 'chain 'A' and resid 517 through 520' Processing helix chain 'A' and resid 524 through 540 removed outlier: 3.510A pdb=" N LEU A 537 " --> pdb=" O ALA A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 548 No H-bonds generated for 'chain 'A' and resid 546 through 548' Processing helix chain 'A' and resid 550 through 555 Processing helix chain 'A' and resid 559 through 572 removed outlier: 4.334A pdb=" N ALA A 567 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N TYR A 568 " --> pdb=" O LEU A 564 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLY A 572 " --> pdb=" O TYR A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 586 removed outlier: 4.104A pdb=" N ALA A 579 " --> pdb=" O THR A 575 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR A 586 " --> pdb=" O HIS A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 654 Processing helix chain 'A' and resid 674 through 676 No H-bonds generated for 'chain 'A' and resid 674 through 676' Processing helix chain 'A' and resid 679 through 683 removed outlier: 3.623A pdb=" N TYR A 683 " --> pdb=" O ALA A 679 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 679 through 683' Processing helix chain 'A' and resid 700 through 704 removed outlier: 3.632A pdb=" N ILE A 704 " --> pdb=" O ALA A 700 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 700 through 704' Processing helix chain 'A' and resid 715 through 718 No H-bonds generated for 'chain 'A' and resid 715 through 718' Processing helix chain 'A' and resid 726 through 730 Processing helix chain 'A' and resid 735 through 737 No H-bonds generated for 'chain 'A' and resid 735 through 737' Processing helix chain 'A' and resid 752 through 762 Processing helix chain 'A' and resid 771 through 773 No H-bonds generated for 'chain 'A' and resid 771 through 773' Processing helix chain 'A' and resid 779 through 781 No H-bonds generated for 'chain 'A' and resid 779 through 781' Processing helix chain 'A' and resid 783 through 791 removed outlier: 3.710A pdb=" N ARG A 790 " --> pdb=" O GLN A 786 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 830 No H-bonds generated for 'chain 'A' and resid 827 through 830' Processing helix chain 'A' and resid 837 through 841 Processing helix chain 'B' and resid 18 through 24 removed outlier: 3.606A pdb=" N LEU B 22 " --> pdb=" O ILE B 18 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU B 23 " --> pdb=" O GLY B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 45 removed outlier: 3.773A pdb=" N ARG B 31 " --> pdb=" O SER B 27 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LEU B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N VAL B 39 " --> pdb=" O THR B 35 " (cutoff:3.500A) Proline residue: B 40 - end of helix Processing helix chain 'B' and resid 50 through 96 removed outlier: 3.693A pdb=" N TRP B 54 " --> pdb=" O GLN B 51 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LEU B 55 " --> pdb=" O ARG B 52 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TRP B 56 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY B 58 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N TRP B 59 " --> pdb=" O TRP B 56 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL B 65 " --> pdb=" O ALA B 62 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA B 66 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TRP B 68 " --> pdb=" O VAL B 65 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL B 73 " --> pdb=" O LEU B 70 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR B 74 " --> pdb=" O ASP B 71 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE B 77 " --> pdb=" O THR B 74 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE B 79 " --> pdb=" O ARG B 76 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU B 81 " --> pdb=" O GLY B 78 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE B 83 " --> pdb=" O GLU B 80 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA B 84 " --> pdb=" O LEU B 81 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLN B 90 " --> pdb=" O ASN B 87 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N HIS B 91 " --> pdb=" O HIS B 88 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL B 93 " --> pdb=" O GLN B 90 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ALA B 94 " --> pdb=" O HIS B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 104 No H-bonds generated for 'chain 'B' and resid 102 through 104' Processing helix chain 'B' and resid 107 through 118 removed outlier: 3.642A pdb=" N ALA B 111 " --> pdb=" O ALA B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 125 No