Starting phenix.real_space_refine on Mon Mar 18 01:50:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uw8_20919/03_2024/6uw8_20919.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uw8_20919/03_2024/6uw8_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_20919/03_2024/6uw8_20919.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uw8_20919/03_2024/6uw8_20919.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uw8_20919/03_2024/6uw8_20919.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uw8_20919/03_2024/6uw8_20919.pdb" } resolution = 4.02 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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 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. 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 10.57, per 1000 atoms: 0.54 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: 8.18 Conformation dependent library (CDL) restraints added in 3.2 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: 1.77 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: 5.64 Time building geometry restraints manager: 8.83 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 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: 1.580 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: 4.740 Check model and map are aligned: 0.240 Set scattering table: 0.150 Process input model: 50.510 Find NCS groups from input model: 1.200 Set up NCS constraints: 0.110 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: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 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 % Allowed : 7.94 % Favored : 92.06 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 433 HIS 0.004 0.001 HIS D 301 PHE 0.014 0.001 PHE A 377 TYR 0.015 0.001 TYR D 594 ARG 0.002 0.000 ARG A 693 *********************** 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 : 2.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ARG cc_start: 0.8648 (ttm110) cc_final: 0.8065 (ttm110) REVERT: A 173 MET cc_start: 0.8845 (mtt) cc_final: 0.8595 (mtt) REVERT: A 255 GLN cc_start: 0.8437 (tm-30) cc_final: 0.7993 (tt0) REVERT: A 501 GLU cc_start: 0.8473 (mm-30) cc_final: 0.7981 (mm-30) REVERT: A 521 TRP cc_start: 0.7785 (t-100) cc_final: 0.7570 (t60) REVERT: A 553 LEU cc_start: 0.9369 (mt) cc_final: 0.9094 (mt) REVERT: A 561 ASN cc_start: 0.8878 (m-40) cc_final: 0.8661 (t0) REVERT: A 574 MET cc_start: 0.7923 (mtt) cc_final: 0.7621 (mtt) REVERT: B 173 MET cc_start: 0.8715 (mtt) cc_final: 0.8361 (mtt) REVERT: B 255 GLN cc_start: 0.8375 (tm-30) cc_final: 0.7933 (tt0) REVERT: B 553 LEU cc_start: 0.9392 (mt) cc_final: 0.9117 (mt) REVERT: B 562 MET cc_start: 0.9022 (mmm) cc_final: 0.8784 (tpp) REVERT: C 143 GLN cc_start: 0.8757 (tp-100) cc_final: 0.8464 (pt0) REVERT: C 255 GLN cc_start: 0.8391 (tm-30) cc_final: 0.8000 (tt0) REVERT: C 371 ARG cc_start: 0.7044 (tmt170) cc_final: 0.6700 (tpt-90) REVERT: C 431 MET cc_start: 0.8892 (ttm) cc_final: 0.8637 (mtm) REVERT: C 501 GLU cc_start: 0.8538 (mm-30) cc_final: 0.7955 (mm-30) REVERT: C 521 TRP cc_start: 0.7880 (t-100) cc_final: 0.7651 (t60) REVERT: C 553 LEU cc_start: 0.9387 (mt) cc_final: 0.9117 (mt) REVERT: C 561 ASN cc_start: 0.8921 (m-40) cc_final: 0.8630 (t0) REVERT: C 677 MET cc_start: 0.7568 (mtp) cc_final: 0.7336 (mtm) REVERT: D 122 ARG cc_start: 0.8569 (ttm110) cc_final: 0.7983 (ttm110) REVERT: D 143 GLN cc_start: 0.8833 (tp-100) cc_final: 0.8632 (mm-40) REVERT: D 173 MET cc_start: 0.8833 (mtt) cc_final: 0.8576 (mtt) REVERT: D 255 GLN cc_start: 0.8479 (tm-30) cc_final: 0.7897 (tt0) REVERT: D 320 MET cc_start: 0.9031 (tpp) cc_final: 0.8804 (tpp) REVERT: D 553 LEU cc_start: 0.9376 (mt) cc_final: 0.9131 (mt) REVERT: D 561 ASN cc_start: 0.8887 (m-40) cc_final: 0.8680 (m-40) REVERT: D 562 MET cc_start: 0.8991 (mmm) cc_final: 0.8603 (tpp) outliers start: 0 outliers final: 0 residues processed: 368 average time/residue: 0.2879 time to fit residues: 158.8456 Evaluate side-chains 233 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 2.