Starting phenix.real_space_refine on Wed Feb 14 07:59:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxi_21438/02_2024/6vxi_21438_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxi_21438/02_2024/6vxi_21438.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxi_21438/02_2024/6vxi_21438.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxi_21438/02_2024/6vxi_21438.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxi_21438/02_2024/6vxi_21438_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxi_21438/02_2024/6vxi_21438_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 5794 2.51 5 N 1456 2.21 5 O 1590 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 96": "NH1" <-> "NH2" Residue "A GLU 138": "OE1" <-> "OE2" Residue "A ARG 147": "NH1" <-> "NH2" Residue "A GLU 159": "OE1" <-> "OE2" Residue "A ARG 160": "NH1" <-> "NH2" Residue "A ARG 246": "NH1" <-> "NH2" Residue "A GLU 285": "OE1" <-> "OE2" Residue "A GLU 344": "OE1" <-> "OE2" Residue "A ARG 426": "NH1" <-> "NH2" Residue "A GLU 451": "OE1" <-> "OE2" Residue "A ARG 482": "NH1" <-> "NH2" Residue "A GLU 585": "OE1" <-> "OE2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B ARG 147": "NH1" <-> "NH2" Residue "B GLU 159": "OE1" <-> "OE2" Residue "B ARG 160": "NH1" <-> "NH2" Residue "B ARG 246": "NH1" <-> "NH2" Residue "B GLU 285": "OE1" <-> "OE2" Residue "B GLU 344": "OE1" <-> "OE2" Residue "B ARG 426": "NH1" <-> "NH2" Residue "B GLU 451": "OE1" <-> "OE2" Residue "B ARG 482": "NH1" <-> "NH2" Residue "B GLU 585": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8898 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4405 Classifications: {'peptide': 566} Link IDs: {'PTRANS': 18, 'TRANS': 547} Chain breaks: 3 Chain: "B" Number of atoms: 4405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4405 Classifications: {'peptide': 566} Link IDs: {'PTRANS': 18, 'TRANS': 547} Chain breaks: 3 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'CLR': 1, 'MIX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.25, per 1000 atoms: 0.59 Number of scatterers: 8898 At special positions: 0 Unit cell: (104.55, 75.03, 127.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 58 16.00 O 1590 8.00 N 1456 7.00 C 5794 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 592 " - pdb=" SG CYS A 608 " distance=2.06 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS B 603 " distance=2.04 Simple disulfide: pdb=" SG CYS B 592 " - pdb=" SG CYS B 608 " distance=2.06 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: 3.33 Conformation dependent library (CDL) restraints added in 1.7 seconds 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2092 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 6 sheets defined 49.8% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.97 Creating SS restraints... Processing helix chain 'A' and resid 86 through 93 removed outlier: 3.788A pdb=" N LEU A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 117 No H-bonds generated for 'chain 'A' and resid 115 through 117' Processing helix chain 'A' and resid 136 through 146 removed outlier: 4.103A pdb=" N SER A 143 " --> pdb=" O ASN A 139 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 146 " --> pdb=" O PHE A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 163 removed outlier: 4.191A pdb=" N GLU A 159 " --> pdb=" O HIS A 155 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ARG A 160 " --> pdb=" O GLU A 156 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE A 161 " --> pdb=" O LYS A 157 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN A 162 " --> pdb=" O ASN A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 173 No H-bonds generated for 'chain 'A' and resid 171 through 173' Processing helix chain 'A' and resid 188 through 198 removed outlier: 3.653A pdb=" N LYS A 192 " --> pdb=" O GLY A 188 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG A 193 " --> pdb=" O GLY A 189 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER A 195 " --> pdb=" O ARG A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 233 removed outlier: 4.660A pdb=" N ASN A 222 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA A 223 " --> pdb=" O THR A 220 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL A 224 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU A 226 " --> pdb=" O ALA A 223 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU A 228 " --> pdb=" O LEU A 225 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET A 231 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS A 233 " --> pdb=" O ARG A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 279 removed outlier: 4.152A pdb=" N GLU A 278 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N SER A 279 " --> pdb=" O GLY A 275 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 274 through 279' Processing helix chain 'A' and resid 290 through 293 No H-bonds generated for 'chain 'A' and resid 290 through 293' Processing helix chain 'A' and resid 331 through 337 removed outlier: 4.539A pdb=" N ILE A 335 " --> pdb=" O LYS A 331 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N TYR A 336 " --> pdb=" O LEU A 332 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 331 through 337' Processing helix chain 'A' and resid 342 through 352 removed outlier: 4.031A pdb=" N ALA A 347 " --> pdb=" O LYS A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 390 removed outlier: 3.599A pdb=" N LYS A 382 " --> pdb=" O ARG A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 412 Processing helix chain 'A' and resid 420 through 445 removed outlier: 4.335A pdb=" N ILE A 423 " --> pdb=" O SER A 420 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N GLN A 424 " --> pdb=" O THR A 421 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ARG A 426 " --> pdb=" O ILE A 423 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ALA