Starting phenix.real_space_refine on Sun Mar 17 13:32:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mz7_24085/03_2024/7mz7_24085_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mz7_24085/03_2024/7mz7_24085.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mz7_24085/03_2024/7mz7_24085.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mz7_24085/03_2024/7mz7_24085.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mz7_24085/03_2024/7mz7_24085_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mz7_24085/03_2024/7mz7_24085_updated.pdb" } resolution = 3.35 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 100 5.16 5 Na 1 4.78 5 C 11744 2.51 5 N 2864 2.21 5 O 3180 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17889 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 4426 Classifications: {'peptide': 545} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 530} Chain: "D" Number of atoms: 4426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 4426 Classifications: {'peptide': 545} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 530} Chain: "B" Number of atoms: 4426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 4426 Classifications: {'peptide': 545} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 530} Chain: "C" Number of atoms: 4426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 4426 Classifications: {'peptide': 545} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 530} Chain: "A" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 47 Unusual residues: {' NA': 1, '6EU': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'6EU': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'6EU': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'6EU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.67, per 1000 atoms: 0.48 Number of scatterers: 17889 At special positions: 0 Unit cell: (129.27, 126.768, 111.756, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 100 16.00 Na 1 11.00 O 3180 8.00 N 2864 7.00 C 11744 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 386 " - pdb=" SG CYS C 390 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.05 Conformation dependent library (CDL) restraints added in 3.2 seconds 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4128 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 96 helices and 4 sheets defined 58.4% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.53 Creating SS restraints... Processing helix chain 'A' and resid 187 through 190 No H-bonds generated for 'chain 'A' and resid 187 through 190' Processing helix chain 'A' and resid 204 through 210 Processing helix chain 'A' and resid 214 through 222 Processing helix chain 'A' and resid 234 through 236 No H-bonds generated for 'chain 'A' and resid 234 through 236' Processing helix chain 'A' and resid 251 through 257 Processing helix chain 'A' and resid 261 through 268 Processing helix chain 'A' and resid 287 through 294 Processing helix chain 'A' and resid 299 through 319 removed outlier: 3.687A pdb=" N PHE A 304 " --> pdb=" O ASP A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 327 No H-bonds generated for 'chain 'A' and resid 325 through 327' Processing helix chain 'A' and resid 336 through 343 Processing helix chain 'A' and resid 346 through 354 removed outlier: 4.007A pdb=" N GLN A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 400 Processing helix chain 'A' and resid 412 through 414 No H-bonds generated for 'chain 'A' and resid 412 through 414' Processing helix chain 'A' and resid 416 through 453 removed outlier: 5.028A pdb=" N LYS A 431 " --> pdb=" O ASP A 427 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ARG A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ILE A 433 " --> pdb=" O PHE A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 499 Processing helix chain 'A' and resid 505 through 508 No H-bonds generated for 'chain 'A' and resid 505 through 508' Processing helix chain 'A' and resid 511 through 531 Processing helix chain 'A' and resid 535 through 556 removed outlier: 3.900A pdb=" N VAL A 542 " --> pdb=" O ALA A 539 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA A 546 " --> pdb=" O PHE A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 598 removed outlier: 3.777A pdb=" N ILE A 564 " --> pdb=" O GLN A 560 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LEU