Starting phenix.real_space_refine (version: dev) on Wed Dec 14 07:38:02 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uw8_20919/12_2022/6uw8_20919.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uw8_20919/12_2022/6uw8_20919.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uw8_20919/12_2022/6uw8_20919.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uw8_20919/12_2022/6uw8_20919.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uw8_20919/12_2022/6uw8_20919.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uw8_20919/12_2022/6uw8_20919.pdb" } resolution = 4.02 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 117": "NH1" <-> "NH2" Residue "A GLU 137": "OE1" <-> "OE2" Residue "A GLU 144": "OE1" <-> "OE2" Residue "A ARG 148": "NH1" <-> "NH2" Residue "A ARG 188": "NH1" <-> "NH2" Residue "A ARG 225": "NH1" <-> "NH2" Residue "A ARG 226": "NH1" <-> "NH2" Residue "A PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 285": "OE1" <-> "OE2" Residue "A ASP 293": "OD1" <-> "OD2" Residue "A ARG 327": "NH1" <-> "NH2" Residue "A GLU 355": "OE1" <-> "OE2" Residue "A ARG 369": "NH1" <-> "NH2" Residue "A GLU 405": "OE1" <-> "OE2" Residue "A PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 462": "NH1" <-> "NH2" Residue "A ARG 464": "NH1" <-> "NH2" Residue "A ARG 567": "NH1" <-> "NH2" Residue "A GLU 631": "OE1" <-> "OE2" Residue "A ARG 690": "NH1" <-> "NH2" Residue "A GLU 704": "OE1" <-> "OE2" Residue "A ARG 714": "NH1" <-> "NH2" Residue "A PHE 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 719": "OE1" <-> "OE2" Residue "A ARG 729": "NH1" <-> "NH2" Residue "B ARG 117": "NH1" <-> "NH2" Residue "B GLU 137": "OE1" <-> "OE2" Residue "B GLU 144": "OE1" <-> "OE2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B ARG 188": "NH1" <-> "NH2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "B ARG 226": "NH1" <-> "NH2" Residue "B PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 285": "OE1" <-> "OE2" Residue "B ASP 293": "OD1" <-> "OD2" Residue "B ARG 327": "NH1" <-> "NH2" Residue "B GLU 355": "OE1" <-> "OE2" Residue "B ARG 369": "NH1" <-> "NH2" Residue "B GLU 405": "OE1" <-> "OE2" Residue "B PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 462": "NH1" <-> "NH2" Residue "B ARG 464": "NH1" <-> "NH2" Residue "B ARG 567": "NH1" <-> "NH2" Residue "B GLU 631": "OE1" <-> "OE2" Residue "B ARG 690": "NH1" <-> "NH2" Residue "B GLU 704": "OE1" <-> "OE2" Residue "B ARG 714": "NH1" <-> "NH2" Residue "B PHE 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 719": "OE1" <-> "OE2" Residue "B ARG 729": "NH1" <-> "NH2" Residue "C ARG 117": "NH1" <-> "NH2" Residue "C GLU 137": "OE1" <-> "OE2" Residue "C GLU 144": "OE1" <-> "OE2" Residue "C ARG 148": "NH1" <-> "NH2" Residue "C ARG 188": "NH1" <-> "NH2" Residue "C ARG 225": "NH1" <-> "NH2" Residue "C ARG 226": "NH1" <-> "NH2" Residue "C PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 285": "OE1" <-> "OE2" Residue "C ASP 293": "OD1" <-> "OD2" Residue "C ARG 327": "NH1" <-> "NH2" Residue "C GLU 355": "OE1" <-> "OE2" Residue "C ARG 369": "NH1" <-> "NH2" Residue "C GLU 405": "OE1" <-> "OE2" Residue "C PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 462": "NH1" <-> "NH2" Residue "C ARG 464": "NH1" <-> "NH2" Residue "C ARG 567": "NH1" <-> "NH2" Residue "C GLU 631": "OE1" <-> "OE2" Residue "C ARG 690": "NH1" <-> "NH2" Residue "C GLU 704": "OE1" <-> "OE2" Residue "C ARG 714": "NH1" <-> "NH2" Residue "C PHE 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 719": "OE1" <-> "OE2" Residue "C ARG 729": "NH1" <-> "NH2" Residue "D ARG 117": "NH1" <-> "NH2" Residue "D GLU 137": "OE1" <-> "OE2" Residue "D GLU 144": "OE1" <-> "OE2" Residue "D ARG 148": "NH1" <-> "NH2" Residue "D ARG 188": "NH1" <-> "NH2" Residue "D ARG 225": "NH1" <-> "NH2" Residue "D ARG 226": "NH1" <-> "NH2" Residue "D PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 285": "OE1" <-> "OE2" Residue "D ASP 293": "OD1" <-> "OD2" Residue "D ARG 327": "NH1" <-> "NH2" Residue "D GLU 355": "OE1" <-> "OE2" Residue "D ARG 369": "NH1" <-> "NH2" Residue "D GLU 405": "OE1" <-> "OE2" Residue "D PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 462": "NH1" <-> "NH2" Residue "D ARG 464": "NH1" <-> "NH2" Residue "D ARG 567": "NH1" <-> "NH2" Residue "D GLU 631": "OE1" <-> "OE2" Residue "D ARG 690": "NH1" <-> "NH2" Residue "D GLU 704": "OE1" <-> "OE2" Residue "D ARG 714": "NH1" <-> "NH2" Residue "D PHE 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 719": "OE1" <-> "OE2" Residue "D ARG 729": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 19640 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4910 Classifications: {'peptide': 602} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 589} Chain breaks: 3 Chain: "B" Number of atoms: 4910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4910 Classifications: {'peptide': 602} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 