Starting phenix.real_space_refine (version: 1.21rc1) on Tue Apr 25 10:34:57 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ysn_10903/04_2023/6ysn_10903_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ysn_10903/04_2023/6ysn_10903.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ysn_10903/04_2023/6ysn_10903.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ysn_10903/04_2023/6ysn_10903.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ysn_10903/04_2023/6ysn_10903_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ysn_10903/04_2023/6ysn_10903_updated.pdb" } resolution = 3.0 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= -0.000 sd= 0.010 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: 6 Type Number sf(0) Gaussians S 116 5.16 5 Cl 4 4.86 5 C 12948 2.51 5 N 3288 2.21 5 O 3476 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 26": "OE1" <-> "OE2" Residue "A GLU 28": "OE1" <-> "OE2" Residue "A GLU 81": "OE1" <-> "OE2" Residue "A GLU 113": "OE1" <-> "OE2" Residue "A ARG 191": "NH1" <-> "NH2" Residue "A ARG 196": "NH1" <-> "NH2" Residue "A ARG 263": "NH1" <-> "NH2" Residue "A GLU 266": "OE1" <-> "OE2" Residue "A ARG 492": "NH1" <-> "NH2" Residue "A ARG 512": "NH1" <-> "NH2" Residue "A ARG 718": "NH1" <-> "NH2" Residue "B GLU 81": "OE1" <-> "OE2" Residue "B GLU 113": "OE1" <-> "OE2" Residue "B ARG 191": "NH1" <-> "NH2" Residue "B ARG 196": "NH1" <-> "NH2" Residue "B GLU 242": "OE1" <-> "OE2" Residue "B ARG 263": "NH1" <-> "NH2" Residue "B GLU 266": "OE1" <-> "OE2" Residue "B GLU 404": "OE1" <-> "OE2" Residue "B ARG 492": "NH1" <-> "NH2" Residue "B ARG 512": "NH1" <-> "NH2" Residue "B ARG 718": "NH1" <-> "NH2" Residue "C GLU 113": "OE1" <-> "OE2" Residue "C ARG 191": "NH1" <-> "NH2" Residue "C ARG 196": "NH1" <-> "NH2" Residue "C ARG 263": "NH1" <-> "NH2" Residue "C GLU 266": "OE1" <-> "OE2" Residue "C GLU 404": "OE1" <-> "OE2" Residue "C ARG 492": "NH1" <-> "NH2" Residue "C ARG 512": "NH1" <-> "NH2" Residue "C ARG 718": "NH1" <-> "NH2" Residue "D GLU 81": "OE1" <-> "OE2" Residue "D GLU 113": "OE1" <-> "OE2" Residue "D ARG 191": "NH1" <-> "NH2" Residue "D ARG 196": "NH1" <-> "NH2" Residue "D ARG 263": "NH1" <-> "NH2" Residue "D GLU 266": "OE1" <-> "OE2" Residue "D GLU 404": "OE1" <-> "OE2" Residue "D ARG 492": "NH1" <-> "NH2" Residue "D ARG 512": "NH1" <-> "NH2" Residue "D ARG 718": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 19844 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4925 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 7 Chain: "B" Number of atoms: 4925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4925 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 7 Chain: "C" Number of atoms: 4925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4925 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 7 Chain: "D" Number of atoms: 4925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4925 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 7 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'PJQ': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'PJQ': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'PJQ': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'PJQ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.46, per 1000 atoms: 0.53 Number of scatterers: 19844 At special positions: 0 Unit cell: (118.77, 118.77, 126.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 4 17.00 S 116 16.00 F 12 9.00 O 3476 8.00 N 3288 7.00 C 12948 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 181 " distance=2.04 Simple disulfide: pdb=" SG CYS B 176 " - pdb=" SG CYS B 181 " distance=2.04 Simple disulfide: pdb=" SG CYS C 176 " - pdb=" SG CYS C 181 " distance=2.04 Simple disulfide: pdb=" SG CYS D 176 " - pdb=" SG CYS D 181 " distance=2.04 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: 7.62 Conformation dependent library (CDL) restraints added in 3.1 seconds 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4664 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 123 helices and 0 sheets defined 57.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.12 Creating SS restraints... Processing helix chain 'A' and resid 32 through 34 No H-bonds generated for 'chain 'A' and resid 32 through 34' Processing helix chain 'A' and resid 73 through 79 Processing helix chain 'A' and resid 99 through 104 Processing helix chain 'A' and resid 111 through 114 No H-bonds generated for 'chain 'A' and resid 111 through 114' Processing helix chain 'A' and resid 145 through 152 Processing helix chain 'A' and resid 155 through 163 Processing helix chain 'A' and resid 179 through 183 Processing helix chain 'A' and resid 191 through 203 Processing helix chain 'A' and resid 206 through 210 Processing helix chain 'A' and resid 216 through 228 Processing helix chain 'A' and resid 230 through 233 No H-bonds generated for 'chain 'A' and resid 230 through 233' Processing helix chain 'A' and resid 238 through 258 removed outlier: 3.803A pdb=" N GLU A 242 " --> pdb=" O LYS A 238 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU A 243 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS A 253 " --> pdb=" O LYS A 249 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU A 256 " --> pdb=" O ALA A 252 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLN A 258 " --> pdb=" O ASP A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 269 No H-bonds generated for 'chain 'A' and resid 266 through 269' Processing helix chain 'A' and resid 290 through 295 Processing helix chain 'A' and resid 305 through 315 removed outlier: 3.501A pdb=" N LEU A 310 " --> pdb=" O ASN A 306 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR A 313 " --> pdb=" O GLN A 309 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 314 " --> pdb=" O LEU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 