A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N CYS A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 641 removed outlier: 3.920A pdb=" N PHE A 640 " --> pdb=" O GLU A 636 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N THR A 641 " --> pdb=" O LEU A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 670 Processing helix chain 'A' and resid 674 through 688 Processing helix chain 'A' and resid 690 through 711 Processing helix chain 'A' and resid 717 through 719 No H-bonds generated for 'chain 'A' and resid 717 through 719' Processing helix chain 'D' and resid 187 through 190 No H-bonds generated for 'chain 'D' and resid 187 through 190' Processing helix chain 'D' and resid 204 through 210 Processing helix chain 'D' and resid 214 through 222 Processing helix chain 'D' and resid 234 through 236 No H-bonds generated for 'chain 'D' and resid 234 through 236' Processing helix chain 'D' and resid 251 through 257 Processing helix chain 'D' and resid 261 through 269 Processing helix chain 'D' and resid 287 through 294 Processing helix chain 'D' and resid 299 through 319 removed outlier: 3.712A pdb=" N PHE D 304 " --> pdb=" O ASP D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 327 No H-bonds generated for 'chain 'D' and resid 325 through 327' Processing helix chain 'D' and resid 336 through 343 Processing helix chain 'D' and resid 346 through 353 Processing helix chain 'D' and resid 395 through 400 Processing helix chain 'D' and resid 412 through 414 No H-bonds generated for 'chain 'D' and resid 412 through 414' Processing helix chain 'D' and resid 416 through 453 removed outlier: 5.074A pdb=" N LYS D 431 " --> pdb=" O ASP D 427 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ARG D 432 " --> pdb=" O ARG D 428 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ILE D 433 " --> pdb=" O PHE D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 499 Processing helix chain 'D' and resid 505 through 508 No H-bonds generated for 'chain 'D' and resid 505 through 508' Processing helix chain 'D' and resid 511 through 531 Processing helix chain 'D' and resid 535 through 556 removed outlier: 3.937A pdb=" N VAL D 538 " --> pdb=" O LYS D 535 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL D 542 " --> pdb=" O ALA D 539 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA D 546 " --> pdb=" O PHE D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 598 removed outlier: 3.605A pdb=" N ILE D 564 " --> pdb=" O GLN D 560 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N TYR D 565 " --> pdb=" O GLN D 561 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N CYS D 578 " --> pdb=" O LEU D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 641 removed outlier: 3.987A pdb=" N PHE D 640 " --> pdb=" O GLU D 636 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N THR D 641 " --> pdb=" O LEU D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 670 Processing helix chain 'D' and resid 674 through 688 Processing helix chain 'D' and resid 690 through 711 Processing helix chain 'D' and resid 717 through 719 No H-bonds generated for 'chain 'D' and resid 717 through 719' Processing helix chain 'B' and resid 187 through 190 No H-bonds generated for 'chain 'B' and resid 187 through 190' Processing helix chain 'B' and resid 204 through 210 Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 234 through 236 No H-bonds generated for 'chain 'B' and resid 234 through 236' Processing helix chain 'B' and resid 251 through 257 Processing helix chain 'B' and resid 261 through 269 Processing helix chain 'B' and resid 287 through 294 Processing helix chain 'B' and resid 299 through 319 removed outlier: 3.778A pdb=" N PHE B 304 " --> pdb=" O ASP B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 327 No H-bonds generated for 'chain 'B' and resid 325 through 327' Processing helix chain 'B' and resid 336 through 343 Processing helix chain 'B' and resid 346 through 354 removed outlier: 3.971A pdb=" N GLN B 354 " --> pdb=" O ALA B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 400 Processing helix chain 'B' and resid 412 through 414 No H-bonds generated for 'chain 'B' and resid 412 through 414' Processing helix chain 'B' and resid 416 through 453 removed outlier: 5.067A pdb=" N LYS B 431 " --> pdb=" O ASP B 427 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ARG B 432 " --> pdb=" O ARG B 