589} Chain breaks: 3 Chain: "C" Number of atoms: 4910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4910 Classifications: {'peptide': 602} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 589} Chain breaks: 3 Chain: "D" Number of atoms: 4910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4910 Classifications: {'peptide': 602} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 589} Chain breaks: 3 Time building chain proxies: 11.10, per 1000 atoms: 0.57 Number of scatterers: 19640 At special positions: 0 Unit cell: (158.4, 157.3, 122.1, 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 116 16.00 O 3464 8.00 N 3260 7.00 C 12800 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.49 Conformation dependent library (CDL) restraints added in 3.1 seconds 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4600 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 4 sheets defined 67.3% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 118 through 130 removed outlier: 3.580A pdb=" N SER A 128 " --> pdb=" O PHE A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 146 Processing helix chain 'A' and resid 154 through 163 Processing helix chain 'A' and resid 170 through 178 removed outlier: 3.603A pdb=" N ASN A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 197 removed outlier: 3.528A pdb=" N ASN A 197 " --> pdb=" O PHE A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 204 Processing helix chain 'A' and resid 217 through 225 removed outlier: 3.721A pdb=" N ILE A 221 " --> pdb=" O THR A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 237 Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 274 through 283 Processing helix chain 'A' and resid 298 through 307 Processing helix chain 'A' and resid 315 through 329 removed outlier: 4.082A pdb=" N ARG A 319 " --> pdb=" O ASP A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 336 removed outlier: 3.549A pdb=" N THR A 336 " --> pdb=" O GLU A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 352 Processing helix chain 'A' and resid 353 through 362 Processing helix chain 'A' and resid 402 through 410 Processing helix chain 'A' and resid 415 through 421 Processing helix chain 'A' and resid 425 through 461 removed outlier: 3.892A pdb=" N PHE A 436 " --> pdb=" O LYS A 432 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N LYS A 438 " --> pdb=" O LYS A 434 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N HIS A 439 " --> pdb=" O LYS A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 507 removed outlier: 6.644A pdb=" N PHE A 489 " --> pdb=" O LEU A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 516 removed outlier: 3.615A pdb=" N SER A 515 " --> pdb=" O ASP A 512 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE A 516 " --> pdb=" O LEU A 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 512 through 516' Processing helix chain 'A' and resid 521 through 542 Processing helix chain 'A' and resid 546 through 561 removed outlier: 4.259A pdb=" N CYS A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA A 554 " --> pdb=" O CYS A 550 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TRP A 559 " --> pdb=" O MET A 555 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA A 560 " --> pdb=" O ALA A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 568 removed outlier: 3.773A pdb=" N GLY A 568 " --> pdb=" O TYR A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 586 removed outlier: 4.157A pdb=" N MET A 578 " --> pdb=" O MET A 574 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ILE A 579 " --> pdb=" O TYR A 575 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLN A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 607 removed outlier: 4.619A pdb=" N VAL A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE A 597 " --> pdb=" O VAL A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 638 removed outlier: 3.770A pdb=" N VAL A 629 " --> pdb=" O PHE A 625 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N LEU A 630 " --> pdb=" O SER A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 666 Processing helix chain 'A' and resid 668 through 686 removed outlier: 4.141A pdb=" N LYS A 686 " --> pdb=" O GLU A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 707 Processing helix chain 'A' and resid 738 through 747 Processing helix chain 'B' and resid 118 through 130 removed outlier: 3.580A pdb=" N SER B 128 " --> pdb=" O PHE B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 146 Processing helix chain 'B' and resid 154 through 163 Processing helix chain 'B' and resid 170 through 178 removed outlier: 3.603A pdb=" N ASN B 178 " --> pdb=" O LYS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 197 removed outlier: 3.528A pdb=" N ASN B 197 " --> pdb=" O PHE B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 204 Processing helix chain 'B' and resid 217 through 225 removed