346 removed outlier: 3.746A pdb=" N LEU A 340 " --> pdb=" O THR A 336 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE A 341 " --> pdb=" O ILE A 337 " (cutoff:3.500A) Proline residue: A 342 - end of helix Processing helix chain 'A' and resid 356 through 358 No H-bonds generated for 'chain 'A' and resid 356 through 358' Processing helix chain 'A' and resid 363 through 379 removed outlier: 3.652A pdb=" N LEU A 375 " --> pdb=" O THR A 371 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 423 removed outlier: 3.710A pdb=" N LEU A 408 " --> pdb=" O GLU A 404 " (cutoff:3.500A) Proline residue: A 409 - end of helix removed outlier: 3.938A pdb=" N GLU A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET A 422 " --> pdb=" O GLU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 453 removed outlier: 3.904A pdb=" N ASN A 443 " --> pdb=" O ASP A 439 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TYR A 446 " --> pdb=" O MET A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 468 No H-bonds generated for 'chain 'A' and resid 466 through 468' Processing helix chain 'A' and resid 474 through 497 removed outlier: 3.533A pdb=" N GLU A 479 " --> pdb=" O THR A 475 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA A 480 " --> pdb=" O LEU A 476 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA A 483 " --> pdb=" O GLU A 479 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A 488 " --> pdb=" O ILE A 484 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER A 490 " --> pdb=" O ASN A 486 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LEU A 493 " --> pdb=" O SER A 489 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N ILE A 494 " --> pdb=" O SER A 490 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N SER A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N PHE A 497 " --> pdb=" O LEU A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 512 removed outlier: 3.588A pdb=" N ARG A 512 " --> pdb=" O ILE A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 542 removed outlier: 3.666A pdb=" N LEU A 538 " --> pdb=" O GLY A 534 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR A 539 " --> pdb=" O LEU A 535 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N TYR A 541 " --> pdb=" O GLN A 537 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N TYR A 542 " --> pdb=" O LEU A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 552 No H-bonds generated for 'chain 'A' and resid 550 through 552' Processing helix chain 'A' and resid 568 through 577 removed outlier: 3.677A pdb=" N GLN A 573 " --> pdb=" O PHE A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 588 Processing helix chain 'A' and resid 597 through 613 Processing helix chain 'A' and resid 616 through 629 removed outlier: 3.692A pdb=" N LEU A 620 " --> pdb=" O LEU A 616 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE A 621 " --> pdb=" O LEU A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 650 removed outlier: 3.555A pdb=" N TRP A 639 " --> pdb=" O ALA A 635 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER A 649 " --> pdb=" O LYS A 645 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N TYR A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 662 No H-bonds generated for 'chain 'A' and resid 659 through 662' Processing helix chain 'A' and resid 705 through 730 removed outlier: 4.139A pdb=" N ASN A 710 " --> pdb=" O SER A 706 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR A 713 " --> pdb=" O GLN A 709 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN A 714 " --> pdb=" O ASN A 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 34 No H-bonds generated for 'chain 'B' and resid 32 through 34' Processing helix chain 'B' and resid 73 through 79 Processing helix chain 'B' and resid 99 through 104 Processing helix chain 'B' and resid 111 through 114 No H-bonds generated for 'chain 'B' and resid 111 through 114' Processing helix chain 'B' and resid 145 through 152 Processing helix chain 'B' and resid 155 through 163 Processing helix chain 'B' and resid 179 through 183 Processing helix chain 'B' and resid 191 through 203 Processing helix chain 'B' and resid 206 through 210 Processing helix chain 'B' and resid 216 through 233 removed outlier: 3.952A pdb=" N LYS B 232 " --> pdb=" O LYS B 228 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL B 233 " --> pdb=" O GLU B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 258 removed outlier: 3.832A pdb=" N GLU B 242 " --> pdb=" O LYS B 238 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU B 243 " --> pdb=" O ALA B 239 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS B 253 " --> pdb=" O LYS B 249 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU B 256 " --> pdb=" O ALA B 252 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLN B 258 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 269 No H-bonds generated for 'chain 'B' and resid 266 through 269' Processing helix chain 'B' and resid 290 through 295 Processing helix chain 'B' and resid 305 through 315 removed outlier: 3.981A pdb=" N THR B 313 " --> pdb=" O GLN B 309 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU B 314 " --> pdb=" O LEU B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 346 removed outlier: 3.811A pdb=" N LEU B 340 " --> pdb=" O THR B 336 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE B 341 " --> pdb=" O ILE B 337 " (cutoff:3.500A) Proline residue: B 342 - end of helix Processing helix chain 'B' and resid 363 through 379 removed outlier: 3.657A pdb=" N LEU B 375 " --> pdb=" O THR B 371 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 423 removed outlier: 3.732A pdb=" N LEU B 408 " --> pdb=" O GLU B 404 " (cutoff:3.500A) Proline residue: B 409 - end of helix removed outlier: 3.500A pdb=" N LYS B 420 " --> pdb=" O TRP B 416 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLU B 421 " --> pdb=" O GLY B 417 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET B 422 " --> pdb=" O GLU B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 453 removed outlier: 3.907A pdb=" N ASN B 443 " --> pdb=" O ASP B 439 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TYR B 446 " --> pdb=" O MET B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 468 No H-bonds generated for 'chain 'B' and resid 466 through 468' Processing helix chain 'B' and resid 474 through 497 removed outlier: 3.555A pdb=" N GLU B 479 " --> pdb=" O THR B 475 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA B 480 " --> pdb=" O LEU B 476 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA B 483 " --> pdb=" O GLU B 479 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU B 488 " --> pdb=" O ILE B 484 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER B 490 " --> pdb=" O ASN B 486 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N LEU B 493 " --> pdb=" O SER B 489 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ILE B 494 " --> pdb=" O SER B 490 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N SER B 495 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N PHE B 497 " --> pdb=" O LEU B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 512 removed outlier: 3.585A pdb=" N ARG B 512 " --> pdb=" O ILE B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 542 removed outlier: 3.677A pdb=" N LEU B 538 " --> pdb=" O GLY B 534 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR B 539 " --> pdb=" O LEU B 535 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N TYR B 541 " --> pdb=" O GLN B 537 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N TYR B 542 " --> pdb=" O LEU B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 552 No H-bonds generated for 'chain 'B' and resid 550 through 552' Processing helix chain 'B' and resid 568 through 577 removed outlier: 3.679A pdb=" N GLN B 573 " --> pdb=" O PHE B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 588 Processing helix chain 'B' and resid 597 through 613 Processing helix chain 'B' and resid 616 through 629 removed outlier: 3.724A pdb=" N LEU B 620 " --> pdb=" O LEU B 616 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE B 621 " --> pdb=" O LEU B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 650 removed outlier: 3.521A pdb=" N TRP B 639 " --> pdb=" O ALA B 635 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER B 649 " --> pdb=" O LYS B 645 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N TYR B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 659 through 662 No H-bonds generated for 'chain 'B' and resid 659 through 662' Processing helix chain 'B' and resid 705 through 731 removed outlier: 4.206A pdb=" N ASN B 710 " --> pdb=" O SER B 706 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR B 713 " --> pdb=" O GLN B 709 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN B 714 " --> pdb=" O ASN B 710 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN B 731 " --> pdb=" O ALA B 727 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 34 No H-bonds generated for 'chain 'C' and resid 32 through 34' Processing helix chain 'C' and resid 73 through 79 Processing helix chain 'C' and resid 99 through 104 Processing helix chain 'C' and resid 111 through 114 No H-bonds generated for 'chain 'C' and resid 111 through 114' Processing helix chain 'C' and resid 145 through 152 Processing helix chain 'C' and resid 155 through 163 Processing helix chain 'C' and resid 179 through 183 Processing helix chain 'C' and resid 191 through 203 Processing helix chain 'C' and resid 206 through 210 Processing helix chain 'C' and resid 216 through 233 removed outlier: 3.942A pdb=" N LYS C 232 " --> pdb=" O LYS C 228 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL C 233 " --> pdb=" O GLU C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 258 removed outlier: 3.725A pdb=" N GLU C 242 " --> pdb=" O LYS C 238 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU C 243 " --> pdb=" O ALA C 239 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS C 253 " --> pdb=" O LYS C 249 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU C 256 " --> pdb=" O ALA C 252 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLN C 258 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 269 No H-bonds generated for 'chain 'C' and resid 266 through 269' Processing helix chain 'C' and resid 290 through 295 Processing helix chain 'C' and resid 305 through 315 removed outlier: 3.504A pdb=" N LEU C 310 " --> pdb=" O ASN C 306 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR C 313 " --> pdb=" O GLN C 309 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU C 314 " --> pdb=" O LEU C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 346 removed outlier: 3.779A pdb=" N LEU C 340 " --> pdb=" O THR C 336 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE C 341 " --> pdb=" O ILE C 337 " (cutoff:3.500A) Proline residue: C 342 - end of helix Processing helix chain 'C' and resid 363 through 379 removed outlier: 3.653A pdb=" N LEU C 375 " --> pdb=" O THR C 371 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR C 376 " --> pdb=" O ALA C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 423 removed outlier: 3.734A pdb=" N LEU C 408 " --> pdb=" O GLU C 404 " (cutoff:3.500A) Proline residue: C 409 - end of helix removed outlier: 3.938A pdb=" N GLU C 421 " --> pdb=" O GLY C 417 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N MET C 422 " --> pdb=" O GLU C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 453 removed outlier: 3.908A pdb=" N ASN C 443 " --> pdb=" O ASP C 439 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TYR C 446 " --> pdb=" O MET C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 468 No H-bonds