428 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE B 433 " --> pdb=" O PHE B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 499 Processing helix chain 'B' and resid 505 through 508 No H-bonds generated for 'chain 'B' and resid 505 through 508' Processing helix chain 'B' and resid 511 through 531 Processing helix chain 'B' and resid 535 through 556 removed outlier: 3.952A pdb=" N VAL B 542 " --> pdb=" O ALA B 539 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA B 546 " --> pdb=" O PHE B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 598 removed outlier: 3.533A pdb=" N TYR B 565 " --> pdb=" O GLN B 561 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N CYS B 578 " --> pdb=" O LEU B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 641 removed outlier: 3.882A pdb=" N PHE B 640 " --> pdb=" O GLU B 636 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N THR B 641 " --> pdb=" O LEU B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 670 Processing helix chain 'B' and resid 674 through 688 Processing helix chain 'B' and resid 690 through 711 Processing helix chain 'C' and resid 187 through 190 No H-bonds generated for 'chain 'C' and resid 187 through 190' Processing helix chain 'C' and resid 204 through 210 Processing helix chain 'C' and resid 214 through 222 Processing helix chain 'C' and resid 234 through 236 No H-bonds generated for 'chain 'C' and resid 234 through 236' Processing helix chain 'C' and resid 251 through 257 Processing helix chain 'C' and resid 261 through 269 Processing helix chain 'C' and resid 287 through 294 Processing helix chain 'C' and resid 299 through 319 removed outlier: 3.770A pdb=" N PHE C 304 " --> pdb=" O ASP C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 327 No H-bonds generated for 'chain 'C' and resid 325 through 327' Processing helix chain 'C' and resid 336 through 343 Processing helix chain 'C' and resid 346 through 353 Processing helix chain 'C' and resid 363 through 365 No H-bonds generated for 'chain 'C' and resid 363 through 365' Processing helix chain 'C' and resid 395 through 400 Processing helix chain 'C' and resid 412 through 414 No H-bonds generated for 'chain 'C' and resid 412 through 414' Processing helix chain 'C' and resid 416 through 453 removed outlier: 5.079A pdb=" N LYS C 431 " --> pdb=" O ASP C 427 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ARG C 432 " --> pdb=" O ARG C 428 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ILE C 433 " --> pdb=" O PHE C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 499 Processing helix chain 'C' and resid 505 through 508 No H-bonds generated for 'chain 'C' and resid 505 through 508' Processing helix chain 'C' and resid 511 through 531 Processing helix chain 'C' and resid 535 through 556 removed outlier: 3.909A pdb=" N VAL C 538 " --> pdb=" O LYS C 535 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL C 542 " --> pdb=" O ALA C 539 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA C 546 " --> pdb=" O PHE C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 598 removed outlier: 3.638A pdb=" N TYR C 565 " --> pdb=" O GLN C 561 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LEU C 577 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N CYS C 578 " --> pdb=" O LEU C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 641 removed outlier: 4.001A pdb=" N PHE C 640 " --> pdb=" O GLU C 636 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N THR C 641 " --> pdb=" O LEU C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 670 Processing helix chain 'C' and resid 674 through 688 Processing helix chain 'C' and resid 690 through 711 Processing helix chain 'C' and resid 717 through 719 No H-bonds generated for 'chain 'C' and resid 717 through 719' Processing sheet with id= A, first strand: chain 'A' and resid 742 through 747 removed outlier: 4.009A pdb=" N TRP A 372 " --> pdb=" O SER A 379 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU A 381 " --> pdb=" O THR A 370 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N THR A 370 " --> pdb=" O LEU A 381 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'D' and resid 742 through 747 removed outlier: 4.076A pdb=" N TRP D 372 " --> pdb=" O SER D 379 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU D 381 " --> pdb=" O THR D 370 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N THR D 370 " --> pdb=" O LEU D 381 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 368 through 370 Processing sheet with id= D, first strand: chain 'C' and resid 742 through 747 removed outlier: 4.033A pdb=" N TRP C 372 " --> pdb=" O SER C 379 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU C 381 " --> pdb=" O THR C 370 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N THR C 370 " --> pdb=" O LEU C 381 " (cutoff:3.500A) 889 hydrogen bonds defined for protein. 