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 0.7980 chunk 181 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 188 optimal weight: 10.0000 chunk 72 optimal weight: 6.9990 chunk 114 optimal weight: 7.9990 chunk 140 optimal weight: 0.9990 chunk 217 optimal weight: 0.7980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN A 197 ASN A 242 ASN ** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 ASN A 452 ASN A 585 HIS B 242 ASN ** B 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 ASN B 585 HIS C 143 GLN C 242 ASN ** C 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 ASN C 585 HIS D 143 GLN D 242 ASN ** D 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 339 ASN D 585 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 20060 Z= 0.227 Angle : 0.560 7.303 27120 Z= 0.294 Chirality : 0.038 0.133 3100 Planarity : 0.004 0.057 3360 Dihedral : 4.738 19.837 2620 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 0.05 % Allowed : 4.89 % Favored : 95.07 % 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: -2.01 (0.16), residues: 2376 helix: -0.49 (0.12), residues: 1596 sheet: -2.95 (0.54), residues: 68 loop : -2.97 (0.20), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 433 HIS 0.006 0.001 HIS B 301 PHE 0.011 0.001 PHE B 377 TYR 0.014 0.001 TYR B 650 ARG 0.008 0.000 ARG A 416 *********************** 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 310 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 309 time to evaluate : 2.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ARG cc_start: 0.8726 (ttm110) cc_final: 0.7794 (ttm110) REVERT: A 142 LEU cc_start: 0.8504 (tp) cc_final: 0.7756 (tp) REVERT: A 173 MET cc_start: 0.8884 (mtt) cc_final: 0.8618 (mtt) REVERT: A 255 GLN cc_start: 0.8329 (tm-30) cc_final: 0.7977 (tt0) REVERT: A 278 VAL cc_start: 0.9374 (t) cc_final: 0.9134 (t) REVERT: A 308 GLU cc_start: 0.7702 (tm-30) cc_final: 0.7058 (tm-30) REVERT: A 419 MET cc_start: 0.9149 (mtp) cc_final: 0.8849 (mtp) REVERT: A 501 GLU cc_start: 0.8456 (mm-30) cc_final: 0.7966 (mm-30) REVERT: A 561 ASN cc_start: 0.9183 (m-40) cc_final: 0.8863 (t0) REVERT: A 574 MET cc_start: 0.7898 (mtt) cc_final: 0.7653 (mtp) REVERT: B 122 ARG cc_start: 0.8754 (ttm110) cc_final: 0.8075 (ttm110) REVERT: B 308 GLU cc_start: 0.7610 (tm-30) cc_final: 0.7065 (tm-30) REVERT: B 562 MET cc_start: 0.9107 (mmm) cc_final: 0.8717 (tpp) REVERT: C 122 ARG cc_start: 0.8685 (ttm110) cc_final: 0.7954 (ttm110) REVERT: C 255 GLN cc_start: 0.8286 (tm-30) cc_final: 0.7982 (tt0) REVERT: C 308 GLU cc_start: 0.7698 (tm-30) cc_final: 0.7013 (tm-30) REVERT: C 419 MET cc_start: 0.9138 (mtp) cc_final: 0.8833 (mtp) REVERT: C 501 GLU cc_start: 0.8539 (mm-30) cc_final: 0.7961 (mm-30) REVERT: C 561 ASN cc_start: 0.9169 (m-40) cc_final: 0.8815 (t0) REVERT: D 122 ARG cc_start: 0.8727 (ttm110) cc_final: 0.7749 (ttm110) REVERT: D 159 MET cc_start: 0.7607 (mmm) cc_final: 0.6998 (mmp) REVERT: D 173 MET cc_start: 0.8867 (mtt) cc_final: 0.8576 (mtt) REVERT: D 255 GLN cc_start: 0.8354 (tm-30) cc_final: 0.7847 (tt0) REVERT: D 278 VAL cc_start: 0.9335 (t) cc_final: 0.9104 (t) REVERT: D 308 GLU cc_start: 0.7663 (tm-30) cc_final: 0.7001 (tm-30) REVERT: D 419 MET cc_start: 0.9137 (mtp) cc_final: 0.8866 (mtp) REVERT: D 561 ASN cc_start: 0.9120 (m-40) cc_final: 0.8825 (t0) REVERT: D 645 GLN cc_start: 0.6885 (pm20) cc_final: 0.6427 (mm110) outliers start: 1 outliers final: 0 residues processed: 309 average time/residue: 0.2765 time to fit residues: 137.4301 Evaluate side-chains 219 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 2.216 ------------------------------------------------------------------------------- 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: 6.9990 chunk 67 optimal weight: 3.9990 chunk 181 optimal weight: 6.9990 chunk 148 optimal weight: 4.9990 chunk 60 optimal weight: 20.0000 chunk 218 optimal weight: 6.9990 chunk 235 optimal weight: 2.9990 chunk 194 optimal weight: 4.9990 chunk 216 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 175 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 430 HIS A 585 HIS B 430 HIS B 561 ASN B 585 HIS C 430 HIS C 585 HIS D 143 GLN D 197 ASN ** D 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 430 HIS D 585 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 20060 Z= 0.365 Angle : 0.654 6.491 27120 Z= 0.338 Chirality : 0.041 0.142 3100 Planarity : 0.004 0.057 3360 Dihedral : 4.803 22.171 2620 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 0.09 % Allowed : 4.89 % Favored : 95.02 % 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: -1.37 (0.17), residues: 2376 helix: 0.03 (0.13), residues: 1592 sheet: -2.57 (0.60), residues: 68 loop : -2.81 (0.21), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 433 HIS 0.008 0.001 HIS B 301 PHE 0.016 0.001 PHE A 601 TYR 0.020 0.002 TYR B 451 ARG 0.007 0.000 ARG A 416 *********************** 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 263 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 261 time to evaluate : 2.