generated for 'chain 'C' and resid 466 through 468' Processing helix chain 'C' and resid 474 through 497 removed outlier: 3.539A pdb=" N GLU C 479 " --> pdb=" O THR C 475 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA C 480 " --> pdb=" O LEU C 476 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA C 483 " --> pdb=" O GLU C 479 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU C 488 " --> pdb=" O ILE C 484 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER C 490 " --> pdb=" O ASN C 486 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N LEU C 493 " --> pdb=" O SER C 489 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N ILE C 494 " --> pdb=" O SER C 490 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N SER C 495 " --> pdb=" O LEU C 491 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LEU C 496 " --> pdb=" O ARG C 492 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N PHE C 497 " --> pdb=" O LEU C 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 504 through 512 removed outlier: 3.585A pdb=" N ARG C 512 " --> pdb=" O ILE C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 542 removed outlier: 3.665A pdb=" N LEU C 538 " --> pdb=" O GLY C 534 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR C 539 " --> pdb=" O LEU C 535 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N TYR C 541 " --> pdb=" O GLN C 537 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N TYR C 542 " --> pdb=" O LEU C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 550 through 552 No H-bonds generated for 'chain 'C' and resid 550 through 552' Processing helix chain 'C' and resid 568 through 577 removed outlier: 3.694A pdb=" N GLN C 573 " --> pdb=" O PHE C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 585 through 588 Processing helix chain 'C' and resid 597 through 613 Processing helix chain 'C' and resid 616 through 629 removed outlier: 3.709A pdb=" N LEU C 620 " --> pdb=" O LEU C 616 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE C 621 " --> pdb=" O LEU C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 650 removed outlier: 3.521A pdb=" N TRP C 639 " --> pdb=" O ALA C 635 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER C 649 " --> pdb=" O LYS C 645 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N TYR C 650 " --> pdb=" O LEU C 646 " (cutoff:3.500A) Processing helix chain 'C' and resid 659 through 662 No H-bonds generated for 'chain 'C' and resid 659 through 662' Processing helix chain 'C' and resid 705 through 731 removed outlier: 4.144A pdb=" N ASN C 710 " --> pdb=" O SER C 706 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR C 713 " --> pdb=" O GLN C 709 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN C 714 " --> pdb=" O ASN C 710 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN C 731 " --> pdb=" O ALA C 727 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 34 No H-bonds generated for 'chain 'D' and resid 32 through 34' Processing helix chain 'D' and resid 73 through 79 Processing helix chain 'D' and resid 99 through 104 Processing helix chain 'D' and resid 111 through 114 No H-bonds generated for 'chain 'D' and resid 111 through 114' Processing helix chain 'D' and resid 145 through 152 Processing helix chain 'D' and resid 155 through 163 Processing helix chain 'D' and resid 179 through 183 Processing helix chain 'D' and resid 191 through 203 Processing helix chain 'D' and resid 206 through 210 Processing helix chain 'D' and resid 216 through 228 Processing helix chain 'D' and resid 230 through 233 No H-bonds generated for 'chain 'D' and resid 230 through 233' Processing helix chain 'D' and resid 238 through 258 removed outlier: 3.822A pdb=" N GLU D 242 " --> pdb=" O LYS D 238 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU D 243 " --> pdb=" O ALA D 239 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS D 253 " --> pdb=" O LYS D 249 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU D 256 " --> pdb=" O ALA D 252 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLN D 258 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 269 No H-bonds generated for 'chain 'D' and resid 266 through 269' Processing helix chain 'D' and resid 290 through 295 Processing helix chain 'D' and resid 305 through 315 removed outlier: 3.983A pdb=" N THR D 313 " --> pdb=" O GLN D 309 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU D 314 " --> pdb=" O LEU D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 346 removed outlier: 3.779A pdb=" N LEU D 340 " --> pdb=" O THR D 336 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE D 341 " --> pdb=" O ILE D 337 " (cutoff:3.500A) Proline residue: D 342 - end of helix Processing helix chain 'D' and resid 363 through 379 removed outlier: 3.655A pdb=" N LEU D 375 " --> pdb=" O THR D 371 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR D 376 " --> pdb=" O ALA D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 423 removed outlier: 3.731A pdb=" N LEU D 408 " --> pdb=" O GLU D 404 " (cutoff:3.500A) Proline residue: D 409 - end of helix removed outlier: 3.938A pdb=" N GLU D 421 " --> pdb=" O GLY D 417 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET D 422 " --> pdb=" O GLU D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 453 removed outlier: 3.907A pdb=" N ASN D 443 " --> pdb=" O ASP D 439 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TYR D 446 " --> pdb=" O MET D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 468 No H-bonds generated for 'chain 'D' and resid 466 through 468' Processing helix chain 'D' and resid 474 through 497 removed outlier: 3.540A pdb=" N GLU D 479 " --> pdb=" O THR D 475 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA D 480 " --> pdb=" O LEU D 476 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA D 483 " --> pdb=" O GLU D 479 