2457 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: 5.22 Time building geometry restraints manager: 7.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2779 1.31 - 1.44: 5279 1.44 - 1.57: 10103 1.57 - 1.71: 15 1.71 - 1.84: 164 Bond restraints: 18340 Sorted by residual: bond pdb=" CAM 6EU A 901 " pdb=" OAC 6EU A 901 " ideal model delta sigma weight residual 1.422 1.195 0.227 2.00e-02 2.50e+03 1.29e+02 bond pdb=" CAM 6EU B 901 " pdb=" OAC 6EU B 901 " ideal model delta sigma weight residual 1.422 1.196 0.226 2.00e-02 2.50e+03 1.28e+02 bond pdb=" CAM 6EU D 901 " pdb=" OAC 6EU D 901 " ideal model delta sigma weight residual 1.422 1.198 0.224 2.00e-02 2.50e+03 1.25e+02 bond pdb=" CAM 6EU C 901 " pdb=" OAC 6EU C 901 " ideal model delta sigma weight residual 1.422 1.201 0.221 2.00e-02 2.50e+03 1.23e+02 bond pdb=" CAV 6EU C 901 " pdb=" CBB 6EU C 901 " ideal model delta sigma weight residual 1.330 1.541 -0.211 2.00e-02 2.50e+03 1.11e+02 ... (remaining 18335 not shown) Histogram of bond angle deviations from ideal: 95.36 - 103.11: 132 103.11 - 110.85: 6470 110.85 - 118.60: 7692 118.60 - 126.34: 10352 126.34 - 134.08: 238 Bond angle restraints: 24884 Sorted by residual: angle pdb=" CAN 6EU D 901 " pdb=" CAJ 6EU D 901 " pdb=" CAO 6EU D 901 " ideal model delta sigma weight residual 115.38 132.49 -17.11 3.00e+00 1.11e-01 3.25e+01 angle pdb=" CAN 6EU A 901 " pdb=" CAJ 6EU A 901 " pdb=" CAO 6EU A 901 " ideal model delta sigma weight residual 115.38 132.35 -16.97 3.00e+00 1.11e-01 3.20e+01 angle pdb=" C SER C 711 " pdb=" N PHE C 712 " pdb=" CA PHE C 712 " ideal model delta sigma weight residual 121.54 131.80 -10.26 1.91e+00 2.74e-01 2.88e+01 angle pdb=" CAN 6EU B 901 " pdb=" CAJ 6EU B 901 " pdb=" CAO 6EU B 901 " ideal model delta sigma weight residual 115.38 131.38 -16.00 3.00e+00 1.11e-01 2.84e+01 angle pdb=" C SER B 711 " pdb=" N PHE B 712 " pdb=" CA PHE B 712 " ideal model delta sigma weight residual 121.54 131.70 -10.16 1.91e+00 2.74e-01 2.83e+01 ... (remaining 24879 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.45: 10214 16.45 - 32.90: 654 32.90 - 49.35: 130 49.35 - 65.80: 32 65.80 - 82.25: 17 Dihedral angle restraints: 11047 sinusoidal: 4619 harmonic: 6428 Sorted by residual: dihedral pdb=" CA PHE A 429 " pdb=" C PHE A 429 " pdb=" N VAL A 430 " pdb=" CA VAL A 430 " ideal model delta harmonic sigma weight residual -180.00 -156.25 -23.75 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA TYR B 653 " pdb=" C TYR B 653 " pdb=" N ASP B 654 " pdb=" CA ASP B 654 " ideal model delta harmonic sigma weight residual 180.00 156.28 23.72 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA TYR C 653 " pdb=" C TYR C 653 " pdb=" N ASP C 654 " pdb=" CA ASP C 654 " ideal model delta harmonic sigma weight residual 180.00 156.33 23.67 0 5.00e+00 4.00e-02 2.24e+01 ... (remaining 11044 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 2760 0.131 - 0.261: 16 0.261 - 0.392: 4 0.392 - 0.522: 8 0.522 - 0.653: 4 Chirality restraints: 2792 Sorted by residual: chirality pdb=" CAJ 6EU A 901 " pdb=" CAK 6EU A 901 " pdb=" CAN 6EU A 901 " pdb=" CAO 6EU A 901 " both_signs ideal model delta sigma weight residual False 2.66 2.00 0.65 2.00e-01 2.50e+01 1.07e+01 chirality pdb=" CAJ 6EU D 901 " pdb=" CAK 6EU D 901 " pdb=" CAN 6EU D 901 " pdb=" CAO 6EU D 901 " both_signs ideal model delta sigma weight residual False 2.66 2.00 0.65 2.00e-01 2.50e+01 1.06e+01 chirality pdb=" CAJ 6EU B 901 " pdb=" CAK 6EU B 901 " pdb=" CAN 6EU B 901 " pdb=" CAO 6EU B 901 " both_signs ideal model delta sigma weight residual False 2.66 2.02 0.64 2.00e-01 2.50e+01 1.03e+01 ... (remaining 2789 not shown) Planarity restraints: 3064 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAM 6EU B 901 " -0.095 2.00e-02 2.50e+03 1.67e-01 2.78e+02 pdb=" CAV 6EU B 901 " 0.289 2.00e-02 2.50e+03 pdb=" CBB 6EU B 901 " -0.094 2.00e-02 2.50e+03 pdb=" CBD 6EU B 901 " -0.099 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAM 6EU C 901 " 0.094 2.00e-02 2.50e+03 1.63e-01 2.66e+02 pdb=" CAV 6EU C 901 " -0.283 2.00e-02 2.50e+03 pdb=" CBB 6EU C 901 " 0.092 2.00e-02 2.50e+03 pdb=" CBD 6EU C 901 " 0.096 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAM 6EU A 901 " -0.092 2.00e-02 2.50e+03 1.61e-01 2.60e+02 pdb=" CAV 6EU A 901 " 0.279 2.00e-02 2.50e+03 pdb=" CBB 6EU A 901 " -0.091 2.00e-02 2.50e+03 pdb=" CBD 6EU A 901 " -0.096 2.00e-02 2.50e+03 ... (remaining 3061 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 211 2.62 - 3.19: 17197 3.19 - 3.76: 27565 3.76 - 4.33: 38641 4.33 - 4.90: 63914 Nonbonded interactions: 147528 Sorted by model distance: nonbonded pdb=" OG1 THR B 731 " pdb=" OD1 ASP B 733 " model vdw 2.046 2.440 nonbonded pdb=" OG1 THR D 731 " pdb=" OD1 ASP D 733 " model vdw 2.077 2.440 nonbonded pdb=" OG1 THR A 731 " pdb=" OD1 ASP A 733 " model vdw 2.110 2.440 nonbonded pdb=" OG1 THR C 731 " pdb=" OD1 ASP C 733 " model vdw 2.126 2.440 nonbonded pdb=" O ILE C 672 " pdb=" ND2 ASN C 676 " model vdw 2.204 2.520 ... (remaining 147523 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 185 through 752 or resid 901)) selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 8.380 Check model and map are aligned: 0.280 Set scattering table: 0.180 Process input model: 46.610 Find NCS groups from input model: 1.320 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: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 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 : 0.013 0.227 18340 Z= 0.822 Angle : 0.958 17.110 24884 Z= 0.482 Chirality : 0.058 0.653 2792 Planarity : 0.008 0.167 3064 Dihedral : 12.078 82.246 6916 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.71 % Favored : 94.11 % Rotamer: Outliers : 0.41 % Allowed : 3.37 % Favored : 96.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.21 (0.18), residues: 2172 helix: 1.16 (0.14), residues: 1348 sheet: -1.26 (0.49), residues: 76 loop : -1.61 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 749 HIS 0.005 0.002 HIS B 320 PHE 0.019 0.002 PHE C 649 TYR 0.019 0.002 TYR D 511 ARG 0.005 0.001 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 725 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 717 time to evaluate : 2.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 ASN cc_start: 0.9013 (t0) cc_final: 0.8737 (t0) REVERT: A 378 HIS cc_start: 0.7733 (p-80) cc_final: 0.7478 (p-80) REVERT: A 394 SER cc_start: 0.8830 (m) cc_final: 0.8522 (p) REVERT: A 420 ARG cc_start: 0.8382 (mtt-85) cc_final: 0.8127 (mtp85) REVERT: A 465 LEU cc_start: 0.8934 (tp) cc_final: 0.8389 (tp) REVERT: A 483 SER cc_start: 0.9511 (m) cc_final: 0.9217 (p) REVERT: A 562 MET cc_start: 0.8673 (mmm) cc_final: 0.8419 (mmm) REVERT: A 687 ASN cc_start: 0.9067 (t0) cc_final: 0.8646 (t0) REVERT: A 688 LYS cc_start: 0.8804 (mmtt) cc_final: 0.8498 (mptt) REVERT: D 236 PHE cc_start: 0.8700 (m-80) cc_final: 0.8500 (m-10) REVERT: D 310 ASN cc_start: 0.8833 (t0) cc_final: 0.8561 (t0) REVERT: D 394 SER cc_start: 0.8931 (m) cc_final: 0.8694 (p) REVERT: D 404 SER cc_start: 0.7732 (m) cc_final: 0.7364 (p) REVERT: D 428 ARG cc_start: 0.8456 (mmt180) cc_final: 0.8036 (mmt180) REVERT: D 536 GLU cc_start: 0.8280 (mp0) cc_final: 0.7735 (mp0) REVERT: D 561 GLN cc_start: 0.8339 (tp40) cc_final: 0.8106 (mp10) REVERT: D 687 ASN cc_start: 0.9092 (t0) cc_final: 0.8680 (t0) REVERT: D 688 LYS cc_start: 0.8549 (mmtm) cc_final: 0.8091 (mmtp) REVERT: D 698 LYS cc_start: 0.9030 (mttp) cc_final: 0.8820 (mttm) REVERT: D 725 LEU cc_start: 0.8750 (mt) cc_final: 0.8541 (mp) REVERT: B 226 ASP cc_start: 0.8483 (t0) cc_final: 0.7862 (t0) REVERT: B 360 PRO cc_start: 0.8619 (Cg_exo) cc_final: 0.7758 (Cg_endo) REVERT: B 363 ARG cc_start: 0.7980 (tpp-160) cc_final: 0.7514 (tpp80) REVERT: B 372 TRP cc_start: 0.8846 (p-90) cc_final: 0.8626 (p-90) REVERT: B 483 SER cc_start: 0.9443 (m) cc_final: 0.9129 (p) REVERT: B 509 ASP cc_start: 0.7565 (OUTLIER) cc_final: 0.7353 (m-30) REVERT: B 562 MET cc_start: 0.8739 (mmm) cc_final: 0.8511 (mmm) REVERT: B 682 MET cc_start: 0.8599 (mtp) cc_final: 0.8224 (mtm) REVERT: B 687 ASN cc_start: 0.9119 (t0) cc_final: 0.8566 (t0) REVERT: C 358 HIS cc_start: 0.7347 (m-70) cc_final: 0.6303 (m-70) REVERT: C 363 ARG cc_start: 0.7902 (tpp-160) cc_final: 0.7238 (mmm-85) REVERT: C 420 ARG cc_start: 0.8305 (mtt-85) cc_final: 0.8081 (mtp85) REVERT: C 652 ASN cc_start: 0.7803 (m-40) cc_final: 0.7467 (t0) REVERT: C 687 ASN cc_start: 0.9141 (t0) cc_final: 0.8759 (t0) REVERT: C 688 LYS cc_start: 0.8704 (mmtt) cc_final: 0.8297 (mptt) outliers start: 8 outliers final: 4 residues processed: 722 average time/residue: 0.3256 time to fit residues: 340.4158 Evaluate side-chains 485 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 480 time to evaluate : 1.