outlier: 3.721A pdb=" N ILE B 221 " --> pdb=" O THR B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 237 Processing helix chain 'B' and resid 264 through 272 Processing helix chain 'B' and resid 274 through 283 Processing helix chain 'B' and resid 298 through 307 Processing helix chain 'B' and resid 315 through 329 removed outlier: 4.083A pdb=" N ARG B 319 " --> pdb=" O ASP B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 336 removed outlier: 3.548A pdb=" N THR B 336 " --> pdb=" O GLU B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 352 Processing helix chain 'B' and resid 353 through 362 Processing helix chain 'B' and resid 402 through 410 Processing helix chain 'B' and resid 415 through 421 Processing helix chain 'B' and resid 425 through 461 removed outlier: 3.893A pdb=" N PHE B 436 " --> pdb=" O LYS B 432 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N LYS B 438 " --> pdb=" O LYS B 434 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N HIS B 439 " --> pdb=" O LYS B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 507 removed outlier: 6.643A pdb=" N PHE B 489 " --> pdb=" O LEU B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 516 removed outlier: 3.616A pdb=" N SER B 515 " --> pdb=" O ASP B 512 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE B 516 " --> pdb=" O LEU B 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 512 through 516' Processing helix chain 'B' and resid 521 through 542 Processing helix chain 'B' and resid 546 through 561 removed outlier: 4.259A pdb=" N CYS B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA B 554 " --> pdb=" O CYS B 550 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N TRP B 559 " --> pdb=" O MET B 555 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 568 removed outlier: 3.773A pdb=" N GLY B 568 " --> pdb=" O TYR B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 586 removed outlier: 4.157A pdb=" N MET B 578 " --> pdb=" O MET B 574 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ILE B 579 " --> pdb=" O TYR B 575 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLN B 580 " --> pdb=" O SER B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 607 removed outlier: 4.619A pdb=" N VAL B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE B 597 " --> pdb=" O VAL B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 638 removed outlier: 3.770A pdb=" N VAL B 629 " --> pdb=" O PHE B 625 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N LEU B 630 " --> pdb=" O SER B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 666 Processing helix chain 'B' and resid 668 through 686 removed outlier: 4.141A pdb=" N LYS B 686 " --> pdb=" O GLU B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 707 Processing helix chain 'B' and resid 738 through 747 Processing helix chain 'C' and resid 118 through 130 removed outlier: 3.580A pdb=" N SER C 128 " --> pdb=" O PHE C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 146 Processing helix chain 'C' and resid 154 through 163 Processing helix chain 'C' and resid 170 through 178 removed outlier: 3.603A pdb=" N ASN C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 197 removed outlier: 3.527A pdb=" N ASN C 197 " --> pdb=" O PHE C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 204 Processing helix chain 'C' and resid 217 through 225 removed outlier: 3.721A pdb=" N ILE C 221 " --> pdb=" O THR C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 237 Processing helix chain 'C' and resid 264 through 272 Processing helix chain 'C' and resid 274 through 283 Processing helix chain 'C' and resid 298 through 307 Processing helix chain 'C' and resid 315 through 329 removed outlier: 4.082A pdb=" N ARG C 319 " --> pdb=" O ASP C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 336 removed outlier: 3.549A pdb=" N THR C 336 " --> pdb=" O GLU C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 352 Processing helix chain 'C' and resid 353 through 362 Processing helix chain 'C' and resid 402 through 410 Processing helix chain 'C' and resid 415 through 421 Processing helix chain 'C' and resid 425 through 461 removed outlier: 3.892A pdb=" N PHE C 436 " --> pdb=" O LYS C 432 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N LYS C 438 " --> pdb=" O LYS C 434 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N HIS C 439 " --> pdb=" O LYS C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 507 removed outlier: 6.644A pdb=" N PHE C 489 " --> pdb=" O LEU C 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 516 removed outlier: 3.615A pdb=" N SER C 515 " --> pdb=" O ASP C 512 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE C 516 " --> pdb=" O LEU C 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 512 through 516' Processing helix chain 'C' and resid 521 through 542 Processing helix chain 'C' and resid 546 through 561 removed outlier: 