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU D 488 " --> pdb=" O ILE D 484 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER D 490 " --> pdb=" O ASN D 486 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N LEU D 493 " --> pdb=" O SER D 489 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N ILE D 494 " --> pdb=" O SER D 490 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N SER D 495 " --> pdb=" O LEU D 491 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N PHE D 497 " --> pdb=" O LEU D 493 " (cutoff:3.500A) Processing helix chain 'D' and resid 504 through 512 removed outlier: 3.589A pdb=" N ARG D 512 " --> pdb=" O ILE D 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 542 removed outlier: 3.675A pdb=" N LEU D 538 " --> pdb=" O GLY D 534 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR D 539 " --> pdb=" O LEU D 535 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N TYR D 541 " --> pdb=" O GLN D 537 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N TYR D 542 " --> pdb=" O LEU D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 550 through 552 No H-bonds generated for 'chain 'D' and resid 550 through 552' Processing helix chain 'D' and resid 568 through 577 removed outlier: 3.677A pdb=" N GLN D 573 " --> pdb=" O PHE D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 585 through 588 Processing helix chain 'D' and resid 597 through 613 Processing helix chain 'D' and resid 616 through 629 removed outlier: 3.720A pdb=" N LEU D 620 " --> pdb=" O LEU D 616 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE D 621 " --> pdb=" O LEU D 617 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 650 removed outlier: 3.532A pdb=" N TRP D 639 " --> pdb=" O ALA D 635 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER D 649 " --> pdb=" O LYS D 645 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N TYR D 650 " --> pdb=" O LEU D 646 " (cutoff:3.500A) Processing helix chain 'D' and resid 659 through 662 No H-bonds generated for 'chain 'D' and resid 659 through 662' Processing helix chain 'D' and resid 705 through 730 removed outlier: 4.152A pdb=" N ASN D 710 " --> pdb=" O SER D 706 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR D 713 " --> pdb=" O GLN D 709 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN D 714 " --> pdb=" O ASN D 710 " (cutoff:3.500A) 728 hydrogen bonds defined for protein. 2172 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: 5.88 Time building geometry restraints manager: 8.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3120 1.30 - 1.43: 5615 1.43 - 1.56: 11385 1.56 - 1.69: 8 1.69 - 1.82: 192 Bond restraints: 20320 Sorted by residual: bond pdb=" C02 PJQ A 901 " pdb=" O01 PJQ A 901 " ideal model delta sigma weight residual 1.222 1.405 -0.183 2.00e-02 2.50e+03 8.34e+01 bond pdb=" C02 PJQ B 901 " pdb=" O01 PJQ B 901 " ideal model delta sigma weight residual 1.222 1.405 -0.183 2.00e-02 2.50e+03 8.34e+01 bond pdb=" C02 PJQ C 901 " pdb=" O01 PJQ C 901 " ideal model delta sigma weight residual 1.222 1.404 -0.182 2.00e-02 2.50e+03 8.28e+01 bond pdb=" C02 PJQ D 801 " pdb=" O01 PJQ D 801 " ideal model delta sigma weight residual 1.222 1.404 -0.182 2.00e-02 2.50e+03 8.27e+01 bond pdb=" C14 PJQ C 901 " pdb=" F16 PJQ C 901 " ideal model delta sigma weight residual 1.334 1.432 -0.098 2.00e-02 2.50e+03 2.40e+01 ... (remaining 20315 not shown) Histogram of bond angle deviations from ideal: 100.18 - 107.19: 642 107.19 - 114.21: 11722 114.21 - 121.23: 10208 121.23 - 128.24: 4771 128.24 - 135.26: 209 Bond angle restraints: 27552 Sorted by residual: angle pdb=" N LEU A 349 " pdb=" CA LEU A 349 " pdb=" C LEU A 349 " ideal model delta sigma weight residual 114.04 108.43 5.61 1.24e+00 6.50e-01 2.04e+01 angle pdb=" N LEU B 349 " pdb=" CA LEU B 349 " pdb=" C LEU B 349 " ideal model delta sigma weight residual 114.04 108.48 5.56 1.24e+00 6.50e-01 2.01e+01 angle pdb=" N LEU D 349 " pdb=" CA LEU D 349 " pdb=" C LEU D 349 " ideal model delta sigma weight residual 114.04 108.50 5.54 1.24e+00 6.50e-01 1.99e+01 angle pdb=" N LEU C 349 " pdb=" CA LEU C 349 " pdb=" C LEU C 349 " ideal model delta sigma weight residual 114.04 108.52 5.52 1.24e+00 6.50e-01 1.98e+01 angle pdb=" C GLU C 28 " pdb=" N LEU C 29 " pdb=" CA LEU C 29 " ideal model delta sigma weight residual 121.19 127.16 -5.97 1.59e+00 3.96e-01 1.41e+01 ... (remaining 27547 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 10829 17.47 - 34.94: 1025 34.94 - 52.40: 188 52.40 - 69.87: 9 69.87 - 87.34: 13 Dihedral angle restraints: 12064 sinusoidal: 4916 harmonic: 7148 Sorted by residual: dihedral pdb=" CA ILE B 346 " pdb=" C ILE B 346 " pdb=" N ALA B 347 " pdb=" CA ALA B 347 " ideal model delta harmonic sigma weight residual 180.00 159.07 20.93 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA ILE D 346 " pdb=" C ILE D 346 " pdb=" N ALA D 347 " pdb=" CA ALA D 347 " ideal model delta harmonic sigma weight residual 180.00 159.10 20.90 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA ILE A 346 " pdb=" C ILE A 346 " pdb=" N ALA A 347 " pdb=" CA ALA A 347 " ideal model delta harmonic sigma weight residual 180.00 159.10 20.90 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 12061 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1938 0.036 - 0.072: 938 0.072 - 0.108: 166 0.108 - 0.144: 49 0.144 - 0.180: 1 Chirality restraints: 3092 Sorted by residual: chirality pdb=" CB ILE B 18 " pdb=" CA ILE B 18 " pdb=" CG1 ILE B 18 " pdb=" CG2 ILE B 18 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.13e-01 chirality pdb=" CA VAL A 458 " pdb=" N VAL A 458 " pdb=" C VAL A 458 " pdb=" CB VAL A 458 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.31e-01 chirality pdb=" CA VAL A 302 " pdb=" N VAL A 302 " pdb=" C VAL A 302 " pdb=" CB VAL A 302 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.28e-01 ... (remaining 3089 not