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain D residue 512 SER Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain C residue 512 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 0.9990 chunk 163 optimal weight: 9.9990 chunk 90 optimal weight: 0.7980 chunk 55 optimal weight: 8.9990 chunk 110 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 chunk 169 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 126 optimal weight: 6.9990 chunk 196 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 ASN D 228 GLN D 393 ASN ** D 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 676 ASN B 393 ASN B 748 ASN C 202 GLN C 393 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18340 Z= 0.180 Angle : 0.602 13.051 24884 Z= 0.310 Chirality : 0.039 0.213 2792 Planarity : 0.004 0.049 3064 Dihedral : 7.429 59.965 2782 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.52 % Favored : 94.29 % Rotamer: Outliers : 1.71 % Allowed : 13.07 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.79 (0.18), residues: 2172 helix: 1.63 (0.14), residues: 1340 sheet: -0.76 (0.51), residues: 76 loop : -1.38 (0.24), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 697 HIS 0.004 0.001 HIS C 358 PHE 0.020 0.001 PHE D 266 TYR 0.024 0.001 TYR D 309 ARG 0.007 0.001 ARG B 420 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 552 time to evaluate : 2.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 ASN cc_start: 0.8872 (t0) cc_final: 0.8651 (t0) REVERT: A 372 TRP cc_start: 0.8254 (p-90) cc_final: 0.8007 (p-90) REVERT: A 391 GLU cc_start: 0.8218 (mp0) cc_final: 0.8011 (pt0) REVERT: A 394 SER cc_start: 0.8829 (m) cc_final: 0.8412 (p) REVERT: A 499 ARG cc_start: 0.8117 (tpp-160) cc_final: 0.7555 (mmt-90) REVERT: A 509 ASP cc_start: 0.7904 (m-30) cc_final: 0.7691 (m-30) REVERT: A 562 MET cc_start: 0.8639 (mmm) cc_final: 0.8372 (mmm) REVERT: D 236 PHE cc_start: 0.8665 (m-80) cc_final: 0.8456 (m-10) REVERT: D 394 SER cc_start: 0.8869 (m) cc_final: 0.8636 (p) REVERT: D 428 ARG cc_start: 0.8358 (mmt180) cc_final: 0.8124 (mmt180) REVERT: D 561 GLN cc_start: 0.8168 (tp40) cc_final: 0.7964 (mp10) REVERT: B 213 ASN cc_start: 0.7964 (t0) cc_final: 0.7549 (t0) REVERT: B 226 ASP cc_start: 0.8450 (t0) cc_final: 0.7834 (t0) REVERT: B 359 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.7204 (tm-30) REVERT: B 360 PRO cc_start: 0.8652 (Cg_exo) cc_final: 0.8416 (Cg_endo) REVERT: B 687 ASN cc_start: 0.9002 (t0) cc_final: 0.8792 (t0) REVERT: C 198 TYR cc_start: 0.7589 (t80) cc_final: 0.7304 (t80) REVERT: C 293 GLU cc_start: 0.8830 (mm-30) cc_final: 0.8610 (mt-10) REVERT: C 460 LEU cc_start: 0.8070 (mt) cc_final: 0.7742 (tp) REVERT: C 509 ASP cc_start: 0.7889 (m-30) cc_final: 0.7665 (m-30) REVERT: C 572 MET cc_start: 0.8104 (mmt) cc_final: 0.7635 (mmt) REVERT: C 687 ASN cc_start: 0.9047 (t0) cc_final: 0.8657 (t0) outliers start: 33 outliers final: 22 residues processed: 566 average time/residue: 0.2849 time to fit residues: 243.7461 Evaluate side-chains 505 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 482 time to evaluate : 1.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 514 ILE Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 359 GLU Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 660 ILE Chi-restraints excluded: chain C residue 722 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 109 optimal weight: 10.0000 chunk 60 optimal weight: 0.0670 chunk 163 optimal weight: 0.0870 chunk 133 optimal weight: 1.9990 chunk 54 optimal weight: 20.0000 chunk 196 optimal weight: 5.9990 chunk 212 optimal weight: 0.8980 chunk 175 optimal weight: 9.9990 chunk 194 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 chunk 157 optimal weight: 4.9990 overall best weight: 1.