4.258A pdb=" N CYS C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA C 554 " --> pdb=" O CYS C 550 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TRP C 559 " --> pdb=" O MET C 555 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA C 560 " --> pdb=" O ALA C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 568 removed outlier: 3.773A pdb=" N GLY C 568 " --> pdb=" O TYR C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 586 removed outlier: 4.158A pdb=" N MET C 578 " --> pdb=" O MET C 574 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ILE C 579 " --> pdb=" O TYR C 575 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLN C 580 " --> pdb=" O SER C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 607 removed outlier: 4.619A pdb=" N VAL C 596 " --> pdb=" O PHE C 592 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE C 597 " --> pdb=" O VAL C 593 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 638 removed outlier: 3.770A pdb=" N VAL C 629 " --> pdb=" O PHE C 625 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N LEU C 630 " --> pdb=" O SER C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 666 Processing helix chain 'C' and resid 668 through 686 removed outlier: 4.141A pdb=" N LYS C 686 " --> pdb=" O GLU C 682 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 707 Processing helix chain 'C' and resid 738 through 747 Processing helix chain 'D' and resid 118 through 130 removed outlier: 3.580A pdb=" N SER D 128 " --> pdb=" O PHE D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 146 Processing helix chain 'D' and resid 154 through 163 Processing helix chain 'D' and resid 170 through 178 removed outlier: 3.603A pdb=" N ASN D 178 " --> pdb=" O LYS D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 197 removed outlier: 3.528A pdb=" N ASN D 197 " --> pdb=" O PHE D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 204 Processing helix chain 'D' and resid 217 through 225 removed outlier: 3.721A pdb=" N ILE D 221 " --> pdb=" O THR D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 237 Processing helix chain 'D' and resid 264 through 272 Processing helix chain 'D' and resid 274 through 283 Processing helix chain 'D' and resid 298 through 307 Processing helix chain 'D' and resid 315 through 329 removed outlier: 4.083A pdb=" N ARG D 319 " --> pdb=" O ASP D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 336 removed outlier: 3.549A pdb=" N THR D 336 " --> pdb=" O GLU D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 352 Processing helix chain 'D' and resid 353 through 362 Processing helix chain 'D' and resid 402 through 410 Processing helix chain 'D' and resid 415 through 421 Processing helix chain 'D' and resid 425 through 461 removed outlier: 3.893A pdb=" N PHE D 436 " --> pdb=" O LYS D 432 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N LYS D 438 " --> pdb=" O LYS D 434 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N HIS D 439 " --> pdb=" O LYS D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 483 through 507 removed outlier: 6.644A pdb=" N PHE D 489 " --> pdb=" O LEU D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 516 removed outlier: 3.615A pdb=" N SER D 515 " --> pdb=" O ASP D 512 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE D 516 " --> pdb=" O LEU D 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 512 through 516' Processing helix chain 'D' and resid 521 through 542 Processing helix chain 'D' and resid 546 through 561 removed outlier: 4.259A pdb=" N CYS D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA D 554 " --> pdb=" O CYS D 550 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N TRP D 559 " --> pdb=" O MET D 555 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA D 560 " --> pdb=" O ALA D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 568 removed outlier: 3.773A pdb=" N GLY D 568 " --> pdb=" O TYR D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 586 removed outlier: 4.158A pdb=" N MET D 578 " --> pdb=" O MET D 574 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ILE D 579 " --> pdb=" O TYR D 575 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLN D 580 " --> pdb=" O SER D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 607 removed outlier: 4.619A pdb=" N VAL D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE D 597 " --> pdb=" O VAL D 593 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 638 removed outlier: 3.770A pdb=" N VAL D 629 " --> pdb=" O PHE D 625 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N LEU D 630 " --> pdb=" O SER D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 666 Processing helix chain 'D' and resid 668 through 686 removed outlier: 4.141A pdb=" N LYS D 686 " --> pdb=" O GLU D 682 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 707 Processing helix chain 'D' and resid 738 through 747 Processing sheet with