shown) Planarity restraints: 3404 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 144 " -0.032 5.00e-02 4.00e+02 4.89e-02 3.83e+00 pdb=" N PRO A 145 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 145 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 145 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 144 " 0.032 5.00e-02 4.00e+02 4.88e-02 3.81e+00 pdb=" N PRO B 145 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 145 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 145 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 144 " -0.032 5.00e-02 4.00e+02 4.87e-02 3.79e+00 pdb=" N PRO D 145 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO D 145 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 145 " -0.027 5.00e-02 4.00e+02 ... (remaining 3401 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1853 2.74 - 3.28: 19092 3.28 - 3.82: 30344 3.82 - 4.36: 40288 4.36 - 4.90: 66507 Nonbonded interactions: 158084 Sorted by model distance: nonbonded pdb=" OG1 THR C 544 " pdb=" OE2 GLU C 549 " model vdw 2.202 2.440 nonbonded pdb=" OG1 THR A 544 " pdb=" OE2 GLU A 549 " model vdw 2.202 2.440 nonbonded pdb=" OG1 THR B 544 " pdb=" OE2 GLU B 549 " model vdw 2.204 2.440 nonbonded pdb=" OG1 THR D 544 " pdb=" OE2 GLU D 549 " model vdw 2.205 2.440 nonbonded pdb=" OH TYR B 374 " pdb=" O SER B 489 " model vdw 2.229 2.440 ... (remaining 158079 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 0.970 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: 5.750 Check model and map are aligned: 0.310 Set scattering table: 0.190 Process input model: 49.320 Find NCS groups from input model: 1.430 Set up NCS constraints: 0.120 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:12.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 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 : 0.006 0.183 20320 Z= 0.396 Angle : 0.707 7.104 27552 Z= 0.409 Chirality : 0.041 0.180 3092 Planarity : 0.005 0.049 3404 Dihedral : 13.657 87.339 7388 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer Outliers : 0.19 % 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: -4.49 (0.14), residues: 2360 helix: -2.95 (0.10), residues: 1596 sheet: None (None), residues: 0 loop : -2.57 (0.20), residues: 764 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 418 time to evaluate : 2.174 Fit side-chains outliers start: 4 outliers final: 9 residues processed: 422 average time/residue: 1.5541 time to fit residues: 726.1166 Evaluate side-chains 289 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 280 time to evaluate : 2.498 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 9 residues processed: 8 average time/residue: 0.3131 time to fit residues: 7.1512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 0.7980 chunk 181 optimal weight: 6.9990 chunk 100 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 122 optimal weight: 0.0370 chunk 97 optimal weight: 0.0030 chunk 188 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 140 optimal weight: 5.9990 chunk 217 optimal weight: 0.7980 overall best weight: 0.5268 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 GLN A 396 GLN A 551 ASN A 629 GLN B 247 GLN B 551 ASN B 629 GLN C 235 ASN C 247 GLN C 551 ASN C 629 GLN D 247 GLN D 551 ASN D 629 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 20320 Z= 0.131 Angle : 0.509 9.111 27552 Z= 0.256 Chirality : 0.038 0.136 3092 Planarity : 0.005 0.050 3404 Dihedral : 5.216 47.545 2632 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer Outliers : 2.13 % 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: -2.68 (0.16), residues: 2360 helix: -1.48 (0.12), residues: 1624 sheet: None (None), residues: 0 loop : -2.10 (0.21), residues: 736 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 267 time to evaluate : 2.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 15 residues processed: 286 average time/residue: 1.3792 time to fit residues: 443.1171 Evaluate side-chains 257 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 242 time to evaluate : 2.457 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 14 residues processed: 1 average time/residue: 0.2381 time to fit residues: 3.6757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 20.0000 chunk 67 optimal weight: 5.9990 chunk 181 optimal weight: 8.9990 chunk 148 optimal weight: 4.9990 chunk 60 optimal weight: 10.0000 chunk 218 optimal weight: 0.2980 chunk 235 optimal weight: 3.9990 chunk 194 optimal weight: 0.5980 chunk 216 optimal weight: 5.9990 chunk 74 optimal weight: 0.6980 chunk 175 optimal weight: 3.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 533 ASN A 551 ASN A 629 GLN B 533 ASN B 551 ASN B 629 GLN C 533 ASN C 551 ASN C 629 GLN D 533 ASN D 551 ASN D 629 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 20320 Z= 0.241 Angle : 0.564 11.060 27552 Z= 0.275 Chirality : 0.040 0.143 3092 Planarity : 0.004 0.049 3404 Dihedral : 5.440 49.821 2632 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer Outliers : 3.53 % 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: -1.96 (0.17), residues: 2360 helix: -0.94 (0.13), residues: 1624 sheet: None (None), residues: 0 loop : -1.81 (0.22), residues: 736 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 266 time to evaluate : 2.