H-bonds generated for 'chain 'B' and resid 122 through 125' Processing helix chain 'B' and resid 132 through 149 removed outlier: 3.543A pdb=" N LEU B 140 " --> pdb=" O THR B 136 " (cutoff:3.500A) Proline residue: B 142 - end of helix Processing helix chain 'B' and resid 154 through 192 removed outlier: 3.713A pdb=" N GLY B 163 " --> pdb=" O ALA B 159 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL B 164 " --> pdb=" O ALA B 160 " (cutoff:3.500A) Proline residue: B 165 - end of helix removed outlier: 3.561A pdb=" N ASP B 182 " --> pdb=" O ALA B 178 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA B 184 " --> pdb=" O ARG B 180 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR B 190 " --> pdb=" O ASP B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 201 Processing helix chain 'B' and resid 203 through 209 Processing helix chain 'B' and resid 212 through 225 Processing helix chain 'B' and resid 230 through 265 Proline residue: B 239 - end of helix removed outlier: 5.916A pdb=" N PHE B 244 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N SER B 245 " --> pdb=" O GLN B 241 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE B 253 " --> pdb=" O GLN B 249 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR B 263 " --> pdb=" O THR B 259 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE B 264 " --> pdb=" O ALA B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 283 Processing helix chain 'B' and resid 285 through 311 removed outlier: 3.506A pdb=" N LEU B 293 " --> pdb=" O ALA B 289 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA B 294 " --> pdb=" O VAL B 290 " (cutoff:3.500A) Proline residue: B 295 - end of helix removed outlier: 3.748A pdb=" N ARG B 306 " --> pdb=" O ALA B 302 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ILE B 307 " --> pdb=" O THR B 303 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY B 308 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL B 310 " --> pdb=" O ARG B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 380 Processing helix chain 'B' and resid 397 through 399 No H-bonds generated for 'chain 'B' and resid 397 through 399' Processing helix chain 'B' and resid 423 through 427 Processing helix chain 'B' and resid 440 through 443 No H-bonds generated for 'chain 'B' and resid 440 through 443' Processing helix chain 'B' and resid 449 through 452 No H-bonds generated for 'chain 'B' and resid 449 through 452' Processing helix chain 'B' and resid 458 through 460 No H-bonds generated for 'chain 'B' and resid 458 through 460' Processing helix chain 'B' and resid 478 through 485 Processing helix chain 'B' and resid 504 through 513 Processing helix chain 'B' and resid 555 through 557 No H-bonds generated for 'chain 'B' and resid 555 through 557' Processing helix chain 'B' and resid 560 through 570 removed outlier: 3.867A pdb=" N PHE B 564 " --> pdb=" O ARG B 560 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 610 through 613 Processing sheet with id= B, first strand: chain 'A' and resid 812 through 815 removed outlier: 6.635A pdb=" N VAL A 797 " --> pdb=" O THR A 639 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N LEU A 641 " --> pdb=" O VAL A 797 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N VAL A 799 " --> pdb=" O LEU A 641 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N GLY A 687 " --> pdb=" O ILE A 768 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N ASP A 770 " --> pdb=" O GLY A 687 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N VAL A 689 " --> pdb=" O ASP A 770 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 615 through 617 removed outlier: 7.579A pdb=" N PHE A 617 " --> pdb=" O GLN A 627 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N GLN A 627 " --> pdb=" O PHE A 617 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 544 through 549 removed outlier: 6.943A pdb=" N PHE B 539 " --> pdb=" O VAL B 546 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ASP B 548 " --> pdb=" O VAL B 537 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N VAL B 537 " --> pdb=" O ASP B 548 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG B 536 " --> pdb=" O THR B 361 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ARG B 521 " --> pdb=" O THR B 362 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N ILE B 364 " --> pdb=" O ARG B 521 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ILE B 523 " --> pdb=" O ILE B 364 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N GLY B 366 " --> pdb=" O ILE B 523 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N SER B 410 " --> pdb=" O LEU B 492 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ASP B 494 " --> pdb=" O SER B 410 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL B 412 " --> pdb=" O ASP B 494 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 337 through 339 removed outlier: 7.359A pdb=" N PHE B 339 " --> pdb=" O ASP B 350 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N ASP B 350 " --> pdb=" O PHE B 339 " (cutoff:3.500A) 352 hydrogen bonds defined for protein. 