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 285 ASN B 310 ASN ** B 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 378 HIS C 560 GLN ** C 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18340 Z= 0.231 Angle : 0.571 13.170 24884 Z= 0.293 Chirality : 0.039 0.162 2792 Planarity : 0.004 0.049 3064 Dihedral : 7.179 59.913 2776 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.80 % Favored : 94.01 % Rotamer: Outliers : 2.80 % Allowed : 14.37 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.71 (0.18), residues: 2172 helix: 1.53 (0.14), residues: 1368 sheet: -0.69 (0.51), residues: 76 loop : -1.46 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 372 HIS 0.003 0.001 HIS B 206 PHE 0.014 0.001 PHE B 304 TYR 0.015 0.001 TYR B 374 ARG 0.005 0.001 ARG C 420 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 497 time to evaluate : 2.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 ASN cc_start: 0.7891 (t0) cc_final: 0.7435 (t0) REVERT: A 310 ASN cc_start: 0.8855 (t0) cc_final: 0.8644 (t0) REVERT: A 343 SER cc_start: 0.9179 (m) cc_final: 0.8919 (m) REVERT: A 372 TRP cc_start: 0.8274 (p-90) cc_final: 0.7978 (p-90) REVERT: A 394 SER cc_start: 0.8880 (m) cc_final: 0.8394 (p) REVERT: A 509 ASP cc_start: 0.7915 (m-30) cc_final: 0.7639 (m-30) REVERT: A 562 MET cc_start: 0.8689 (mmm) cc_final: 0.8323 (mmt) REVERT: D 236 PHE cc_start: 0.8672 (m-80) cc_final: 0.8356 (m-10) REVERT: D 394 SER cc_start: 0.8910 (m) cc_final: 0.8634 (p) REVERT: D 428 ARG cc_start: 0.8376 (mmt180) cc_final: 0.8156 (mmt180) REVERT: D 464 LYS cc_start: 0.8286 (mmtt) cc_final: 0.8045 (mmmt) REVERT: D 684 GLU cc_start: 0.7524 (tp30) cc_final: 0.7312 (tp30) REVERT: B 213 ASN cc_start: 0.7857 (t0) cc_final: 0.7519 (t0) REVERT: B 226 ASP cc_start: 0.8462 (t0) cc_final: 0.7821 (t0) REVERT: B 360 PRO cc_start: 0.8668 (Cg_exo) cc_final: 0.8253 (Cg_endo) REVERT: B 372 TRP cc_start: 0.8439 (p-90) cc_final: 0.8088 (p-90) REVERT: B 491 ARG cc_start: 0.9035 (mmm160) cc_final: 0.8262 (ttp-170) REVERT: B 687 ASN cc_start: 0.9087 (t0) cc_final: 0.8801 (t0) REVERT: B 691 GLN cc_start: 0.8171 (mp10) cc_final: 0.7928 (mp10) REVERT: B 746 GLU cc_start: 0.8363 (tp30) cc_final: 0.8162 (tm-30) REVERT: C 198 TYR cc_start: 0.7654 (t80) cc_final: 0.7364 (t80) REVERT: C 372 TRP cc_start: 0.8675 (p-90) cc_final: 0.8301 (p-90) REVERT: C 378 HIS cc_start: 0.7116 (OUTLIER) cc_final: 0.6725 (p-80) REVERT: C 460 LEU cc_start: 0.8066 (mt) cc_final: 0.7823 (tp) REVERT: C 491 ARG cc_start: 0.9024 (mmm160) cc_final: 0.8616 (mtp85) REVERT: C 509 ASP cc_start: 0.7885 (m-30) cc_final: 0.7634 (m-30) REVERT: C 562 MET cc_start: 0.8645 (tpp) cc_final: 0.8186 (mmt) outliers start: 54 outliers final: 36 residues processed: 524 average time/residue: 0.2679 time to fit residues: 216.2038 Evaluate side-chains 504 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 467 time to evaluate : 1.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 358 HIS Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 514 ILE Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 741 CYS Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 378 HIS Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 512 SER Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 660 ILE Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 704 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 194 optimal weight: 6.9990 chunk 147 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 21 optimal weight: 0.4980 chunk 93 optimal weight: 2.9990 chunk 131 optimal weight: 0.9990 chunk 197 optimal weight: 2.9990 chunk 208 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 186 optimal weight: 2.9990 chunk 56 optimal weight: 9.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 ASN B 727 GLN C 378 HIS C 560 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18340 Z= 0.209 Angle : 0.550 10.692 24884 Z= 0.283 Chirality : 0.038 0.160 2792 Planarity : 0.004 0.050 3064 Dihedral : 6.996 59.952 2776 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.76 % Favored : 94.06 % Rotamer: Outliers : 3.27 % Allowed : 15.30 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.81 (0.18), residues: 2172 helix: 1.60 (0.14), residues: 1368 sheet: -0.49 (0.54), residues: 76 loop : -1.43 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 372 HIS 0.020 0.001 HIS C 378 PHE 0.015 0.001 PHE A 496 TYR 0.012 0.001 TYR A 309 ARG 0.004 0.000 ARG C 420 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 480 time to evaluate : 2.