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 76 outliers final: 30 residues processed: 307 average time/residue: 1.3788 time to fit residues: 475.5726 Evaluate side-chains 291 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 261 time to evaluate : 2.334 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 25 residues processed: 5 average time/residue: 0.1794 time to fit residues: 4.9777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 6.9990 chunk 164 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 104 optimal weight: 6.9990 chunk 146 optimal weight: 2.9990 chunk 219 optimal weight: 0.8980 chunk 231 optimal weight: 0.6980 chunk 114 optimal weight: 0.7980 chunk 207 optimal weight: 10.0000 chunk 62 optimal weight: 0.5980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 ASN A 629 GLN B 235 ASN B 551 ASN B 629 GLN B 711 GLN C 551 ASN C 629 GLN D 551 ASN D 629 GLN D 711 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 20320 Z= 0.154 Angle : 0.503 10.263 27552 Z= 0.245 Chirality : 0.038 0.159 3092 Planarity : 0.004 0.048 3404 Dihedral : 5.378 59.971 2632 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer Outliers : 3.11 % 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: -1.27 (0.17), residues: 2360 helix: -0.45 (0.13), residues: 1620 sheet: None (None), residues: 0 loop : -1.47 (0.23), residues: 740 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 263 time to evaluate : 2.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 25 residues processed: 306 average time/residue: 1.4166 time to fit residues: 485.7530 Evaluate side-chains 265 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 240 time to evaluate : 2.345 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 23 residues processed: 2 average time/residue: 0.1928 time to fit residues: 3.9693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 0.1980 chunk 131 optimal weight: 8.9990 chunk 3 optimal weight: 10.0000 chunk 172 optimal weight: 4.9990 chunk 95 optimal weight: 6.9990 chunk 197 optimal weight: 0.4980 chunk 160 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 118 optimal weight: 2.9990 chunk 208 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 GLN A 533 ASN A 551 ASN A 629 GLN A 711 GLN B 235 ASN B 247 GLN B 533 ASN B 551 ASN B 629 GLN B 711 GLN C 247 GLN C 533 ASN C 551 ASN C 629 GLN C 711 GLN D 247 GLN D 533 ASN D 551 ASN D 629 GLN D 711 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 20320 Z= 0.182 Angle : 0.517 10.730 27552 Z= 0.250 Chirality : 0.039 0.139 3092 Planarity : 0.004 0.046 3404 Dihedral : 4.938 48.188 2632 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer Outliers : 3.06 % 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 (0.18), residues: 2360 helix: -0.24 (0.13), residues: 1620 sheet: None (None), residues: 0 loop : -1.33 (0.23), residues: 740 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 244 time to evaluate : 2.418 Fit side-chains outliers start: 66 outliers final: 33 residues processed: 284 average time/residue: 1.3854 time to fit residues: 443.7648 Evaluate side-chains 278 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 245 time to evaluate : 2.338 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 24 residues processed: 9 average time/residue: 1.1373 time to fit residues: 14.9479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 1.9990 chunk 208 optimal weight: 0.6980 chunk 45 optimal weight: 5.9990 chunk 136 optimal weight: 8.9990 chunk 57 optimal weight: 6.9990 chunk 232 optimal weight: 2.9990 chunk 192 optimal weight: 0.8980 chunk 107 optimal weight: 0.0370 chunk 19 optimal weight: 4.9990 chunk 76 optimal weight: 7.9990 chunk 121 optimal weight: 20.0000 overall best weight: 1.3262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 GLN A 533 ASN A 551 ASN A 629 GLN A 711 GLN B 235 ASN B 533 ASN B 551 ASN B 629 GLN B 711 GLN C 235 ASN C 247 GLN C 533 ASN C 551 ASN C 629 GLN C 711 GLN D 533 ASN D 551 ASN D 629 GLN D 711 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 20320 Z= 0.180 Angle : 0.507 10.776 27552 Z= 0.246 Chirality : 0.038 0.137 3092 Planarity : 0.004 0.046 3404 Dihedral : 4.871 48.642 2632 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer Outliers : 2.88 % 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: -0.78 (0.18), residues: 2360 helix: -0.10 (0.13), residues: 1620 sheet: None (None), residues: 0 loop : -1.24 (0.23), residues: 740 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 238 time to evaluate : 2.460 Fit side-chains outliers start: 62 outliers final: 35 residues processed: 278 average time/residue: 1.3043 time to fit residues: 410.3933 Evaluate side-chains 266 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 231 time to evaluate : 2.308 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 27 residues processed: 8 average time/residue: 0.2054 time to fit residues: 6.1342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 0.0770 chunk 26 optimal weight: 0.9990 chunk 132 optimal weight: 7.9990 chunk 169 optimal weight: 0.3980 chunk 131 optimal weight: 4.9990 chunk 195 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 chunk 231 optimal weight: 3.9990 chunk 144 optimal weight: 10.0000 chunk 141 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.8944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 GLN A 533 ASN A 551 ASN A 629 GLN A 711 GLN B 235 ASN B 533 ASN B 551 ASN B 629 GLN B 711 GLN C 235 ASN C 247 GLN C 533 ASN C 551 ASN C 629 GLN C 711 GLN D 443 ASN D 533 ASN D 551 ASN D 629 GLN D 711 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 20320 Z= 0.141 Angle : 0.472 10.029 27552 Z= 0.231 Chirality : 0.037 0.134 3092 Planarity : 0.004 0.046 3404 Dihedral : 4.685 47.762 2632 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer Outliers : 2.83 % 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: -0.45 (0.18), residues: 2360 helix: 0.18 (0.14), residues: 1616 sheet: None (None), residues: 0 loop : -1.16 (0.23), residues: 744 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 230 time to evaluate : 2.449 Fit side-chains outliers start: 61 outliers final: 39 residues processed: 266 average time/residue: 1.4056 time to fit residues: 423.2834 Evaluate side-chains 264 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 225 time to evaluate : 2.479 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 29 residues processed: 13 average time/residue: 0.9143 