966 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: 2.43 Time building geometry restraints manager: 3.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 1405 1.27 - 1.41: 2094 1.41 - 1.54: 5206 1.54 - 1.67: 81 1.67 - 1.80: 25 Bond restraints: 8811 Sorted by residual: bond pdb=" O3A ANP A 901 " pdb=" PB ANP A 901 " ideal model delta sigma weight residual 1.700 1.550 0.150 2.00e-02 2.50e+03 5.61e+01 bond pdb=" C LYS B 486 " pdb=" O LYS B 486 " ideal model delta sigma weight residual 1.235 1.141 0.093 1.26e-02 6.30e+03 5.48e+01 bond pdb=" C VAL B 270 " pdb=" O VAL B 270 " ideal model delta sigma weight residual 1.240 1.171 0.068 1.26e-02 6.30e+03 2.95e+01 bond pdb=" N3B ANP A 901 " pdb=" PG ANP A 901 " ideal model delta sigma weight residual 1.795 1.689 0.106 2.00e-02 2.50e+03 2.79e+01 bond pdb=" C THR B 269 " pdb=" O THR B 269 " ideal model delta sigma weight residual 1.233 1.164 0.069 1.32e-02 5.74e+03 2.71e+01 ... (remaining 8806 not shown) Histogram of bond angle deviations from ideal: 99.74 - 106.62: 269 106.62 - 113.49: 5075 113.49 - 120.36: 3421 120.36 - 127.23: 3164 127.23 - 134.10: 114 Bond angle restraints: 12043 Sorted by residual: angle pdb=" N GLY B 388 " pdb=" CA GLY B 388 " pdb=" C GLY B 388 " ideal model delta sigma weight residual 110.21 119.62 -9.41 9.10e-01 1.21e+00 1.07e+02 angle pdb=" C THR B 267 " pdb=" CA THR B 267 " pdb=" CB THR B 267 " ideal model delta sigma weight residual 110.96 123.88 -12.92 1.54e+00 4.22e-01 7.04e+01 angle pdb=" N ALA B 442 " pdb=" CA ALA B 442 " pdb=" C ALA B 442 " ideal model delta sigma weight residual 114.64 102.34 12.30 1.52e+00 4.33e-01 6.55e+01 angle pdb=" N ILE B 531 " pdb=" CA ILE B 531 " pdb=" C ILE B 531 " ideal model delta sigma weight residual 113.71 106.97 6.74 9.50e-01 1.11e+00 5.03e+01 angle pdb=" N GLN A 454 " pdb=" CA GLN A 454 " pdb=" C GLN A 454 " ideal model delta sigma weight residual 114.16 104.32 9.84 1.48e+00 4.57e-01 4.42e+01 ... (remaining 12038 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 4714 17.31 - 34.62: 409 34.62 - 51.93: 64 51.93 - 69.25: 11 69.25 - 86.56: 7 Dihedral angle restraints: 5205 sinusoidal: 1944 harmonic: 3261 Sorted by residual: dihedral pdb=" C THR B 267 " pdb=" N THR B 267 " pdb=" CA THR B 267 " pdb=" CB THR B 267 " ideal model delta harmonic sigma weight residual -122.00 -139.89 17.89 0 2.50e+00 1.60e-01 5.12e+01 dihedral pdb=" CA ARG B 389 " pdb=" C ARG B 389 " pdb=" N VAL B 390 " pdb=" CA VAL B 390 " ideal model delta harmonic sigma weight residual 180.00 151.95 28.05 0 5.00e+00 4.00e-02 3.15e+01 dihedral pdb=" CA SER B 368 " pdb=" C SER B 368 " pdb=" N GLY B 369 " pdb=" CA GLY B 369 " ideal model delta harmonic sigma weight residual 180.00 152.37 27.63 0 5.00e+00 4.00e-02 3.05e+01 ... (remaining 5202 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 1422 0.115 - 0.229: 37 0.229 - 0.344: 5 0.344 - 0.459: 1 0.459 - 0.573: 1 Chirality restraints: 1466 Sorted by residual: chirality pdb=" CA THR B 267 " pdb=" N THR B 267 " pdb=" C THR B 267 " pdb=" CB THR B 267 " both_signs ideal model delta sigma weight residual False 2.53 1.95 0.57 2.00e-01 2.50e+01 8.22e+00 chirality pdb=" CA LEU B 268 " pdb=" N LEU B 268 " pdb=" C LEU B 268 " pdb=" CB LEU B 268 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 3.14e+00 chirality pdb=" CA LYS B 486 " pdb=" N LYS B 486 " pdb=" C LYS B 486 " pdb=" CB LYS B 486 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.81e+00 ... (remaining 1463 not shown) Planarity restraints: 1537 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 836 " -0.022 2.00e-02 2.50e+03 4.32e-02 1.87e+01 pdb=" C ARG A 836 " 0.075 2.00e-02 2.50e+03 pdb=" O ARG A 836 " -0.028 2.00e-02 2.50e+03 pdb=" N TYR A 837 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 342 " 0.019 2.00e-02 2.50e+03 3.84e-02 1.48e+01 pdb=" C ASP B 342 " -0.066 2.00e-02 2.50e+03 pdb=" O ASP B 342 " 0.025 2.00e-02 2.50e+03 pdb=" N GLY B 343 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 545 " 0.047 5.00e-02 4.00e+02 7.17e-02 8.22e+00 pdb=" N PRO A 546 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 546 