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ARG cc_start: 0.8798 (ttm110) cc_final: 0.7823 (ttm110) REVERT: A 142 LEU cc_start: 0.8623 (tp) cc_final: 0.8265 (tp) REVERT: A 173 MET cc_start: 0.8900 (mtt) cc_final: 0.8664 (mtt) REVERT: A 255 GLN cc_start: 0.8410 (tm-30) cc_final: 0.8052 (tt0) REVERT: A 308 GLU cc_start: 0.7573 (tm-30) cc_final: 0.6982 (tm-30) REVERT: A 495 MET cc_start: 0.8574 (mtt) cc_final: 0.8234 (mtp) REVERT: A 561 ASN cc_start: 0.9187 (m-40) cc_final: 0.8896 (t0) REVERT: B 122 ARG cc_start: 0.8708 (ttm110) cc_final: 0.7871 (ttm110) REVERT: B 173 MET cc_start: 0.8773 (mtt) cc_final: 0.8555 (mtt) REVERT: B 308 GLU cc_start: 0.7475 (tm-30) cc_final: 0.6854 (tm-30) REVERT: C 122 ARG cc_start: 0.8675 (ttm110) cc_final: 0.7845 (ttm110) REVERT: C 255 GLN cc_start: 0.8384 (tm-30) cc_final: 0.8031 (tt0) REVERT: C 308 GLU cc_start: 0.7586 (tm-30) cc_final: 0.6964 (tm-30) REVERT: C 561 ASN cc_start: 0.9184 (m-40) cc_final: 0.8914 (t0) REVERT: D 122 ARG cc_start: 0.8690 (ttm110) cc_final: 0.7738 (ttm110) REVERT: D 159 MET cc_start: 0.7813 (mmm) cc_final: 0.7275 (mmp) REVERT: D 173 MET cc_start: 0.8939 (mtt) cc_final: 0.8671 (mtt) REVERT: D 255 GLN cc_start: 0.8386 (tm-30) cc_final: 0.7922 (tt0) REVERT: D 308 GLU cc_start: 0.7609 (tm-30) cc_final: 0.7016 (tm-30) REVERT: D 419 MET cc_start: 0.9223 (mtp) cc_final: 0.8938 (mtp) REVERT: D 495 MET cc_start: 0.7996 (mmt) cc_final: 0.7522 (tpp) REVERT: D 561 ASN cc_start: 0.9227 (m-40) cc_final: 0.8977 (t0) outliers start: 2 outliers final: 1 residues processed: 261 average time/residue: 0.2677 time to fit residues: 112.7673 Evaluate side-chains 204 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 203 time to evaluate : 2.224 ------------------------------------------------------------------------------- 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: 9.9990 chunk 164 optimal weight: 0.7980 chunk 113 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 146 optimal weight: 4.9990 chunk 219 optimal weight: 0.4980 chunk 231 optimal weight: 0.4980 chunk 114 optimal weight: 5.9990 chunk 207 optimal weight: 2.9990 chunk 62 optimal weight: 10.0000 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 523 HIS 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: 0.8201 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 20060 Z= 0.156 Angle : 0.511 7.701 27120 Z= 0.264 Chirality : 0.036 0.140 3100 Planarity : 0.004 0.060 3360 Dihedral : 4.304 19.691 2620 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 0.05 % Allowed : 2.91 % Favored : 97.04 % 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: -0.74 (0.17), residues: 2376 helix: 0.49 (0.13), residues: 1596 sheet: -2.17 (0.65), residues: 68 loop : -2.54 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 433 HIS 0.009 0.001 HIS B 301 PHE 0.016 0.001 PHE B 193 TYR 0.013 0.001 TYR A 594 ARG 0.003 0.000 ARG C 337 *********************** 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 328 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 327 time to evaluate : 2.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ARG cc_start: 0.8769 (ttm110) cc_final: 0.7772 (ttm110) REVERT: A 173 MET cc_start: 0.8836 (mtt) cc_final: 0.8495 (mtt) REVERT: A 255 GLN cc_start: 0.8367 (tm-30) cc_final: 0.7936 (tt0) REVERT: A 308 GLU cc_start: 0.7544 (tm-30) cc_final: 0.7126 (tm-30) REVERT: A 320 MET cc_start: 0.9130 (tpp) cc_final: 0.8849 (tpp) REVERT: A 495 MET cc_start: 0.8473 (mtt) cc_final: 0.8164 (mtp) REVERT: A 501 GLU cc_start: 0.8514 (mm-30) cc_final: 0.7951 (mm-30) REVERT: A 561 ASN cc_start: 0.9178 (m-40) cc_final: 0.8840 (t0) REVERT: A 574 MET cc_start: 0.7896 (mtt) cc_final: 0.7661 (mtp) REVERT: A 589 LYS cc_start: 0.8437 (ttmt) cc_final: 0.8228 (mmtt) REVERT: B 122 ARG cc_start: 0.8684 (ttm110) cc_final: 0.7921 (ttm110) REVERT: B 255 GLN cc_start: 0.8388 (tm-30) cc_final: 0.7851 (tt0) REVERT: B 574 MET cc_start: 0.7967 (mmm) cc_final: 0.7585 (mmm) REVERT: C 122 ARG cc_start: 0.8627 (ttm110) cc_final: 0.7852 (ttm110) REVERT: C 255 GLN cc_start: 0.8359 (tm-30) cc_final: 0.7951 (tt0) REVERT: C 282 MET cc_start: 0.7268 (ptt) cc_final: 0.7026 (ptt) REVERT: C 308 GLU cc_start: 0.7561 (tm-30) cc_final: 0.7118 (tm-30) REVERT: C 501 GLU cc_start: 0.8558 (mm-30) cc_final: 0.8111 (mm-30) REVERT: C 561 ASN cc_start: 0.9159 (m-40) cc_final: 0.8813 (t0) REVERT: C 574 MET cc_start: 0.7933 (mmm) cc_final: 0.7500 (mmm) REVERT: C 589 LYS cc_start: 0.8459 (ttmt) cc_final: 0.8245 (mmtt) REVERT: C 677 MET cc_start: 0.7431 (mtp) cc_final: 0.7183 (mtm) REVERT: D 122 ARG cc_start: 0.8678 (ttm110) cc_final: 0.7677 (ttm110) REVERT: D 139 LEU cc_start: 0.8814 (tt) cc_final: 