time to fit residues: 17.5698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 147 optimal weight: 10.0000 chunk 157 optimal weight: 0.7980 chunk 114 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 181 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 ASN A 270 ASN A 533 ASN A 551 ASN A 629 GLN A 711 GLN B 235 ASN B 247 GLN B 270 ASN B 533 ASN B 551 ASN B 629 GLN B 711 GLN C 235 ASN C 270 ASN C 533 ASN C 551 ASN C 629 GLN C 711 GLN D 235 ASN D 247 GLN D 270 ASN D 533 ASN D 551 ASN D 629 GLN D 711 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.036 20320 Z= 0.323 Angle : 0.590 11.696 27552 Z= 0.285 Chirality : 0.042 0.147 3092 Planarity : 0.004 0.047 3404 Dihedral : 5.147 49.473 2632 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer Outliers : 3.15 % 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: -0.80 (0.17), residues: 2360 helix: -0.12 (0.13), residues: 1616 sheet: None (None), residues: 0 loop : -1.22 (0.23), residues: 744 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 243 time to evaluate : 2.498 Fit side-chains outliers start: 68 outliers final: 32 residues processed: 279 average time/residue: 1.3301 time to fit residues: 420.5060 Evaluate side-chains 268 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 236 time to evaluate : 2.293 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 24 residues processed: 8 average time/residue: 0.1859 time to fit residues: 6.0345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 3.9990 chunk 221 optimal weight: 0.7980 chunk 202 optimal weight: 2.9990 chunk 215 optimal weight: 0.9980 chunk 129 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 169 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 194 optimal weight: 0.9990 chunk 203 optimal weight: 3.9990 chunk 214 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 533 ASN A 551 ASN A 629 GLN A 711 GLN B 235 ASN B 533 ASN B 551 ASN B 629 GLN B 711 GLN C 235 ASN C 533 ASN C 551 ASN C 629 GLN C 711 GLN D 533 ASN D 551 ASN D 629 GLN D 711 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 20320 Z= 0.148 Angle : 0.481 10.219 27552 Z= 0.236 Chirality : 0.038 0.134 3092 Planarity : 0.004 0.046 3404 Dihedral : 4.766 47.586 2632 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer Outliers : 2.13 % 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: -0.36 (0.18), residues: 2360 helix: 0.24 (0.14), residues: 1616 sheet: None (None), residues: 0 loop : -1.10 (0.23), residues: 744 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 223 time to evaluate : 2.416 Fit side-chains outliers start: 46 outliers final: 29 residues processed: 254 average time/residue: 1.2838 time to fit residues: 370.1769 Evaluate side-chains 249 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 220 time to evaluate : 2.117 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 25 residues processed: 4 average time/residue: 0.4084 time to fit residues: 5.3291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 2.9990 chunk 227 optimal weight: 5.9990 chunk 139 optimal weight: 4.9990 chunk 108 optimal weight: 0.6980 chunk 158 optimal weight: 5.9990 chunk 239 optimal weight: 1.9990 chunk 220 optimal weight: 5.9990 chunk 190 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 147 optimal weight: 0.8980 chunk 116 optimal weight: 6.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 ASN A 247 GLN A 533 ASN A 551 ASN A 629 GLN A 711 GLN B 235 ASN B 247 GLN B 533 ASN B 551 ASN B 629 GLN C 235 ASN C 533 ASN C 551 ASN C 629 GLN C 711 GLN D 235 ASN D 247 GLN D 533 ASN D 551 ASN D 629 GLN D 711 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 20320 Z= 0.255 Angle : 0.552 11.529 27552 Z= 0.267 Chirality : 0.040 0.143 3092 Planarity : 0.004 0.047 3404 Dihedral : 5.022 49.274 2632 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer Outliers : 2.18 % 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: -0.51 (0.18), residues: 2360 helix: 0.11 (0.13), residues: 1612 sheet: None (None), residues: 0 loop : -1.12 (0.23), residues: 748 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 224 time to evaluate : 2.351 Fit side-chains outliers start: 47 outliers final: 27 residues processed: 252 average time/residue: 1.3006 time to fit residues: 373.2322 Evaluate side-chains 249 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 222 time to evaluate : 2.389 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 24 residues processed: 3 average time/residue: 0.2050 time to fit residues: 4.5431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 3.9990 chunk 202 optimal weight: 0.7980 chunk 58 optimal weight: 9.9990 chunk 175 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 190 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 195 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 ASN A 533 ASN A 551 ASN A 629 GLN A 711 GLN B 235 ASN B 533 ASN B 551 ASN B 629 GLN C 235 ASN C 533 ASN C 551 ASN C 629 GLN C 711 GLN D 235 ASN D 533 ASN D 551 ASN D 629 GLN D 711 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.176544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.137013 restraints weight = 18924.510| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.34 r_work: 0.2921 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 20320 Z= 0.239 Angle : 0.542 11.268 27552 Z= 0.263 Chirality : 0.040 0.141 3092 Planarity : 0.004 0.048 3404 Dihedral : 5.007 48.982 2632 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer Outliers : 1.95 % 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: -0.53 (0.18), residues: 2360 helix: 0.09 (0.13), residues: 1616 sheet: None (None), residues: 0 loop : -1.12 (0.23), residues: 744 =============================================================================== Job complete usr+sys time: 6772.28 seconds wall clock time: 121 minutes 15.51 seconds (7275.51 seconds total)