A 427 " --> pdb=" O GLN A 424 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLY A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL A 429 " --> pdb=" O ARG A 426 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU A 430 " --> pdb=" O ALA A 427 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU A 433 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR A 434 " --> pdb=" O PHE A 431 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR A 435 " --> pdb=" O PHE A 432 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N SER A 440 " --> pdb=" O GLN A 437 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N SER A 441 " --> pdb=" O CYS A 438 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL A 442 " --> pdb=" O PHE A 439 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER A 443 " --> pdb=" O SER A 440 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA A 444 " --> pdb=" O SER A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 461 Processing helix chain 'A' and resid 466 through 477 removed outlier: 3.520A pdb=" N SER A 476 " --> pdb=" O GLY A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 482 No H-bonds generated for 'chain 'A' and resid 479 through 482' Processing helix chain 'A' and resid 484 through 497 removed outlier: 5.028A pdb=" N PHE A 489 " --> pdb=" O PRO A 485 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE A 492 " --> pdb=" O ILE A 488 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N PHE A 495 " --> pdb=" O CYS A 491 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N MET A 496 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 528 removed outlier: 3.642A pdb=" N THR A 512 " --> pdb=" O VAL A 508 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA A 528 " --> pdb=" O ALA A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 542 removed outlier: 3.935A pdb=" N MET A 541 " --> pdb=" O ALA A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 549 No H-bonds generated for 'chain 'A' and resid 546 through 549' Processing helix chain 'A' and resid 563 through 570 removed outlier: 3.933A pdb=" N TRP A 567 " --> pdb=" O SER A 563 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU A 568 " --> pdb=" O TRP A 564 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N GLN A 569 " --> pdb=" O LEU A 565 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N TYR A 570 " --> pdb=" O SER A 566 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 563 through 570' Processing helix chain 'A' and resid 573 through 583 Processing helix chain 'A' and resid 610 through 617 removed outlier: 3.510A pdb=" N LYS A 616 " --> pdb=" O GLU A 612 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLN A 617 " --> pdb=" O TYR A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 649 removed outlier: 4.305A pdb=" N LYS A 628 " --> pdb=" O GLY A 625 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL A 631 " --> pdb=" O LYS A 628 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ALA A 634 " --> pdb=" O VAL A 631 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N CYS A 635 " --> pdb=" O ALA A 632 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL A 638 " --> pdb=" O CYS A 635 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ILE A 639 " --> pdb=" O MET A 636 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR A 642 " --> pdb=" O ILE A 639 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ILE A 643 " --> pdb=" O PHE A 640 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR A 645 " --> pdb=" O THR A 642 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU A 648 " --> pdb=" O TYR A 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 93 removed outlier: 3.787A pdb=" N LEU B 90 " --> pdb=" O LYS B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 117 No H-bonds generated for 'chain 'B' and resid 115 through 117' Processing helix chain 'B' and resid 136 through 146 removed outlier: 4.103A pdb=" N SER B 143 " --> pdb=" O ASN B 139 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU B 146 " --> pdb=" O PHE B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 163 removed outlier: 4.191A pdb=" N GLU B 159 " --> pdb=" O HIS B 155 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ARG B 160 " --> pdb=" O GLU B 156 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE B 161 " --> pdb=" O LYS B 157 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN B 162 " --> pdb=" O ASN B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 173 No H-bonds generated for 'chain 'B' and resid 171 through 173' Processing helix chain 'B' and resid 188 through 198 removed outlier: 3.653A pdb=" N LYS B 192 " --> pdb=" O GLY B 188 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG B 193 " --> pdb=" O GLY B 189 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER B 195 " --> pdb=" O ARG B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 233 removed outlier: 4.660A pdb=" N ASN B 222 " --> pdb=" O SER B 219 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA B 223 " --> pdb=" O THR B 220 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL B 224 " --> pdb=" O ALA B 221 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU B 226 " --> pdb=" O ALA B 223 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU B 228 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET B 231 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS B 233 " --> pdb=" O ARG B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 279 removed outlier: 4.152A pdb=" N GLU B 278 " --> pdb=" O LEU B 274 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N SER B 279 " --> pdb=" O GLY B 275 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 274 through 279' Processing helix chain 'B' and resid 290 through 293 No H-bonds generated for 'chain 'B' and resid 290 through 293' Processing helix chain 