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 546 " 0.039 5.00e-02 4.00e+02 ... (remaining 1534 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1213 2.75 - 3.29: 8642 3.29 - 3.82: 13678 3.82 - 4.36: 17567 4.36 - 4.90: 29568 Nonbonded interactions: 70668 Sorted by model distance: nonbonded pdb=" NH2 ARG A 364 " pdb=" OG1 THR B 228 " model vdw 2.209 2.520 nonbonded pdb=" OG SER B 27 " pdb=" OD1 ASP B 71 " model vdw 2.220 2.440 nonbonded pdb=" N3B ANP A 901 " pdb=" O2A ANP A 901 " model vdw 2.251 2.520 nonbonded pdb=" OD1 ASN B 221 " pdb=" N ALA B 222 " model vdw 2.273 2.520 nonbonded pdb=" O LEU B 70 " pdb=" OG1 THR B 74 " model vdw 2.285 2.440 ... (remaining 70663 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.470 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: 12.820 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 25.850 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 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:11.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 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 0.150 8811 Z= 0.537 Angle : 1.023 17.912 12043 Z= 0.626 Chirality : 0.056 0.573 1466 Planarity : 0.005 0.072 1537 Dihedral : 13.628 86.558 3103 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.36 % Favored : 90.20 % Rotamer Outliers : 0.68 % Cbeta Deviations : 0.38 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.21 (0.19), residues: 1143 helix: -3.11 (0.15), residues: 698 sheet: -3.96 (0.47), residues: 60 loop : -3.68 (0.26), residues: 385 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 71 time to evaluate : 1.061 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 76 average time/residue: 1.5160 time to fit residues: 122.2199 Evaluate side-chains 45 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 42 time to evaluate : 1.031 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 1 average time/residue: 0.2491 time to fit residues: 1.6864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 47 optimal weight: 0.0020 chunk 29 optimal weight: 0.4980 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 103 optimal weight: 0.3980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 HIS A 463 GLN A 597 HIS A 743 ASN A 752 GLN A 802 HIS B 11 ASN B 109 ASN B 237 GLN B 241 GLN B 426 ASN B 533 HIS B 568 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 8811 Z= 0.186 Angle : 0.664 10.770 12043 Z= 0.340 Chirality : 0.042 0.137 1466 Planarity : 0.005 0.065 1537 Dihedral : 5.724 30.829 1251 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.87 % Favored : 91.95 % Rotamer Outliers : 1.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.42 (0.22), residues: 1143 helix: -1.64 (0.18), residues: 708 sheet: -2.95 (0.51), residues: 70 loop : -3.12 (0.28), residues: 365 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 63 time to evaluate : 1.017 Fit side-chains outliers start: 17 outliers final: 3 residues processed: 75 average time/residue: 0.9810 time to fit residues: 80.4278 Evaluate side-chains 56 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 53 time to evaluate : 1.018 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 0.1467 time to fit residues: 1.5348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 6.9990 chunk 32 optimal weight: 0.4980 chunk 86 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 103 optimal weight: 0.0020 chunk 112 optimal weight: 1.9990 chunk 92 optimal weight: 0.0470 chunk 102 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 overall best weight: 0.4886 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 GLN A 743 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 8811 Z= 0.163 Angle : 0.603 7.870 12043 Z= 0.305 Chirality : 0.041 0.136 1466 Planarity : 0.004 0.062 1537 Dihedral : 5.234 28.893 1251 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.52 % Favored : 92.39 % Rotamer Outliers : 2.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.24), residues: 1143 helix: -0.79 (0.19), residues: 709 sheet: -2.15 (0.56), residues: 70 loop : -2.80 (0.29), residues: 364 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 56 time to evaluate : 1.249 Fit side-chains outliers start: 25 outliers final: 10 residues processed: 74 average time/residue: 1.0520 time to fit residues: 84.9194 Evaluate side-chains 56 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 46 time to evaluate : 1.026 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 9 residues processed: 1 average time/residue: 1.8529 time to fit residues: 3.2916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 104 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 743 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 8811 Z= 0.229 Angle : 0.619 9.441 12043 Z= 0.311 Chirality : 0.042 0.148 1466 Planarity : 0.004 0.063 1537 Dihedral : 5.124 29.246 1251 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.52 % Favored : 92.39 % Rotamer Outliers : 2.