0.8167 (tt) REVERT: D 143 GLN cc_start: 0.8771 (tp40) cc_final: 0.8466 (pt0) REVERT: D 159 MET cc_start: 0.7707 (mmm) cc_final: 0.7163 (mmp) REVERT: D 255 GLN cc_start: 0.8350 (tm-30) cc_final: 0.7841 (tt0) REVERT: D 308 GLU cc_start: 0.7664 (tm-30) cc_final: 0.7183 (tm-30) REVERT: D 419 MET cc_start: 0.9197 (mtp) cc_final: 0.8855 (mtp) REVERT: D 561 ASN cc_start: 0.9236 (m-40) cc_final: 0.8870 (t0) REVERT: D 574 MET cc_start: 0.7968 (mmm) cc_final: 0.7530 (mmm) REVERT: D 589 LYS cc_start: 0.8425 (ttmt) cc_final: 0.8195 (mmtt) outliers start: 1 outliers final: 0 residues processed: 327 average time/residue: 0.2703 time to fit residues: 141.7873 Evaluate side-chains 218 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 2.167 ------------------------------------------------------------------------------- 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: 0.9980 chunk 131 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 172 optimal weight: 0.2980 chunk 95 optimal weight: 1.9990 chunk 197 optimal weight: 9.9990 chunk 160 optimal weight: 0.6980 chunk 0 optimal weight: 20.0000 chunk 118 optimal weight: 0.5980 chunk 208 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 297 ASN ** 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 523 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 20060 Z= 0.127 Angle : 0.491 6.372 27120 Z= 0.253 Chirality : 0.036 0.138 3100 Planarity : 0.003 0.062 3360 Dihedral : 4.048 17.280 2620 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % 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: -0.32 (0.17), residues: 2376 helix: 0.77 (0.13), residues: 1600 sheet: -1.89 (0.67), residues: 68 loop : -2.32 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 433 HIS 0.007 0.000 HIS B 301 PHE 0.007 0.001 PHE D 506 TYR 0.012 0.001 TYR B 594 ARG 0.011 0.000 ARG D 416 *********************** 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 366 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 366 time to evaluate : 2.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ARG cc_start: 0.8747 (ttm110) cc_final: 0.7782 (ttm110) REVERT: A 255 GLN cc_start: 0.8360 (tm-30) cc_final: 0.7904 (tt0) REVERT: A 306 VAL cc_start: 0.9158 (t) cc_final: 0.8954 (t) REVERT: A 308 GLU cc_start: 0.7628 (tm-30) cc_final: 0.7354 (tm-30) REVERT: A 495 MET cc_start: 0.8378 (mtt) cc_final: 0.8039 (mtp) REVERT: A 501 GLU cc_start: 0.8477 (mm-30) cc_final: 0.7981 (mm-30) REVERT: A 561 ASN cc_start: 0.9222 (m-40) cc_final: 0.8898 (t0) REVERT: A 635 LEU cc_start: 0.9262 (tp) cc_final: 0.8937 (tt) REVERT: A 684 VAL cc_start: 0.7245 (t) cc_final: 0.6927 (t) REVERT: B 122 ARG cc_start: 0.8656 (ttm110) cc_final: 0.7908 (ttm110) REVERT: B 255 GLN cc_start: 0.8374 (tm-30) cc_final: 0.7851 (tt0) REVERT: B 300 LEU cc_start: 0.9094 (mt) cc_final: 0.8742 (mt) REVERT: B 411 THR cc_start: 0.8462 (p) cc_final: 0.8208 (p) REVERT: B 574 MET cc_start: 0.7903 (mmm) cc_final: 0.7546 (mmm) REVERT: B 635 LEU cc_start: 0.9206 (tp) cc_final: 0.8907 (tt) REVERT: B 735 ASN cc_start: 0.8575 (p0) cc_final: 0.8373 (p0) REVERT: C 122 ARG cc_start: 0.8601 (ttm110) cc_final: 0.7709 (ttm110) REVERT: C 255 GLN cc_start: 0.8356 (tm-30) cc_final: 0.7943 (tt0) REVERT: C 282 MET cc_start: 0.7307 (ptt) cc_final: 0.7092 (ptt) REVERT: C 306 VAL cc_start: 0.9159 (t) cc_final: 0.8911 (t) REVERT: C 308 GLU cc_start: 0.7640 (tm-30) cc_final: 0.7323 (tm-30) REVERT: C 419 MET cc_start: 0.9160 (mtp) cc_final: 0.8813 (mtp) REVERT: C 501 GLU cc_start: 0.8497 (mm-30) cc_final: 0.7840 (mm-30) REVERT: C 561 ASN cc_start: 0.9225 (m-40) cc_final: 0.8827 (t0) REVERT: D 122 ARG cc_start: 0.8659 (ttm110) cc_final: 0.7683 (ttm110) REVERT: D 255 GLN cc_start: 0.8348 (tm-30) cc_final: 0.7866 (tt0) REVERT: D 306 VAL cc_start: 0.9165 (t) cc_final: 0.8900 (t) REVERT: D 308 GLU cc_start: 0.7596 (tm-30) cc_final: 0.7171 (tm-30) REVERT: D 501 GLU cc_start: 0.8594 (mm-30) cc_final: 0.7986 (mm-30) REVERT: D 561 ASN cc_start: 0.9221 (m-40) cc_final: 0.8926 (t0) REVERT: D 635 LEU cc_start: 0.9359 (tp) cc_final: 0.9127 (tt) outliers start: 0 outliers final: 0 residues processed: 366 average time/residue: 0.2767 time to fit residues: 161.1866 Evaluate side-chains 242 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 2.418 ------------------------------------------------------------------------------- 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: 3.9990 chunk 208 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 136 optimal weight: 10.0000 chunk 57 optimal weight: 0.6980 chunk 232 optimal weight: 1.9990 chunk 