'B' and resid 331 through 337 removed outlier: 4.538A pdb=" N ILE B 335 " --> pdb=" O LYS B 331 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N TYR B 336 " --> pdb=" O LEU B 332 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL B 337 " --> pdb=" O ALA B 333 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 331 through 337' Processing helix chain 'B' and resid 342 through 352 removed outlier: 4.031A pdb=" N ALA B 347 " --> pdb=" O LYS B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 390 removed outlier: 3.599A pdb=" N LYS B 382 " --> pdb=" O ARG B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 412 Processing helix chain 'B' and resid 420 through 445 removed outlier: 4.334A pdb=" N ILE B 423 " --> pdb=" O SER B 420 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N GLN B 424 " --> pdb=" O THR B 421 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ARG B 426 " --> pdb=" O ILE B 423 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ALA B 427 " --> pdb=" O GLN B 424 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLY B 428 " --> pdb=" O ASN B 425 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL B 429 " --> pdb=" O ARG B 426 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU B 430 " --> pdb=" O ALA B 427 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU B 433 " --> pdb=" O LEU B 430 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR B 434 " --> pdb=" O PHE B 431 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR B 435 " --> pdb=" O PHE B 432 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N SER B 440 " --> pdb=" O GLN B 437 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N SER B 441 " --> pdb=" O CYS B 438 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL B 442 " --> pdb=" O PHE B 439 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER B 443 " --> pdb=" O SER B 440 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA B 444 " --> pdb=" O SER B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 461 Processing helix chain 'B' and resid 466 through 477 removed outlier: 3.520A pdb=" N SER B 476 " --> pdb=" O GLY B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 482 No H-bonds generated for 'chain 'B' and resid 479 through 482' Processing helix chain 'B' and resid 484 through 497 removed outlier: 5.028A pdb=" N PHE B 489 " --> pdb=" O PRO B 485 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE B 492 " --> pdb=" O ILE B 488 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE B 495 " --> pdb=" O CYS B 491 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N MET B 496 " --> pdb=" O ILE B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 528 removed outlier: 3.641A pdb=" N THR B 512 " --> pdb=" O VAL B 508 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA B 528 " --> pdb=" O ALA B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 542 removed outlier: 3.934A pdb=" N MET B 541 " --> pdb=" O ALA B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 549 No H-bonds generated for 'chain 'B' and resid 546 through 549' Processing helix chain 'B' and resid 563 through 570 removed outlier: 3.932A pdb=" N TRP B 567 " --> pdb=" O SER B 563 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU B 568 " --> pdb=" O TRP B 564 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N GLN B 569 " --> pdb=" O LEU B 565 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N TYR B 570 " --> pdb=" O SER B 566 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 563 through 570' Processing helix chain 'B' and resid 573 through 583 Processing helix chain 'B' and resid 610 through 617 removed outlier: 3.510A pdb=" N LYS B 616 " --> pdb=" O GLU B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 649 removed outlier: 4.305A pdb=" N LYS B 628 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL B 631 " --> pdb=" O LYS B 628 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ALA B 634 " --> pdb=" O VAL B 631 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N CYS B 635 " --> pdb=" O ALA B 632 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL B 638 " --> pdb=" O CYS B 635 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ILE B 639 " --> pdb=" O MET B 636 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR B 642 " --> pdb=" O ILE B 639 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ILE B 643 " --> pdb=" O PHE B 640 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR B 645 " --> pdb=" O THR B 642 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU B 648 " --> pdb=" O TYR B 645 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 37 through 40 removed outlier: 3.533A pdb=" N ASP A 105 " --> pdb=" O HIS A 40 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 75 through 77 removed outlier: 6.370A pdb=" N ILE A 238 " --> pdb=" O ASN A 76 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N GLY A 122 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N ASP A 210 " --> pdb=" O GLY A 122 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL A 124 " --> pdb=" O ASP A 210 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 256 through 260 removed outlier: 3.540A pdb=" N PHE A 266 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ALA A 260 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N LEU A 264 " --> pdb=" O ALA A 260 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 37 through 40 removed outlier: 3.534A pdb=" N ASP B 105 " --> pdb=" O HIS B 40 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 75 through 77 removed outlier: 6.372A pdb=" N ILE B 238 " --> pdb=" O ASN B 76 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N GLY B 122 " --> pdb=" O PHE B 208 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N ASP B 210 " --> pdb=" O GLY B 122 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL B 124 " --> pdb=" O ASP B 210 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 256 through 260 removed outlier: 3.540A pdb=" N PHE B 266 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ALA B 260 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N LEU B 264 " --> pdb=" O ALA B 260 " (cutoff:3.500A) 269 hydrogen bonds defined for protein. 