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.24), residues: 1143 helix: -0.44 (0.20), residues: 705 sheet: -1.79 (0.58), residues: 70 loop : -2.62 (0.29), residues: 368 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 51 time to evaluate : 1.044 Fit side-chains outliers start: 23 outliers final: 11 residues processed: 72 average time/residue: 1.1271 time to fit residues: 87.9511 Evaluate side-chains 58 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 47 time to evaluate : 1.057 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 10 residues processed: 1 average time/residue: 1.9008 time to fit residues: 3.3412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 1 optimal weight: 0.4980 chunk 82 optimal weight: 0.5980 chunk 45 optimal weight: 0.4980 chunk 94 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 56 optimal weight: 4.9990 chunk 98 optimal weight: 0.3980 chunk 27 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 627 GLN A 743 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 8811 Z= 0.164 Angle : 0.583 7.414 12043 Z= 0.293 Chirality : 0.040 0.135 1466 Planarity : 0.004 0.063 1537 Dihedral : 4.922 27.840 1251 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.09 % Favored : 92.83 % Rotamer Outliers : 2.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.25), residues: 1143 helix: -0.14 (0.20), residues: 710 sheet: -1.45 (0.62), residues: 70 loop : -2.49 (0.30), residues: 363 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 54 time to evaluate : 1.011 Fit side-chains outliers start: 24 outliers final: 10 residues processed: 76 average time/residue: 1.1250 time to fit residues: 92.7759 Evaluate side-chains 57 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 47 time to evaluate : 0.971 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 10 residues processed: 0 time to fit residues: 1.4062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 3.9990 chunk 99 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 110 optimal weight: 3.9990 chunk 91 optimal weight: 0.0060 chunk 51 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 GLN A 627 GLN A 743 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 8811 Z= 0.178 Angle : 0.588 7.599 12043 Z= 0.294 Chirality : 0.041 0.146 1466 Planarity : 0.004 0.062 1537 Dihedral : 4.830 28.463 1251 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.35 % Favored : 92.56 % Rotamer Outliers : 2.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.25), residues: 1143 helix: 0.07 (0.20), residues: 711 sheet: -1.09 (0.62), residues: 77 loop : -2.39 (0.31), residues: 355 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 50 time to evaluate : 1.032 Fit side-chains outliers start: 25 outliers final: 9 residues processed: 71 average time/residue: 1.0911 time to fit residues: 84.5996 Evaluate side-chains 60 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 51 time to evaluate : 1.021 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 9 residues processed: 0 time to fit residues: 1.3595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 80 optimal weight: 0.5980 chunk 92 optimal weight: 0.0060 chunk 61 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 GLN A 627 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 8811 Z= 0.227 Angle : 0.615 7.857 12043 Z= 0.307 Chirality : 0.042 0.160 1466 Planarity : 0.004 0.063 1537 Dihedral : 4.892 27.178 1251 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.52 % Favored : 92.39 % Rotamer Outliers : 2.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.25), residues: 1143 helix: 0.15 (0.20), residues: 706 sheet: -0.99 (0.62), residues: 77 loop : -2.32 (0.31), residues: 360 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 50 time to evaluate : 1.034 Fit side-chains outliers start: 22 outliers final: 11 residues processed: 69 average time/residue: 1.2244 time to fit residues: 91.4023 Evaluate side-chains 55 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 44 time to evaluate : 1.040 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 10 residues processed: 1 average time/residue: 1.1747 time to fit residues: 2.5879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 86 optimal weight: 0.9990 chunk 99 optimal weight: 0.6980 chunk 105 optimal weight: 7.