id=AA1, first strand: chain 'A' and resid 376 through 382 removed outlier: 5.267A pdb=" N THR A 378 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU A 389 " --> pdb=" O THR A 378 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TRP A 380 " --> pdb=" O SER A 387 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 376 through 382 removed outlier: 5.268A pdb=" N THR B 378 " --> pdb=" O LEU B 389 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU B 389 " --> pdb=" O THR B 378 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TRP B 380 " --> pdb=" O SER B 387 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 376 through 382 removed outlier: 5.267A pdb=" N THR C 378 " --> pdb=" O LEU C 389 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU C 389 " --> pdb=" O THR C 378 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TRP C 380 " --> pdb=" O SER C 387 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 376 through 382 removed outlier: 5.267A pdb=" N THR D 378 " --> pdb=" O LEU D 389 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU D 389 " --> pdb=" O THR D 378 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TRP D 380 " --> pdb=" O SER D 387 " (cutoff:3.500A) 1084 hydrogen bonds defined for protein. 3192 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.81 Time building geometry restraints manager: 8.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6154 1.34 - 1.46: 4591 1.46 - 1.58: 9115 1.58 - 1.70: 4 1.70 - 1.82: 196 Bond restraints: 20060 Sorted by residual: bond pdb=" CA ARG C 118 " pdb=" C ARG C 118 " ideal model delta sigma weight residual 1.524 1.601 -0.077 1.16e-02 7.43e+03 4.43e+01 bond pdb=" CA ARG B 118 " pdb=" C ARG B 118 " ideal model delta sigma weight residual 1.524 1.600 -0.076 1.16e-02 7.43e+03 4.29e+01 bond pdb=" CA ARG A 118 " pdb=" C ARG A 118 " ideal model delta sigma weight residual 1.524 1.590 -0.066 1.16e-02 7.43e+03 3.25e+01 bond pdb=" CA ARG D 118 " pdb=" C ARG D 118 " ideal model delta sigma weight residual 1.524 1.590 -0.066 1.16e-02 7.43e+03 3.24e+01 bond pdb=" C VAL A 154 " pdb=" N PRO A 155 " ideal model delta sigma weight residual 1.336 1.391 -0.055 1.20e-02 6.94e+03 2.07e+01 ... (remaining 20055 not shown) Histogram of bond angle deviations from ideal: 99.22 - 106.21: 333 106.21 - 113.19: 10753 113.19 - 120.17: 8089 120.17 - 127.16: 7744 127.16 - 134.14: 201 Bond angle restraints: 27120 Sorted by residual: angle pdb=" N LEU B 119 " pdb=" CA LEU B 119 " pdb=" C LEU B 119 " ideal model delta sigma weight residual 111.71 122.89 -11.18 1.15e+00 7.56e-01 9.45e+01 angle pdb=" N LEU C 119 " pdb=" CA LEU C 119 " pdb=" C LEU C 119 " ideal model delta sigma weight residual 111.71 122.85 -11.14 1.15e+00 7.56e-01 9.38e+01 angle pdb=" N LEU A 119 " pdb=" CA LEU A 119 " pdb=" C LEU A 119 " ideal model delta sigma weight residual 111.71 122.08 -10.37 1.15e+00 7.56e-01 8.13e+01 angle pdb=" N LEU D 119 " pdb=" CA LEU D 119 " pdb=" C LEU D 119 " ideal model delta sigma weight residual 111.71 122.07 -10.36 1.15e+00 7.56e-01 8.11e+01 angle pdb=" N ARG C 118 " pdb=" CA ARG C 118 " pdb=" C ARG C 118 " ideal model delta sigma weight residual 112.68 121.04 -8.36 1.33e+00 5.65e-01 3.95e+01 ... (remaining 27115 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.20: 10166 15.20 - 30.39: 1294 30.39 - 45.59: 388 45.59 - 60.78: 44 60.78 - 75.98: 24 Dihedral angle restraints: 11916 sinusoidal: 4832 harmonic: 7084 Sorted by residual: dihedral pdb=" C ARG B 118 " pdb=" N ARG B 118 " pdb=" CA ARG B 118 " pdb=" CB ARG B 118 " ideal model delta harmonic sigma weight residual -122.60 -134.59 11.99 0 2.50e+00 1.60e-01 2.30e+01 dihedral pdb=" C ARG C 118 " pdb=" N ARG C 118 " pdb=" CA ARG C 118 " pdb=" CB ARG C 118 " ideal model delta harmonic sigma weight residual -122.60 -134.58 11.98 0 2.50e+00 1.60e-01 2.30e+01 dihedral pdb=" CA GLU B 687 " pdb=" C GLU B 687 " pdb=" N SER B 688 " pdb=" CA SER B 688 " ideal model delta harmonic sigma weight residual -180.00 -158.06 -21.94 0 5.00e+00 4.00e-02 1.93e+01 ... (remaining 11913 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 2820 0.086 - 0.172: 259 0.172 - 0.257: 13 0.257 - 0.343: 4 0.343 - 0.429: 4 Chirality restraints: 3100 Sorted by residual: chirality pdb=" CA ARG B 118 " pdb=" N ARG B 118 " pdb=" C ARG B 118 " pdb=" CB ARG B 118 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.60e+00 chirality pdb=" CA ARG C 118 " pdb=" N ARG C 118 " pdb=" C ARG C 118 " pdb=" CB ARG C 118 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.56e+00 chirality pdb=" CA ARG A 118 " pdb=" N ARG A 118 " pdb=" C ARG A 118 " pdb=" CB ARG A 118 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.46e+00 ... (remaining 3097 not shown) Planarity restraints: 3360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG C 118 " 0.013 2.00e-02 2.50e+03 2.63e-02 6.93e+00 pdb=" C ARG C 118 " -0.045 2.00e-02 2.50e+03 pdb=" O ARG C 