633 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: 2.36 Time building geometry restraints manager: 3.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1384 1.29 - 1.42: 2375 1.42 - 1.55: 5230 1.55 - 1.68: 7 1.68 - 1.81: 94 Bond restraints: 9090 Sorted by residual: bond pdb=" CAY MIX B 701 " pdb=" NAU MIX B 701 " ideal model delta sigma weight residual 1.342 1.491 -0.149 2.00e-02 2.50e+03 5.58e+01 bond pdb=" CAZ MIX B 701 " pdb=" NAV MIX B 701 " ideal model delta sigma weight residual 1.343 1.465 -0.122 2.00e-02 2.50e+03 3.74e+01 bond pdb=" CBA MIX B 701 " pdb=" CBE MIX B 701 " ideal model delta sigma weight residual 1.442 1.554 -0.112 2.00e-02 2.50e+03 3.13e+01 bond pdb=" CBA MIX B 701 " pdb=" OAA MIX B 701 " ideal model delta sigma weight residual 1.254 1.156 0.098 2.00e-02 2.50e+03 2.43e+01 bond pdb=" CBB MIX B 701 " pdb=" CBD MIX B 701 " ideal model delta sigma weight residual 1.459 1.552 -0.093 2.00e-02 2.50e+03 2.18e+01 ... (remaining 9085 not shown) Histogram of bond angle deviations from ideal: 99.21 - 106.25: 195 106.25 - 113.29: 5017 113.29 - 120.33: 3755 120.33 - 127.37: 3267 127.37 - 134.41: 78 Bond angle restraints: 12312 Sorted by residual: angle pdb=" C ASP A 217 " pdb=" N SER A 218 " pdb=" CA SER A 218 " ideal model delta sigma weight residual 121.54 128.93 -7.39 1.91e+00 2.74e-01 1.50e+01 angle pdb=" C ASP B 217 " pdb=" N SER B 218 " pdb=" CA SER B 218 " ideal model delta sigma weight residual 121.54 128.90 -7.36 1.91e+00 2.74e-01 1.48e+01 angle pdb=" N SER A 218 " pdb=" CA SER A 218 " pdb=" C SER A 218 " ideal model delta sigma weight residual 110.80 118.07 -7.27 2.13e+00 2.20e-01 1.16e+01 angle pdb=" N SER B 218 " pdb=" CA SER B 218 " pdb=" C SER B 218 " ideal model delta sigma weight residual 110.80 118.05 -7.25 2.13e+00 2.20e-01 1.16e+01 angle pdb=" C ILE B 108 " pdb=" N ASN B 109 " pdb=" CA ASN B 109 " ideal model delta sigma weight residual 121.54 127.90 -6.36 1.91e+00 2.74e-01 1.11e+01 ... (remaining 12307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 4782 17.79 - 35.59: 517 35.59 - 53.38: 139 53.38 - 71.18: 18 71.18 - 88.97: 11 Dihedral angle restraints: 5467 sinusoidal: 2207 harmonic: 3260 Sorted by residual: dihedral pdb=" CB CYS A 603 " pdb=" SG CYS A 603 " pdb=" SG CYS B 603 " pdb=" CB CYS B 603 " ideal model delta sinusoidal sigma weight residual 93.00 18.11 74.89 1 1.00e+01 1.00e-02 7.10e+01 dihedral pdb=" CB CYS A 592 " pdb=" SG CYS A 592 " pdb=" SG CYS A 608 " pdb=" CB CYS A 608 " ideal model delta sinusoidal sigma weight residual 93.00 40.22 52.78 1 1.00e+01 1.00e-02 3.79e+01 dihedral pdb=" CB CYS B 592 " pdb=" SG CYS B 592 " pdb=" SG CYS B 608 " pdb=" CB CYS B 608 " ideal model delta sinusoidal sigma weight residual 93.00 40.23 52.77 1 1.00e+01 1.00e-02 3.79e+01 ... (remaining 5464 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1043 0.057 - 0.114: 312 0.114 - 0.172: 57 0.172 - 0.229: 8 0.229 - 0.286: 6 Chirality restraints: 1426 Sorted by residual: chirality pdb=" C13 CLR B 702 " pdb=" C12 CLR B 702 " pdb=" C14 CLR B 702 " pdb=" C17 CLR B 702 " both_signs ideal model delta sigma weight residual False -2.93 -2.65 -0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" C13 CLR A 701 " pdb=" C12 CLR A 701 " pdb=" C14 CLR A 701 " pdb=" C17 CLR A 701 " both_signs ideal model delta sigma weight residual False -2.93 -2.65 -0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CB ILE B 487 " pdb=" CA ILE B 487 " pdb=" CG1 ILE B 487 " pdb=" CG2 ILE B 487 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 1423 not shown) Planarity restraints: 1519 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 429 " -0.009 2.00e-02 2.50e+03 1.88e-02 3.54e+00 pdb=" C VAL A 429 " 0.033 2.00e-02 2.50e+03 pdb=" O VAL A 429 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU A 430 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 429 " 0.009 2.00e-02 2.50e+03 1.86e-02 3.47e+00 pdb=" C VAL B 429 " -0.032 2.00e-02 2.50e+03 pdb=" O VAL B 429 " 0.012 2.00e-02 2.50e+03 pdb=" N LEU B 430 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 622 " 0.029 5.00e-02 4.00e+02 4.34e-02 3.01e+00 pdb=" N PRO A 623 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 623 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 623 " 0.024 5.00e-02 4.00e+02 ... (remaining 1516 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 2715 2.81 - 3.33: 8209 3.33 - 3.85: 14459 3.85 - 4.38: 17279 4.38 - 4.90: 29255 Nonbonded interactions: 71917 Sorted by model distance: nonbonded pdb=" OG1 THR B 133 " pdb=" OD1 ASN B 387 " model vdw 2.281 2.440 nonbonded pdb=" OG1 THR A 133 " pdb=" OD1 ASN A 387 " model vdw 2.282 2.440 nonbonded pdb=" OH TYR B 494 " pdb=" O LYS B 500 " model vdw 2.297 2.440 nonbonded pdb=" OH TYR A 494 " pdb=" O LYS A 500 " model vdw 2.297 2.440 nonbonded pdb=" OD1 ASN B 436 " pdb=" OAD MIX B 701 " model vdw 2.306 2.440 ... (remaining 71912 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' and resid 35 through 654) selection = (chain 'B' and resid 35 through 654) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.430 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: 0.000 Extract box with map and model: 2.090 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 27.080 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.040 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 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 0.149 9090 Z= 0.551 Angle : 0.998 11.139 12312 Z= 0.502 Chirality : 0.058 0.286 1426 Planarity : 0.005 0.043 1519 Dihedral : 