192 optimal weight: 9.9990 chunk 107 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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 452 ASN B 561 ASN ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 452 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20060 Z= 0.244 Angle : 0.580 9.340 27120 Z= 0.295 Chirality : 0.038 0.140 3100 Planarity : 0.004 0.054 3360 Dihedral : 4.194 18.437 2620 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % 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: -0.37 (0.17), residues: 2376 helix: 0.74 (0.13), residues: 1596 sheet: -1.93 (0.69), residues: 68 loop : -2.34 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 433 HIS 0.002 0.001 HIS A 745 PHE 0.019 0.001 PHE C 193 TYR 0.015 0.001 TYR A 451 ARG 0.007 0.000 ARG D 416 *********************** 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 318 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 318 time to evaluate : 1.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ARG cc_start: 0.8746 (ttm110) cc_final: 0.7746 (ttm110) REVERT: A 255 GLN cc_start: 0.8377 (tm-30) cc_final: 0.7953 (tt0) REVERT: A 306 VAL cc_start: 0.9196 (t) cc_final: 0.8930 (t) REVERT: A 308 GLU cc_start: 0.7610 (tm-30) cc_final: 0.7160 (tm-30) REVERT: A 501 GLU cc_start: 0.8535 (mm-30) cc_final: 0.7812 (mm-30) REVERT: A 574 MET cc_start: 0.8035 (mmm) cc_final: 0.7711 (mmm) REVERT: B 122 ARG cc_start: 0.8634 (ttm110) cc_final: 0.7832 (ttm110) REVERT: B 255 GLN cc_start: 0.8374 (tm-30) cc_final: 0.7903 (tt0) REVERT: B 592 PHE cc_start: 0.7790 (t80) cc_final: 0.7290 (t80) REVERT: C 122 ARG cc_start: 0.8578 (ttm110) cc_final: 0.7803 (ttm110) REVERT: C 255 GLN cc_start: 0.8375 (tm-30) cc_final: 0.7979 (tt0) REVERT: C 308 GLU cc_start: 0.7654 (tm-30) cc_final: 0.7184 (tm-30) REVERT: C 419 MET cc_start: 0.9182 (mtp) cc_final: 0.8842 (mtp) REVERT: C 495 MET cc_start: 0.8546 (mtt) cc_final: 0.8165 (mtp) REVERT: C 501 GLU cc_start: 0.8538 (mm-30) cc_final: 0.8018 (mm-30) REVERT: C 561 ASN cc_start: 0.9210 (m-40) cc_final: 0.8906 (t0) REVERT: C 562 MET cc_start: 0.9060 (mmm) cc_final: 0.8839 (tpp) REVERT: C 702 GLU cc_start: 0.7572 (tp30) cc_final: 0.7264 (tm-30) REVERT: D 122 ARG cc_start: 0.8650 (ttm110) cc_final: 0.7674 (ttm110) REVERT: D 255 GLN cc_start: 0.8368 (tm-30) cc_final: 0.7909 (tt0) REVERT: D 306 VAL cc_start: 0.9172 (t) cc_final: 0.8899 (t) REVERT: D 308 GLU cc_start: 0.7635 (tm-30) cc_final: 0.7169 (tm-30) outliers start: 0 outliers final: 0 residues processed: 318 average time/residue: 0.2753 time to fit residues: 138.0609 Evaluate side-chains 203 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 2.211 ------------------------------------------------------------------------------- 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: 4.9990 chunk 26 optimal weight: 4.9990 chunk 132 optimal weight: 10.0000 chunk 169 optimal weight: 0.8980 chunk 131 optimal weight: 2.9990 chunk 195 optimal weight: 6.9990 chunk 129 optimal weight: 9.9990 chunk 231 optimal weight: 4.9990 chunk 144 optimal weight: 1.9990 chunk 141 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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** ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20060 Z= 0.261 Angle : 0.592 8.631 27120 Z= 0.303 Chirality : 0.039 0.141 3100 Planarity : 0.004 0.051 3360 Dihedral : 4.308 18.988 2620 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % 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: -0.31 (0.17), residues: 2376 helix: 0.74 (0.13), residues: 1596 sheet: 0.13 (0.84), residues: 48 loop : -2.36 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 433 HIS 0.007 0.001 HIS B 301 PHE 0.016 0.001 PHE D 193 TYR 0.014 0.001 TYR D 575 ARG 0.006 0.000 ARG B 416 *********************** 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 295 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 295 time to evaluate : 2.