118 " 0.018 2.00e-02 2.50e+03 pdb=" N LEU C 119 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 118 " 0.013 2.00e-02 2.50e+03 2.62e-02 6.88e+00 pdb=" C ARG B 118 " -0.045 2.00e-02 2.50e+03 pdb=" O ARG B 118 " 0.018 2.00e-02 2.50e+03 pdb=" N LEU B 119 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 118 " 0.011 2.00e-02 2.50e+03 2.36e-02 5.56e+00 pdb=" C ARG A 118 " -0.041 2.00e-02 2.50e+03 pdb=" O ARG A 118 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU A 119 " 0.013 2.00e-02 2.50e+03 ... (remaining 3357 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 802 2.72 - 3.26: 19047 3.26 - 3.81: 30996 3.81 - 4.35: 36239 4.35 - 4.90: 61846 Nonbonded interactions: 148930 Sorted by model distance: nonbonded pdb=" NH2 ARG B 117 " pdb=" NH1 ARG B 118 " model vdw 2.173 3.200 nonbonded pdb=" NH2 ARG C 117 " pdb=" NH1 ARG C 118 " model vdw 2.175 3.200 nonbonded pdb=" NH2 ARG D 117 " pdb=" NH1 ARG D 118 " model vdw 2.203 3.200 nonbonded pdb=" NH2 ARG A 117 " pdb=" NH1 ARG A 118 " model vdw 2.207 3.200 nonbonded pdb=" O LEU C 268 " pdb=" OG1 THR C 272 " model vdw 2.286 2.440 ... (remaining 148925 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 116 5.16 5 C 12800 2.51 5 N 3260 2.21 5 O 3464 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.730 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: 0.020 Extract box with map and model: 5.810 Check model and map are aligned: 0.330 Convert atoms to be neutral: 0.190 Process input model: 49.310 Find NCS groups from input model: 1.280 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 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 : 0.005 0.083 20060 Z= 0.318 Angle : 0.900 11.178 27120 Z= 0.522 Chirality : 0.053 0.429 3100 Planarity : 0.006 0.059 3360 Dihedral : 14.813 75.977 7316 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 8.33 % 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: -4.15 (0.13), residues: 2376 helix: -2.28 (0.09), residues: 1576 sheet: -4.05 (0.39), residues: 76 loop : -3.29 (0.19), residues: 724 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 368 time to evaluate : 2.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 368 average time/residue: 0.3189 time to fit residues: 176.6923 Evaluate side-chains 219 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 2.571 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 0.9990 chunk 181 optimal weight: 0.0170 chunk 100 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 122 optimal weight: 4.9990 chunk 97 optimal weight: 8.9990 chunk 188 optimal weight: 6.9990 chunk 72 optimal weight: 8.9990 chunk 114 optimal weight: 0.8980 chunk 140 optimal weight: 0.9990 chunk 217 optimal weight: 10.0000 overall best weight: 1.1824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN A 197 ASN A 242 ASN A 339 ASN A 452 ASN A 561 ASN A 585 HIS B 242 ASN B 339 ASN B 585 HIS C 242 ASN C 339 ASN C 561 ASN C 585 HIS D 143 GLN D 197 ASN D 242 ASN D 339 ASN D 585 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.042 20060 Z= 0.159 Angle : 0.518 7.128 27120 Z= 0.273 Chirality : 0.036 0.130 3100 Planarity : 0.004 0.057 3360 Dihedral : 4.603 19.101 2620 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.16), residues: 2376 helix: -0.47 (0.12), residues: 1600 sheet: -2.86 (0.53), residues: 68 loop : -2.93 (0.20), residues: 708 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 335 time to evaluate : 2.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 335 average time/residue: 0.2713 time to fit residues: 146.2426 Evaluate side-chains 212 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 211 time to evaluate : 2.392 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2029 time to fit residues: 3.6032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 181 optimal weight: 7.9990 chunk 148 optimal weight: 0.9980 chunk 60 optimal weight: 20.0000 chunk 218 optimal weight: 1.9990 chunk 235 optimal weight: 2.9990 chunk 194 optimal weight: 4.9990 chunk 216 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 175 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 430 HIS A 561 ASN B 430 HIS B 452 ASN B 561 ASN C 430 HIS C 452 ASN C 561 ASN D 430 HIS D 561 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 20060 Z= 0.167 Angle : 0.511 6.934 27120 Z= 0.264 Chirality : 0.036 0.135 3100 Planarity : 0.004 0.058 3360 Dihedral : 4.273 18.665 2620 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.17), residues: 2376 helix: 0.28 (0.13), residues: 1600 sheet: -2.23 (0.62), residues: 68 loop : -2.68 (0.21), residues: 708 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 311 time to evaluate : 2.