15.952 88.972 3366 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.50 % Favored : 90.32 % Rotamer: Outliers : 2.07 % Allowed : 11.83 % Favored : 86.10 % 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: -6.00 (0.17), residues: 1116 helix: -4.44 (0.09), residues: 566 sheet: -4.21 (0.49), residues: 44 loop : -3.26 (0.24), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 379 HIS 0.003 0.001 HIS A 375 PHE 0.021 0.003 PHE B 432 TYR 0.019 0.002 TYR A 463 ARG 0.006 0.001 ARG A 184 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 255 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 MET cc_start: 0.7721 (ttm) cc_final: 0.7503 (mtp) REVERT: A 230 ARG cc_start: 0.7886 (mtm-85) cc_final: 0.7601 (mtm110) REVERT: A 341 PHE cc_start: 0.7454 (m-80) cc_final: 0.7193 (m-80) REVERT: A 509 MET cc_start: 0.8156 (ttt) cc_final: 0.7923 (ttt) REVERT: A 565 LEU cc_start: 0.8828 (tt) cc_final: 0.8616 (tt) REVERT: A 636 MET cc_start: 0.8425 (tpp) cc_final: 0.8222 (mmm) REVERT: B 230 ARG cc_start: 0.7997 (mtm-85) cc_final: 0.7715 (mtm110) REVERT: B 353 SER cc_start: 0.5781 (OUTLIER) cc_final: 0.5362 (p) REVERT: B 424 GLN cc_start: 0.8856 (tm-30) cc_final: 0.8617 (tm-30) REVERT: B 481 MET cc_start: 0.7821 (mmm) cc_final: 0.7463 (ttt) REVERT: B 523 MET cc_start: 0.9116 (ttt) cc_final: 0.8809 (ttp) REVERT: B 605 TYR cc_start: 0.6641 (m-80) cc_final: 0.5992 (m-10) REVERT: B 636 MET cc_start: 0.8495 (tpp) cc_final: 0.8176 (mmm) outliers start: 20 outliers final: 4 residues processed: 267 average time/residue: 0.2145 time to fit residues: 77.6230 Evaluate side-chains 180 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 175 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 544 CYS Chi-restraints excluded: chain B residue 561 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 2.9990 chunk 84 optimal weight: 8.9990 chunk 47 optimal weight: 0.9980 chunk 28 optimal weight: 10.0000 chunk 57 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS A 109 ASN A 158 ASN A 267 HIS A 393 GLN A 457 HIS A 583 HIS A 629 ASN B 40 HIS B 109 ASN B 158 ASN B 267 HIS B 393 GLN B 457 HIS B 583 HIS B 629 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 9090 Z= 0.311 Angle : 0.725 10.646 12312 Z= 0.365 Chirality : 0.043 0.172 1426 Planarity : 0.005 0.031 1519 Dihedral : 6.875 47.641 1355 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.71 % Favored : 92.11 % Rotamer: Outliers : 3.11 % Allowed : 21.47 % Favored : 75.41 % 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: -4.54 (0.20), residues: 1116 helix: -2.83 (0.16), residues: 566 sheet: -4.22 (0.48), residues: 48 loop : -3.01 (0.24), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 379 HIS 0.003 0.001 HIS B 583 PHE 0.025 0.002 PHE B 117 TYR 0.017 0.002 TYR A 605 ARG 0.007 0.000 ARG B 236 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 196 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 PHE cc_start: 0.7098 (t80) cc_final: 0.6892 (t80) REVERT: A 454 LEU cc_start: 0.8642 (tt) cc_final: 0.8352 (tt) REVERT: A 509 MET cc_start: 0.8402 (ttt) cc_final: 0.8125 (ttt) REVERT: A 565 LEU cc_start: 0.8923 (tt) cc_final: 0.8576 (tt) REVERT: A 612 GLU cc_start: 0.7595 (mp0) cc_final: 0.7371 (mp0) REVERT: A 636 MET cc_start: 0.8755 (tpp) cc_final: 0.8493 (mmm) REVERT: B 230 ARG cc_start: 0.8291 (mtm-85) cc_final: 0.8085 (mtm110) REVERT: B 385 PHE cc_start: 0.7608 (t80) cc_final: 0.7349 (t80) REVERT: B 454 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8634 (tp) REVERT: B 523 MET cc_start: 0.9064 (ttt) cc_final: 0.8861 (ttt) REVERT: B 605 TYR cc_start: 0.6652 (m-80) cc_final: 0.6347 (m-10) REVERT: B 612 GLU cc_start: 0.8042 (mp0) cc_final: 0.7694 (mp0) REVERT: B 636 MET cc_start: 0.8779 (tpp) cc_final: 0.8458 (mmm) outliers start: 30 outliers final: 21 residues processed: 213 average time/residue: 0.1879 time to fit residues: 56.8330 Evaluate side-chains 196 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 174 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 643 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 84 optimal weight: 8.9990 chunk 69 optimal weight: 0.0870 chunk 28 optimal weight: 8.9990 chunk 101 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 81 optimal weight: 20.0000 chunk 100 optimal weight: 3.9990 overall best weight: 1.2562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9090 Z= 0.195 Angle : 0.617 9.979 12312 Z= 0.305 Chirality : 0.041 0.189 1426 Planarity : 0.004 0.036 1519 Dihedral : 5.929 39.990 1352 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.44 % Favored : 92.38 % Rotamer: Outliers : 4.46 % Allowed : 22.72 % Favored : 72.82 % 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: -3.68 (0.22), residues: 1116 helix: -1.89 (0.19), residues: 568 sheet: -3.70 (0.56), residues: 44 loop : -2.94 (0.25), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 379 HIS 0.002 0.000 HIS B 267 PHE 0.014 0.002 PHE A 240 TYR 0.017 0.001 TYR A 276 ARG 0.003 0.000 ARG A 236 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 196 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 509 MET cc_start: 0.8468 (ttt) cc_final: 0.8219 (ttt) REVERT: A 523 MET cc_start: 0.8832 (ttt) cc_final: 0.8613 (ttt) REVERT: A 585 GLU cc_start: 0.8245 (tp30) cc_final: 0.8041 (tp30) REVERT: A 636 MET cc_start: 0.8703 (tpp) cc_final: 0.8486 (mmm) REVERT: B 211 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7740 (mp0) REVERT: B 230 ARG cc_start: 0.8398 (mtm-85) cc_final: 0.8040 (mtm110) REVERT: B 252 LEU cc_start: 0.8605 (tp) cc_final: 0.8160 (tt) REVERT: B 523 MET cc_start: 0.8957 (ttt) cc_final: 0.8678 (ttp) REVERT: B 527 ILE cc_start: 0.9200 (pt) cc_final: 0.8983 (pt) REVERT: B 605 TYR cc_start: 0.6491 (m-80) cc_final: 0.6290 (m-10) REVERT: B 612 GLU cc_start: 0.8106 (mp0) cc_final: 0.7894 (mp0) REVERT: B 636 MET cc_start: 0.8775 (tpp) cc_final: 0.8481 (mmm) outliers