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ARG cc_start: 0.8741 (ttm110) cc_final: 0.7742 (ttm110) REVERT: A 159 MET cc_start: 0.8111 (mmp) cc_final: 0.7879 (mmm) REVERT: A 255 GLN cc_start: 0.8353 (tm-30) cc_final: 0.7956 (tt0) REVERT: A 306 VAL cc_start: 0.9126 (t) cc_final: 0.8863 (t) REVERT: A 308 GLU cc_start: 0.7591 (tm-30) cc_final: 0.7165 (tm-30) REVERT: A 411 THR cc_start: 0.8680 (p) cc_final: 0.8243 (p) REVERT: A 495 MET cc_start: 0.8499 (mtt) cc_final: 0.8097 (mtp) REVERT: A 574 MET cc_start: 0.8111 (mmm) cc_final: 0.7780 (mmm) REVERT: A 702 GLU cc_start: 0.7663 (tm-30) cc_final: 0.7450 (tm-30) REVERT: B 122 ARG cc_start: 0.8618 (ttm110) cc_final: 0.7787 (ttm110) REVERT: B 255 GLN cc_start: 0.8392 (tm-30) cc_final: 0.7907 (tt0) REVERT: B 592 PHE cc_start: 0.7803 (t80) cc_final: 0.7459 (t80) REVERT: C 122 ARG cc_start: 0.8550 (ttm110) cc_final: 0.7847 (ttm110) REVERT: C 255 GLN cc_start: 0.8366 (tm-30) cc_final: 0.7988 (tt0) REVERT: C 308 GLU cc_start: 0.7626 (tm-30) cc_final: 0.7157 (tm-30) REVERT: C 419 MET cc_start: 0.9201 (mtp) cc_final: 0.8879 (mtp) REVERT: C 495 MET cc_start: 0.8498 (mtt) cc_final: 0.8166 (mtp) REVERT: C 501 GLU cc_start: 0.8488 (mm-30) cc_final: 0.7818 (mm-30) REVERT: C 562 MET cc_start: 0.8989 (mmm) cc_final: 0.8688 (tpp) REVERT: C 574 MET cc_start: 0.8067 (mmm) cc_final: 0.7843 (mmm) REVERT: C 702 GLU cc_start: 0.7674 (tp30) cc_final: 0.7105 (tm-30) REVERT: D 122 ARG cc_start: 0.8661 (ttm110) cc_final: 0.7678 (ttm110) REVERT: D 139 LEU cc_start: 0.8877 (tt) cc_final: 0.8193 (tt) REVERT: D 143 GLN cc_start: 0.8793 (tp40) cc_final: 0.8510 (pt0) REVERT: D 255 GLN cc_start: 0.8387 (tm-30) cc_final: 0.7915 (tt0) REVERT: D 306 VAL cc_start: 0.9155 (t) cc_final: 0.8916 (t) REVERT: D 308 GLU cc_start: 0.7590 (tm-30) cc_final: 0.7148 (tm-30) REVERT: D 562 MET cc_start: 0.8732 (mtm) cc_final: 0.8435 (mtp) REVERT: D 574 MET cc_start: 0.8119 (mmt) cc_final: 0.7875 (mmm) REVERT: D 702 GLU cc_start: 0.7501 (tm-30) cc_final: 0.7281 (tm-30) outliers start: 0 outliers final: 0 residues processed: 295 average time/residue: 0.2864 time to fit residues: 133.3717 Evaluate side-chains 206 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 2.280 ------------------------------------------------------------------------------- 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: 1.9990 chunk 92 optimal weight: 0.8980 chunk 138 optimal weight: 0.8980 chunk 69 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 157 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 181 optimal weight: 0.0570 overall best weight: 1.1702 ------------------------------------------------------------------------------- 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 452 ASN A 561 ASN ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 561 ASN D 197 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: 0.8189 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 20060 Z= 0.160 Angle : 0.529 7.618 27120 Z= 0.271 Chirality : 0.037 0.140 3100 Planarity : 0.003 0.050 3360 Dihedral : 4.120 16.995 2620 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % 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: -0.17 (0.18), residues: 2376 helix: 0.87 (0.13), residues: 1596 sheet: -1.85 (0.72), residues: 68 loop : -2.20 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 433 HIS 0.007 0.001 HIS B 301 PHE 0.024 0.001 PHE A 193 TYR 0.014 0.001 TYR A 594 ARG 0.006 0.000 ARG B 416 *********************** 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 305 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 305 time to evaluate : 2.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ARG cc_start: 0.8721 (ttm110) cc_final: 0.7750 (ttm110) REVERT: A 139 LEU cc_start: 0.8836 (tt) cc_final: 0.8157 (tt) REVERT: A 143 GLN cc_start: 0.8728 (tp40) cc_final: 0.8470 (pt0) REVERT: A 159 MET cc_start: 0.8091 (mmp) cc_final: 0.7886 (mmm) REVERT: A 255 GLN cc_start: 0.8372 (tm-30) cc_final: 0.7947 (tt0) REVERT: A 306 VAL cc_start: 0.9132 (t) cc_final: 0.8871 (t) REVERT: A 308 GLU cc_start: 0.7633 (tm-30) cc_final: 0.7190 (tm-30) REVERT: A 495 MET cc_start: 0.8487 (mtt) cc_final: 0.8099 (mtp) REVERT: A 592 PHE cc_start: 0.8166 (t80) cc_final: 0.7832 (t80) REVERT: A 702 GLU cc_start: 0.7589 (tm-30) cc_final: 0.7274 (tm-30) REVERT: B 122 ARG cc_start: 0.8580 (ttm110) cc_final: 0.7832 (ttm110) REVERT: B 159 MET cc_start: 0.8147 (mmp) cc_final: 0.7878 (mmm) REVERT: B 255 GLN cc_start: 0.8396 (tm-30) cc_final: 0.7898 (tt0) REVERT: B 702 GLU cc_start: 0.7476 (tm-30) cc_final: 0.7169 (tm-30) REVERT: C 122 ARG cc_start: 0.8540 (ttm110) cc_final: 0.7679 (ttm110) REVERT: C 255 GLN cc_start: 0.8294 (tm-30) cc_final: 0.7925 (tt0) REVERT: C 306 VAL cc_start: 0.9156 (t) cc_final: 0.8855 (t) REVERT: C 308 GLU cc_start: 0.7667 (tm-30) cc_final: 0.7214 (tm-30) REVERT: C 419 MET cc_start: 0.9189 (mtp) cc_final: 0.8788 (mtp) REVERT: C 495 MET cc_start: 0.8471 (mtt) cc_final: 0.8115 (mtp) REVERT: C 702 GLU cc_start: 0.7548 (tp30) cc_final: 0.7061 (tm-30) REVERT: D 122 ARG cc_start: 0.8653 (ttm110) cc_final: 0.7979 (ttm110) REVERT: D 139 LEU cc_start: 0.8802 (tt) cc_final: 0.8151 (tt) REVERT: D 143 GLN cc_start: 0.8769 (tp40) cc_final: 0.8506 (pt0) REVERT: D 255 GLN cc_start: 0.8354 (tm-30) cc_final: 0.7887 (tt0) REVERT: D 306 VAL cc_start: 0.9143 (t) cc_final: 0.8903 (t) REVERT: D 308 GLU cc_start: 0.7631 (tm-30) cc_final: 0.7210 (tm-30) REVERT: D 411 THR cc_start: 0.8360 (p) cc_final: 0.8147 (p) REVERT: D 495 MET cc_start: 0.8468 (mtt) cc_final: 0.8060 (mtp) REVERT: D 562 MET cc_start: 0.8681 (mtm) cc_final: 0.8445 (mtp) outliers start: 0 outliers final: 0 residues processed: 305 average time/residue: 0.2710 time to fit residues: 131.9606 Evaluate side-chains 227 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 227 time to evaluate : 2.