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 GLN A 627 GLN A 743 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 8811 Z= 0.212 Angle : 0.611 9.241 12043 Z= 0.302 Chirality : 0.042 0.146 1466 Planarity : 0.004 0.062 1537 Dihedral : 4.858 27.917 1251 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.52 % Favored : 92.39 % Rotamer Outliers : 2.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.25), residues: 1143 helix: 0.20 (0.20), residues: 709 sheet: -0.87 (0.62), residues: 77 loop : -2.27 (0.31), residues: 357 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 45 time to evaluate : 1.017 Fit side-chains outliers start: 18 outliers final: 10 residues processed: 60 average time/residue: 1.0612 time to fit residues: 69.6663 Evaluate side-chains 52 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 42 time to evaluate : 0.940 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 10 residues processed: 0 time to fit residues: 1.2603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.0050 chunk 102 optimal weight: 0.0020 chunk 105 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 80 optimal weight: 0.0030 chunk 31 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 overall best weight: 0.3412 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 GLN A 627 GLN A 660 HIS A 743 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 8811 Z= 0.143 Angle : 0.584 9.375 12043 Z= 0.290 Chirality : 0.040 0.139 1466 Planarity : 0.004 0.062 1537 Dihedral : 4.684 28.055 1251 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.91 % Favored : 93.00 % Rotamer Outliers : 1.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.26), residues: 1143 helix: 0.42 (0.21), residues: 712 sheet: -0.70 (0.64), residues: 77 loop : -2.10 (0.32), residues: 354 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 50 time to evaluate : 1.060 Fit side-chains outliers start: 16 outliers final: 8 residues processed: 65 average time/residue: 1.0956 time to fit residues: 77.5007 Evaluate side-chains 57 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 49 time to evaluate : 1.011 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 1.4579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 71 optimal weight: 0.8980 chunk 96 optimal weight: 0.7980 chunk 27 optimal weight: 0.0010 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 GLN A 627 GLN A 743 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 8811 Z= 0.182 Angle : 0.600 9.122 12043 Z= 0.296 Chirality : 0.041 0.148 1466 Planarity : 0.004 0.061 1537 Dihedral : 4.668 27.579 1251 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.26 % Favored : 92.65 % Rotamer Outliers : 1.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.26), residues: 1143 helix: 0.48 (0.20), residues: 713 sheet: -0.67 (0.63), residues: 77 loop : -2.09 (0.32), residues: 353 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 47 time to evaluate : 1.111 Fit side-chains outliers start: 11 outliers final: 8 residues processed: 56 average time/residue: 1.1702 time to fit residues: 71.1789 Evaluate side-chains 54 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 46 time to evaluate : 0.985 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 7 residues processed: 1 average time/residue: 0.2324 time to fit residues: 1.6333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 0.0270 chunk 13 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 0.0980 chunk 79 optimal weight: 0.0980 chunk 5 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 overall best weight: 0.3438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 GLN A 627 GLN B 203 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.110686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.090929 restraints weight = 13786.017| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.20 r_work: 0.3046 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 8811 Z= 0.141 Angle : 0.577 9.584 12043 Z= 0.285 Chirality : 0.040 0.131 1466 Planarity : 0.004 0.060 1537 Dihedral : 4.544 26.508 1251 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.91 % Favored : 93.00 % Rotamer Outliers : 1.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.26), residues: 1143 helix: 0.68 (0.21), residues: 712 sheet: -0.53 (0.64), residues: 77 loop : -1.98 (0.32), residues: 354 =============================================================================== Job complete usr+sys time: 2638.26 seconds wall clock time: 47 minutes 43.92 seconds (2863.92 seconds total)