start: 43 outliers final: 28 residues processed: 223 average time/residue: 0.1771 time to fit residues: 57.3050 Evaluate side-chains 203 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 174 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 544 CYS Chi-restraints excluded: chain B residue 561 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 68 optimal weight: 9.9990 chunk 102 optimal weight: 2.9990 chunk 108 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 96 optimal weight: 0.1980 chunk 29 optimal weight: 7.9990 chunk 90 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9090 Z= 0.160 Angle : 0.580 9.932 12312 Z= 0.286 Chirality : 0.040 0.168 1426 Planarity : 0.003 0.039 1519 Dihedral : 5.287 39.810 1352 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.35 % Favored : 92.47 % Rotamer: Outliers : 4.05 % Allowed : 23.86 % Favored : 72.10 % 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: -3.22 (0.23), residues: 1116 helix: -1.41 (0.21), residues: 562 sheet: -3.58 (0.55), residues: 48 loop : -2.82 (0.26), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 379 HIS 0.002 0.000 HIS A 583 PHE 0.021 0.002 PHE B 266 TYR 0.017 0.001 TYR A 276 ARG 0.002 0.000 ARG B 236 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 200 time to evaluate : 1.018 Fit side-chains revert: symmetry clash REVERT: A 40 HIS cc_start: 0.7917 (OUTLIER) cc_final: 0.7710 (t-90) REVERT: A 138 GLU cc_start: 0.8320 (mp0) cc_final: 0.7989 (mp0) REVERT: A 198 MET cc_start: 0.7754 (mtp) cc_final: 0.7484 (mtp) REVERT: A 509 MET cc_start: 0.8443 (ttt) cc_final: 0.8202 (ttt) REVERT: A 523 MET cc_start: 0.8870 (ttt) cc_final: 0.8646 (ttt) REVERT: A 565 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8624 (tt) REVERT: A 585 GLU cc_start: 0.8181 (tp30) cc_final: 0.7940 (tp30) REVERT: A 636 MET cc_start: 0.8730 (tpp) cc_final: 0.8495 (mmm) REVERT: B 252 LEU cc_start: 0.8533 (tp) cc_final: 0.8081 (tt) REVERT: B 452 LYS cc_start: 0.8730 (tttp) cc_final: 0.8470 (tttm) REVERT: B 458 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.6834 (mp0) REVERT: B 523 MET cc_start: 0.8915 (ttt) cc_final: 0.8694 (ttt) REVERT: B 565 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8736 (tt) REVERT: B 585 GLU cc_start: 0.8314 (tp30) cc_final: 0.7892 (tp30) REVERT: B 636 MET cc_start: 0.8785 (tpp) cc_final: 0.8509 (mmm) outliers start: 39 outliers final: 23 residues processed: 224 average time/residue: 0.1694 time to fit residues: 55.7194 Evaluate side-chains 214 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 187 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 299 ASN Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 544 CYS Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 565 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 80 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 chunk 92 optimal weight: 0.3980 chunk 74 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 0.8980 chunk 97 optimal weight: 0.1980 chunk 27 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 391 ASN A 582 GLN ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9090 Z= 0.193 Angle : 0.605 11.900 12312 Z= 0.296 Chirality : 0.041 0.186 1426 Planarity : 0.003 0.040 1519 Dihedral : 5.113 40.119 1352 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.53 % Favored : 92.38 % Rotamer: Outliers : 4.77 % Allowed : 24.38 % Favored : 70.85 % 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: -2.92 (0.24), residues: 1116 helix: -1.17 (0.21), residues: 560 sheet: -3.31 (0.58), residues: 48 loop : -2.68 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 627 HIS 0.012 0.001 HIS B 40 PHE 0.016 0.002 PHE B 250 TYR 0.015 0.001 TYR A 605 ARG 0.006 0.000 ARG B 230 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 193 time to evaluate : 1.047 Fit side-chains revert: symmetry clash REVERT: A 40 HIS cc_start: 0.7971 (OUTLIER) cc_final: 0.7758 (t-90) REVERT: A 198 MET cc_start: 0.7600 (mtp) cc_final: 0.7342 (mtp) REVERT: A 416 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8679 (pp) REVERT: A 454 LEU cc_start: 0.9034 (tp) cc_final: 0.8584 (tt) REVERT: A 458 GLU cc_start: 0.7572 (mt-10) cc_final: 0.7082 (mp0) REVERT: A 509 MET cc_start: 0.8492 (ttt) cc_final: 0.8244 (ttt) REVERT: A 565 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8628 (tt) REVERT: A 636 MET cc_start: 0.8774 (tpp) cc_final: 0.8499 (mmm) REVERT: B 252 LEU cc_start: 0.8533 (tp) cc_final: 0.8096 (tt) REVERT: B 452 LYS cc_start: 0.8814 (tttp) cc_final: 0.8023 (ttmt) REVERT: B 458 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.6954 (mt-10) REVERT: B 523 MET cc_start: 0.8948 (ttt) cc_final: 0.8744 (ttt) REVERT: B 565 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8736 (tt) REVERT: B 636 MET cc_start: 0.8818 (tpp) cc_final: 0.8496 (mmm) outliers start: 46 outliers final: 29 residues processed: 224 average time/residue: 0.1574 time to fit residues: 52.7029 Evaluate side-chains 220 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 186 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 299 ASN Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 643 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 chunk 63 optimal weight: 7.9990 chunk 26 optimal weight: 0.3980 chunk 108 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 50 optimal weight: 0.0470 chunk 9 optimal weight: 2.9990 chunk 35 optimal weight: 0.0570 chunk 56 optimal weight: 10.0000 chunk 104 optimal weight: 1.9990 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9090 Z= 0.163 Angle : 0.583 9.944 12312 Z= 0.283 Chirality : 0.041 0.177 1426 Planarity : 0.003 0.041 1519 Dihedral : 4.920 39.858 1352 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.17 % Favored : 92.74 % Rotamer: Outliers : 4.98 % Allowed : 23.86 % Favored : 71.16 % 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: -2.71 (0.24), residues: 1116 helix: -1.02 (0.22), residues: 562 sheet: -2.80 (0.61), residues: 46 loop : -2.61 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 627 HIS 0.008 0.001 HIS B 40 PHE 0.024 0.002 PHE B 266 TYR 0.015 0.001 TYR A 605 ARG 0.004 0.000 ARG B 230 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 197 time to evaluate : 1.051 Fit side-chains revert: symmetry clash REVERT: A 454 LEU cc_start: 0.9016 (tp) cc_final: 0.8485 (tt) REVERT: A 565 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8742 (tt) REVERT: A 636 MET cc_start: 0.8759 (tpp) cc_final: 0.8535 (mmm) REVERT: B 199 GLU cc_start: 0.7435 (mp0) cc_final: 0.7143 (mp0) REVERT: B 211 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7646 (mp0) REVERT: B 452 LYS cc_start: 0.8813 (tttp) cc_final: 0.8012 (ttmt) REVERT: B 458 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.6897 (mt-10) REVERT: B 523 MET cc_start: 0.8946 (ttt) cc_final: 0.8706 (ttt) REVERT: B 540 LEU cc_start: 0.8145 (tp) cc_final: 0.7931 (tp) REVERT: B 565 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8820 (tt) REVERT: B 612 GLU cc_start: 0.8133 (mp0) cc_final: 0.7833 (mp0) REVERT: B 636 MET cc_start: 0.8795 (tpp) cc_final: 0.8480 (mmm) outliers start: 48 outliers final: 33 residues processed: 230 average time/residue: 0.1598 time to fit residues: 54.9239 Evaluate side-chains 220 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 183 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 299 ASN Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 544 CYS Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 643 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.0020 chunk 61 optimal weight: 8.9990 chunk 79 optimal weight: 6.9990 chunk 91 optimal weight: 8.9990 chunk 60 optimal weight: 1.9990 chunk 107 optimal weight: 0.0370 chunk 67 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.2072 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9090 Z= 0.193 Angle : 0.618 8.845 12312 Z= 0.303 Chirality : 0.041 0.204 1426 Planarity : 0.003 0.043 1519 Dihedral : 4.944 40.351 1352 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 5.39 % Allowed : 24.38 % Favored : 70.23 % 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: -2.60 (0.24), residues: 1116 helix: -0.91 (0.22), residues: 554 sheet: -2.51 (0.64), residues: 46 loop : -2.59 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 627 HIS 0.013 0.001 HIS A 40 PHE 0.021 0.002 PHE A 250 TYR 0.019 0.001 TYR A 276 ARG 0.003 0.000 ARG B 230 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 194 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 GLU cc_start: 0.8179 (mp0) cc_final: 0.7941 (mp0) REVERT: A 565 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8621 (tt) REVERT: B 199 GLU cc_start: 0.7437 (mp0) cc_final: 0.7167 (mp0) REVERT: B 211 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7592 (mp0) REVERT: B 458 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.6967 (mt-10) REVERT: B 523 MET cc_start: 0.8962 (ttt) cc_final: 0.8705 (ttt) REVERT: B 540 LEU cc_start: 0.8219 (tp) cc_final: 0.8018 (tp) REVERT: B 565 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8786 (tt) REVERT: B 612 GLU cc_start: 0.8189 (mp0) cc_final: 0.7941 (mp0) outliers start: 52 outliers final: 41 residues processed: 233 average time/residue: 0.1642 time to fit residues: 56.6520 Evaluate side-chains 226 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 181 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 592 CYS Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 299 ASN Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 544 CYS Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 592 CYS Chi-restraints excluded: chain B residue 643 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 8.9990 chunk 32 optimal weight: 3.9990 chunk 21 optimal weight: 9.9990 chunk 20 optimal weight: 7.9990 chunk 68 optimal weight: 8.9990 chunk 73 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 84 optimal weight: 8.9990 chunk 98 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 9090 Z= 0.400 Angle : 0.767 8.953 12312 Z= 0.384 Chirality : 0.048 0.344 1426 Planarity : 0.004 0.043 1519 Dihedral : 6.034 41.515 1352 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.68 % Favored : 90.14 % Rotamer: Outliers : 5.29 % Allowed : 24.79 % Favored : 69.92 % 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: -2.73 (0.24), residues: 1116 helix: -1.22 (0.21), residues: 574 sheet: -2.89 (0.60), residues: 48 loop : -2.36 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 627 HIS 0.010 0.001 HIS A 40 PHE 0.021 0.003 PHE B 266 TYR 0.023 0.002 TYR A 605 ARG 0.004 0.001 ARG B 426 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 192 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 MET cc_start: 0.7837 (mtp) cc_final: 0.7461 (mtp) REVERT: A 565 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8597 (tt) REVERT: B 211 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7657 (mp0) REVERT: B 405 LEU cc_start: 0.9465 (tp) cc_final: 0.9239 (mt) REVERT: B 446 GLU cc_start: 0.6385 (tm-30) cc_final: 0.6176 (tm-30) REVERT: B 458 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7162 (mt-10) REVERT: B 523 MET cc_start: 0.8974 (ttt) cc_final: 0.8688 (ttp) REVERT: B 565 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8611 (tt) REVERT: B 608 CYS cc_start: 0.5376 (p) cc_final: 0.5059 (p) REVERT: B 612 GLU cc_start: 0.8249 (mp0) cc_final: 0.7917 (mp0) outliers start: 51 outliers final: 38 residues processed: 227 average time/residue: 0.1604 time to fit residues: 54.4879 Evaluate side-chains 225 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 183 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 592 CYS Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 299 ASN Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 592 CYS