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 311 average time/residue: 0.2726 time to fit residues: 135.9096 Evaluate side-chains 204 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 2.478 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 0.9980 chunk 164 optimal weight: 5.9990 chunk 113 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 chunk 146 optimal weight: 3.9990 chunk 219 optimal weight: 6.9990 chunk 231 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 207 optimal weight: 5.9990 chunk 62 optimal weight: 8.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 ASN B 561 ASN B 646 GLN ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 561 ASN ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 561 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 20060 Z= 0.226 Angle : 0.554 7.684 27120 Z= 0.285 Chirality : 0.038 0.138 3100 Planarity : 0.004 0.059 3360 Dihedral : 4.242 18.318 2620 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.17), residues: 2376 helix: 0.55 (0.13), residues: 1596 sheet: -1.93 (0.67), residues: 68 loop : -2.53 (0.22), residues: 712 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 306 time to evaluate : 2.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 306 average time/residue: 0.2767 time to fit residues: 138.4668 Evaluate side-chains 206 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 2.419 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 0.8980 chunk 131 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 172 optimal weight: 0.9980 chunk 95 optimal weight: 6.9990 chunk 197 optimal weight: 0.0470 chunk 160 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 118 optimal weight: 0.9990 chunk 208 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 overall best weight: 1.1882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 ASN ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 561 ASN ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 561 ASN ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 561 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.044 20060 Z= 0.149 Angle : 0.497 8.004 27120 Z= 0.257 Chirality : 0.036 0.138 3100 Planarity : 0.004 0.062 3360 Dihedral : 4.039 17.228 2620 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.17), residues: 2376 helix: 0.76 (0.13), residues: 1596 sheet: -1.84 (0.68), residues: 68 loop : -2.36 (0.22), residues: 712 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 345 time to evaluate : 2.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 345 average time/residue: 0.2788 time to fit residues: 154.1298 Evaluate side-chains 232 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 232 time to evaluate : 2.546 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 2.9990 chunk 208 optimal weight: 5.9990 chunk 45 optimal weight: 0.5980 chunk 136 optimal weight: 4.9990 chunk 57 optimal weight: 0.0170 chunk 232 optimal weight: 2.9990 chunk 192 optimal weight: 20.0000 chunk 107 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 121 optimal weight: 8.9990 overall best weight: 1.5224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 ASN ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 561 ASN ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 561 ASN ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 561 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 20060 Z= 0.175 Angle : 0.524 8.742 27120 Z= 0.270 Chirality : 0.037 0.138 3100 Planarity : 0.004 0.064 3360 Dihedral : 4.005 17.455 2620 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.17), residues: 2376 helix: 0.88 (0.13), residues: 1596 sheet: -1.79 (0.70), residues: 68 loop : -2.33 (0.22), residues: 712 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 323 time to evaluate : 2.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 323 average time/residue: 0.2643 time to fit residues: 138.5614 Evaluate side-chains 226 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 226 time to evaluate : 2.307 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 132 optimal weight: 10.0000 chunk 169 optimal weight: 0.9990 chunk 131 optimal weight: 4.9990 chunk 195 optimal weight: 0.9980 chunk 129 optimal weight: 9.9990 chunk 231 optimal weight: 4.9990 chunk 144 optimal weight: 2.9990 chunk 141 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 561 ASN ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 197 ASN ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 561 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 20060 Z= 0.149 Angle : 0.505 7.773 27120 Z= 0.262 Chirality : 0.036 0.141 3100 Planarity : 0.004 0.061 3360 Dihedral : 3.946 15.369 2620 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.17), residues: 2376 helix: 0.97 (0.13), residues: 1596 sheet: -1.72 (0.71), residues: 68 loop : -2.24 (0.22), residues: 712 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 325 time to evaluate : 2.