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 3.9990 chunk 221 optimal weight: 5.9990 chunk 202 optimal weight: 0.5980 chunk 215 optimal weight: 6.9990 chunk 129 optimal weight: 9.9990 chunk 93 optimal weight: 5.9990 chunk 169 optimal weight: 0.9990 chunk 66 optimal weight: 9.9990 chunk 194 optimal weight: 5.9990 chunk 203 optimal weight: 0.9980 chunk 214 optimal weight: 5.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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** ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20060 Z= 0.262 Angle : 0.601 7.695 27120 Z= 0.307 Chirality : 0.039 0.141 3100 Planarity : 0.004 0.047 3360 Dihedral : 4.258 17.848 2620 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % 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: -0.17 (0.17), residues: 2376 helix: 0.83 (0.13), residues: 1596 sheet: 0.39 (0.89), residues: 48 loop : -2.29 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 433 HIS 0.007 0.001 HIS B 301 PHE 0.021 0.001 PHE D 538 TYR 0.015 0.001 TYR D 451 ARG 0.005 0.000 ARG D 416 *********************** 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 289 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 289 time to evaluate : 2.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ARG cc_start: 0.8738 (ttm110) cc_final: 0.7736 (ttm110) REVERT: A 139 LEU cc_start: 0.8828 (tt) cc_final: 0.8137 (tt) REVERT: A 143 GLN cc_start: 0.8905 (tp40) cc_final: 0.8621 (pt0) REVERT: A 159 MET cc_start: 0.8131 (mmp) cc_final: 0.7926 (mmm) REVERT: A 255 GLN cc_start: 0.8388 (tm-30) cc_final: 0.7969 (tt0) REVERT: A 306 VAL cc_start: 0.9181 (t) cc_final: 0.8918 (t) REVERT: A 308 GLU cc_start: 0.7567 (tm-30) cc_final: 0.7114 (tm-30) REVERT: A 495 MET cc_start: 0.8554 (mtt) cc_final: 0.8154 (mtp) REVERT: A 592 PHE cc_start: 0.8151 (t80) cc_final: 0.7831 (t80) REVERT: A 702 GLU cc_start: 0.7619 (tm-30) cc_final: 0.7296 (tm-30) REVERT: B 122 ARG cc_start: 0.8601 (ttm110) cc_final: 0.7765 (ttm110) REVERT: B 255 GLN cc_start: 0.8383 (tm-30) cc_final: 0.7908 (tt0) REVERT: C 122 ARG cc_start: 0.8552 (ttm110) cc_final: 0.7674 (ttm110) REVERT: C 255 GLN cc_start: 0.8343 (tm-30) cc_final: 0.7952 (tt0) REVERT: C 306 VAL cc_start: 0.9167 (t) cc_final: 0.8915 (t) REVERT: C 308 GLU cc_start: 0.7552 (tm-30) cc_final: 0.7054 (tm-30) REVERT: C 419 MET cc_start: 0.9214 (mtp) cc_final: 0.8869 (mtp) REVERT: C 495 MET cc_start: 0.8509 (mtt) cc_final: 0.8162 (mtp) REVERT: D 122 ARG cc_start: 0.8671 (ttm110) cc_final: 0.7691 (ttm110) REVERT: D 139 LEU cc_start: 0.8880 (tt) cc_final: 0.8268 (tt) REVERT: D 143 GLN cc_start: 0.8784 (tp40) cc_final: 0.8557 (pt0) REVERT: D 255 GLN cc_start: 0.8388 (tm-30) cc_final: 0.7916 (tt0) REVERT: D 306 VAL cc_start: 0.9161 (t) cc_final: 0.8912 (t) REVERT: D 308 GLU cc_start: 0.7610 (tm-30) cc_final: 0.7154 (tm-30) REVERT: D 419 MET cc_start: 0.9128 (mtm) cc_final: 0.8819 (mtp) REVERT: D 495 MET cc_start: 0.8488 (mtt) cc_final: 0.8122 (mtp) REVERT: D 562 MET cc_start: 0.8769 (mtm) cc_final: 0.8557 (mtp) outliers start: 0 outliers final: 0 residues processed: 289 average time/residue: 0.2644 time to fit residues: 122.6733 Evaluate side-chains 204 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 2.379 ------------------------------------------------------------------------------- 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: 6.9990 chunk 227 optimal weight: 5.9990 chunk 139 optimal weight: 5.9990 chunk 108 optimal weight: 9.9990 chunk 158 optimal weight: 10.0000 chunk 239 optimal weight: 1.9990 chunk 220 optimal weight: 0.9990 chunk 190 optimal weight: 0.0770 chunk 19 optimal weight: 0.0070 chunk 147 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 overall best weight: 1.4162 ------------------------------------------------------------------------------- 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 417 HIS A 561 ASN ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8202 