Chi-restraints excluded: chain B residue 643 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 2.9990 chunk 100 optimal weight: 7.9990 chunk 103 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 78 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 chunk 90 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9090 Z= 0.184 Angle : 0.650 10.399 12312 Z= 0.317 Chirality : 0.043 0.308 1426 Planarity : 0.003 0.042 1519 Dihedral : 5.331 40.446 1352 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 4.67 % Allowed : 25.62 % Favored : 69.71 % 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: -2.46 (0.25), residues: 1116 helix: -0.96 (0.22), residues: 554 sheet: -2.57 (0.61), residues: 48 loop : -2.28 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 627 HIS 0.006 0.001 HIS A 40 PHE 0.025 0.002 PHE B 266 TYR 0.021 0.001 TYR A 276 ARG 0.002 0.000 ARG B 230 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 199 time to evaluate : 0.926 Fit side-chains revert: symmetry clash REVERT: A 138 GLU cc_start: 0.8325 (mp0) cc_final: 0.7914 (mp0) REVERT: A 198 MET cc_start: 0.7667 (mtp) cc_final: 0.7183 (mtp) REVERT: A 454 LEU cc_start: 0.9051 (tp) cc_final: 0.8775 (tp) REVERT: A 565 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8678 (tt) REVERT: A 636 MET cc_start: 0.8774 (tpp) cc_final: 0.8208 (mtp) REVERT: B 211 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7589 (mp0) REVERT: B 446 GLU cc_start: 0.6472 (tm-30) cc_final: 0.6173 (tm-30) REVERT: B 458 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.7098 (mp0) REVERT: B 523 MET cc_start: 0.8997 (ttt) cc_final: 0.8648 (ttp) REVERT: B 540 LEU cc_start: 0.8237 (tp) cc_final: 0.7908 (tp) REVERT: B 565 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8733 (tt) REVERT: B 608 CYS cc_start: 0.5196 (p) cc_final: 0.4911 (p) REVERT: B 636 MET cc_start: 0.8759 (tpp) cc_final: 0.8429 (mtp) outliers start: 45 outliers final: 35 residues processed: 223 average time/residue: 0.1571 time to fit residues: 52.4230 Evaluate side-chains 227 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 188 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 592 CYS Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 299 ASN Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 592 CYS Chi-restraints excluded: chain B residue 643 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 102 optimal weight: 0.5980 chunk 88 optimal weight: 0.0870 chunk 9 optimal weight: 5.9990 chunk 68 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 70 optimal weight: 10.0000 chunk 94 optimal weight: 4.9990 overall best weight: 2.3364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 9090 Z= 0.305 Angle : 0.704 10.373 12312 Z= 0.348 Chirality : 0.045 0.288 1426 Planarity : 0.004 0.043 1519 Dihedral : 5.590 39.458 1352 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.23 % Favored : 90.68 % Rotamer: Outliers : 4.77 % Allowed : 25.52 % Favored : 69.71 % 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: -2.54 (0.25), residues: 1116 helix: -1.04 (0.21), residues: 568 sheet: -2.61 (0.60), residues: 48 loop : -2.31 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 627 HIS 0.006 0.001 HIS A 40 PHE 0.026 0.002 PHE B 250 TYR 0.020 0.002 TYR A 276 ARG 0.004 0.000 ARG B 426 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 190 time to evaluate : 0.954 Fit side-chains revert: symmetry clash REVERT: A 565 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8588 (tt) REVERT: B 211 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7656 (mp0) REVERT: B 446 GLU cc_start: 0.6397 (tm-30) cc_final: 0.6165 (tm-30) REVERT: B 458 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.7032 (mp0) REVERT: B 523 MET cc_start: 0.8978 (ttt) cc_final: 0.8713 (ttp) REVERT: B 540 LEU cc_start: 0.8415 (tp) cc_final: 0.8148 (tp) REVERT: B 565 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8380 (tt) outliers start: 46 outliers final: 38 residues processed: 217 average time/residue: 0.1598 time to fit residues: 51.9245 Evaluate side-chains 228 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 186 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 299 ASN Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 592 CYS Chi-restraints excluded: chain B residue 643 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 10.0000 chunk 81 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 chunk 24 optimal weight: 8.9990 chunk 88 optimal weight: 0.1980 chunk 37 optimal weight: 4.9990 chunk 91 optimal weight: 7.9990 chunk 11 optimal weight: 7.9990 chunk 16 optimal weight: 0.8980 chunk 78 optimal weight: 6.9990 chunk 5 optimal weight: 0.1980 overall best weight: 2.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.157184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.124225 restraints weight = 13601.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.124229 restraints weight = 8301.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.124451 restraints weight = 6505.576| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 9090 Z= 0.337 Angle : 0.747 10.901 12312 Z= 0.366 Chirality : 0.046 0.280 1426 Planarity : 0.004 0.042 1519 Dihedral : 5.770 39.674 1352 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.42 % Favored : 91.49 % Rotamer: Outliers : 4.67 % Allowed : 25.83 % Favored : 69.50 % 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: -2.60 (0.24), residues: 1116 helix: -1.13 (0.21), residues: 574 sheet: -2.67 (0.59), residues: 48 loop : -2.29 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 627 HIS 0.006 0.001 HIS A 40 PHE 0.025 0.002 PHE A 250 TYR 0.022 0.002 TYR A 276 ARG 0.004 0.000 ARG B 426 =============================================================================== Job complete usr+sys time: 1906.85 seconds wall clock time: 35 minutes 38.90 seconds (2138.90 seconds total)