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 325 average time/residue: 0.2714 time to fit residues: 143.3998 Evaluate side-chains 232 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 232 time to evaluate : 2.557 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.4073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 0.6980 chunk 92 optimal weight: 0.9990 chunk 138 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 45 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 147 optimal weight: 2.9990 chunk 157 optimal weight: 10.0000 chunk 114 optimal weight: 0.0870 chunk 21 optimal weight: 3.9990 chunk 181 optimal weight: 7.9990 overall best weight: 0.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 561 ASN ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 561 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 20060 Z= 0.129 Angle : 0.520 9.362 27120 Z= 0.264 Chirality : 0.036 0.162 3100 Planarity : 0.003 0.056 3360 Dihedral : 3.844 14.350 2620 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.17), residues: 2376 helix: 1.07 (0.13), residues: 1588 sheet: -1.65 (0.72), residues: 68 loop : -2.24 (0.22), residues: 720 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 342 time to evaluate : 2.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 342 average time/residue: 0.2726 time to fit residues: 154.4044 Evaluate side-chains 240 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 240 time to evaluate : 3.128 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 4.9990 chunk 221 optimal weight: 8.9990 chunk 202 optimal weight: 0.7980 chunk 215 optimal weight: 0.9990 chunk 129 optimal weight: 9.9990 chunk 93 optimal weight: 4.9990 chunk 169 optimal weight: 0.7980 chunk 66 optimal weight: 9.9990 chunk 194 optimal weight: 7.9990 chunk 203 optimal weight: 0.9980 chunk 214 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 HIS ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 561 ASN ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 20060 Z= 0.165 Angle : 0.547 9.688 27120 Z= 0.278 Chirality : 0.037 0.174 3100 Planarity : 0.003 0.054 3360 Dihedral : 3.868 14.910 2620 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.18), residues: 2376 helix: 1.11 (0.13), residues: 1584 sheet: -1.60 (0.73), residues: 68 loop : -2.22 (0.22), residues: 724 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 310 time to evaluate : 2.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 310 average time/residue: 0.2628 time to fit residues: 134.4896 Evaluate side-chains 225 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 2.408 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 9.9990 chunk 227 optimal weight: 6.9990 chunk 139 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 158 optimal weight: 10.0000 chunk 239 optimal weight: 9.9990 chunk 220 optimal weight: 2.9990 chunk 190 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 585 HIS ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 561 ASN B 585 HIS ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 561 ASN C 585 HIS ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 20060 Z= 0.218 Angle : 0.587 9.723 27120 Z= 0.298 Chirality : 0.038 0.192 3100 Planarity : 0.004 0.052 3360 Dihedral : 4.008 16.009 2620 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.18), residues: 2376 helix: 1.07 (0.13), residues: 1588 sheet: 0.61 (0.86), residues: 48 loop : -2.24 (0.22), residues: 740 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 299 time to evaluate : 2.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 300 average time/residue: 0.2650 time to fit residues: 131.2868 Evaluate side-chains 213 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 2.486 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.4192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 1.9990 chunk 202 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 chunk 175 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 190 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 195 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 35 optimal weight: 0.0470 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 561 ASN ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 417 HIS ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.117100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.092043 restraints weight = 40199.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.094102 restraints weight = 27055.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.095523 restraints weight = 20627.166| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 20060 Z= 0.136 Angle : 0.537 8.899 27120 Z= 0.275 Chirality : 0.037 0.142 3100 Planarity : 0.003 0.054 3360 Dihedral : 3.861 15.482 2620 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.18), residues: 2376 helix: 1.15 (0.13), residues: 1584 sheet: -1.52 (0.75), residues: 68 loop : -2.11 (0.22), residues: 724 =============================================================================== Job complete usr+sys time: 3453.92 seconds wall clock time: 64 minutes 17.17 seconds (3857.17 seconds total)