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20060 Z= 0.175 Angle : 0.554 7.341 27120 Z= 0.283 Chirality : 0.037 0.142 3100 Planarity : 0.003 0.049 3360 Dihedral : 4.124 16.370 2620 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % 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: -0.04 (0.17), residues: 2376 helix: 0.94 (0.13), residues: 1596 sheet: 0.48 (0.89), residues: 48 loop : -2.23 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 433 HIS 0.007 0.001 HIS B 301 PHE 0.027 0.001 PHE A 193 TYR 0.013 0.001 TYR B 575 ARG 0.005 0.000 ARG B 416 ********************** 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 301 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 301 time to evaluate : 2.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ARG cc_start: 0.8729 (ttm110) cc_final: 0.8052 (ttm110) REVERT: A 139 LEU cc_start: 0.8846 (tt) cc_final: 0.8188 (tt) REVERT: A 143 GLN cc_start: 0.8879 (tp40) cc_final: 0.8588 (pt0) REVERT: A 255 GLN cc_start: 0.8390 (tm-30) cc_final: 0.7972 (tt0) REVERT: A 306 VAL cc_start: 0.9162 (t) cc_final: 0.8923 (t) REVERT: A 308 GLU cc_start: 0.7629 (tm-30) cc_final: 0.7225 (tm-30) REVERT: A 495 MET cc_start: 0.8547 (mtt) cc_final: 0.8069 (mtp) REVERT: A 574 MET cc_start: 0.8174 (mmt) cc_final: 0.7907 (mmm) REVERT: A 592 PHE cc_start: 0.8059 (t80) cc_final: 0.7766 (t80) REVERT: A 702 GLU cc_start: 0.7543 (tm-30) cc_final: 0.7098 (tm-30) REVERT: B 122 ARG cc_start: 0.8581 (ttm110) cc_final: 0.7826 (ttm110) REVERT: B 255 GLN cc_start: 0.8374 (tm-30) cc_final: 0.7890 (tt0) REVERT: C 122 ARG cc_start: 0.8542 (ttm110) cc_final: 0.7681 (ttm110) REVERT: C 255 GLN cc_start: 0.8348 (tm-30) cc_final: 0.7923 (tt0) REVERT: C 306 VAL cc_start: 0.9150 (t) cc_final: 0.8897 (t) REVERT: C 308 GLU cc_start: 0.7645 (tm-30) cc_final: 0.7186 (tm-30) REVERT: C 411 THR cc_start: 0.8428 (p) cc_final: 0.8219 (p) REVERT: C 419 MET cc_start: 0.9201 (mtp) cc_final: 0.8805 (mtp) REVERT: C 495 MET cc_start: 0.8476 (mtt) cc_final: 0.8110 (mtp) REVERT: C 676 LEU cc_start: 0.8339 (mm) cc_final: 0.8125 (mt) REVERT: D 122 ARG cc_start: 0.8664 (ttm110) cc_final: 0.7714 (ttm110) REVERT: D 139 LEU cc_start: 0.8762 (tt) cc_final: 0.8155 (tt) REVERT: D 143 GLN cc_start: 0.8781 (tp40) cc_final: 0.8538 (pt0) REVERT: D 255 GLN cc_start: 0.8359 (tm-30) cc_final: 0.7884 (tt0) REVERT: D 306 VAL cc_start: 0.9146 (t) cc_final: 0.8904 (t) REVERT: D 308 GLU cc_start: 0.7567 (tm-30) cc_final: 0.7159 (tm-30) REVERT: D 419 MET cc_start: 0.9132 (mtm) cc_final: 0.8849 (mtp) REVERT: D 495 MET cc_start: 0.8451 (mtt) cc_final: 0.8080 (mtp) REVERT: D 574 MET cc_start: 0.7986 (mmm) cc_final: 0.7710 (mmm) outliers start: 0 outliers final: 0 residues processed: 301 average time/residue: 0.2657 time to fit residues: 127.9929 Evaluate side-chains 226 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 226 time to evaluate : 2.182 ------------------------------------------------------------------------------- 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: 0.9980 chunk 202 optimal weight: 0.4980 chunk 58 optimal weight: 1.9990 chunk 175 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 52 optimal weight: 0.0050 chunk 190 optimal weight: 0.8980 chunk 79 optimal weight: 0.1980 chunk 195 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- 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** A 561 ASN ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 417 HIS C 561 ASN ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 417 HIS D 561 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.117173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.092834 restraints weight = 40297.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.094679 restraints weight = 27903.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.095964 restraints weight = 21773.079| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3423 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= 0.124 Angle : 0.522 7.863 27120 Z= 0.267 Chirality : 0.036 0.140 3100 Planarity : 0.003 0.048 3360 Dihedral : 3.901 15.545 2620 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % 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: 1.07 (0.13), residues: 1596 sheet: -1.48 (0.77), residues: 68 loop : -2.17 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 433 HIS 0.006 0.000 HIS B 301 PHE 0.031 0.001 PHE D 193 TYR 0.013 0.001 TYR D 594 ARG 0.006 0.000 ARG B 416 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3511.31 seconds wall clock time: 64 minutes 48.00 seconds (3888.00 seconds total)