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 GLU cc_start: 0.8737 (mm-30) cc_final: 0.8534 (mt-10) REVERT: A 310 ASN cc_start: 0.8843 (t0) cc_final: 0.8605 (t0) REVERT: A 343 SER cc_start: 0.9184 (m) cc_final: 0.8917 (m) REVERT: A 372 TRP cc_start: 0.8238 (p-90) cc_final: 0.7837 (p-90) REVERT: A 394 SER cc_start: 0.8844 (m) cc_final: 0.8304 (p) REVERT: A 420 ARG cc_start: 0.8416 (mtp85) cc_final: 0.8176 (mtp85) REVERT: A 445 MET cc_start: 0.9444 (mmm) cc_final: 0.9192 (mmm) REVERT: A 509 ASP cc_start: 0.7938 (m-30) cc_final: 0.7671 (m-30) REVERT: A 562 MET cc_start: 0.8675 (mmm) cc_final: 0.8279 (mmt) REVERT: A 572 MET cc_start: 0.8684 (OUTLIER) cc_final: 0.8419 (mmm) REVERT: A 652 ASN cc_start: 0.8086 (OUTLIER) cc_final: 0.7859 (t0) REVERT: D 211 ARG cc_start: 0.8876 (mmp80) cc_final: 0.8587 (mmt180) REVERT: D 236 PHE cc_start: 0.8641 (m-80) cc_final: 0.8275 (m-10) REVERT: D 394 SER cc_start: 0.8840 (m) cc_final: 0.8540 (p) REVERT: D 464 LYS cc_start: 0.8292 (mmtt) cc_final: 0.8049 (mmmt) REVERT: B 213 ASN cc_start: 0.7894 (t0) cc_final: 0.7248 (t0) REVERT: B 216 LEU cc_start: 0.9506 (mt) cc_final: 0.9106 (mt) REVERT: B 226 ASP cc_start: 0.8444 (t0) cc_final: 0.7817 (t0) REVERT: B 491 ARG cc_start: 0.9044 (mmm160) cc_final: 0.8341 (ttp-170) REVERT: B 687 ASN cc_start: 0.9055 (t0) cc_final: 0.8821 (t0) REVERT: C 198 TYR cc_start: 0.7635 (t80) cc_final: 0.7302 (t80) REVERT: C 304 PHE cc_start: 0.8672 (OUTLIER) cc_final: 0.7620 (p90) REVERT: C 323 LEU cc_start: 0.8203 (tp) cc_final: 0.7941 (tp) REVERT: C 378 HIS cc_start: 0.7032 (OUTLIER) cc_final: 0.6638 (p-80) REVERT: C 460 LEU cc_start: 0.8069 (mt) cc_final: 0.7825 (tp) REVERT: C 552 MET cc_start: 0.8338 (tpp) cc_final: 0.8123 (tpp) outliers start: 63 outliers final: 45 residues processed: 511 average time/residue: 0.2722 time to fit residues: 214.5518 Evaluate side-chains 514 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 465 time to evaluate : 2.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 541 MET Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 311 GLU Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 358 HIS Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 514 ILE Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 681 LEU Chi-restraints excluded: chain D residue 741 CYS Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 378 HIS Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 512 SER Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 560 GLN Chi-restraints excluded: chain C residue 660 ILE Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 704 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 173 optimal weight: 1.9990 chunk 118 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 155 optimal weight: 0.9990 chunk 86 optimal weight: 8.9990 chunk 178 optimal weight: 0.9980 chunk 144 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 106 optimal weight: 0.5980 chunk 187 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 206 HIS ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 676 ASN B 223 ASN B 652 ASN C 378 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18340 Z= 0.172 Angle : 0.534 14.304 24884 Z= 0.274 Chirality : 0.038 0.160 2792 Planarity : 0.003 0.051 3064 Dihedral : 6.736 59.139 2776 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.31 % Favored : 93.55 % Rotamer: Outliers : 2.85 % Allowed : 16.60 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.92 (0.19), residues: 2172 helix: 1.67 (0.14), residues: 1364 sheet: -0.28 (0.57), residues: 76 loop : -1.37 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 372 HIS 0.012 0.001 HIS C 378 PHE 0.015 0.001 PHE A 304 TYR 0.013 0.001 TYR A 309 ARG 0.004 0.000 ARG B 420 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 488 time to evaluate : 2.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 GLU cc_start: 0.8730 (mm-30) cc_final: 0.8527 (mt-10) REVERT: A 310 ASN cc_start: 0.8829 (t0) cc_final: 0.8587 (t0) REVERT: A 343 SER cc_start: 0.9168 (m) cc_final: 0.8901 (m) REVERT: A 372 TRP cc_start: 0.8209 (p-90) cc_final: 0.7794 (p-90) REVERT: A 394 SER cc_start: 0.8809 (m) cc_final: 0.8282 (p) REVERT: A 420 ARG cc_start: 0.8414 (mtp85) cc_final: 0.8124 (mtp85) REVERT: A 445 MET cc_start: 0.9473 (mmm) cc_final: 0.9230 (mmm) REVERT: A 509 ASP cc_start: 0.7906 (m-30) cc_final: 0.7694 (m-30) REVERT: A 562 MET cc_start: 0.8678 (mmm) cc_final: 0.8259 (mmt) REVERT: A 652 ASN cc_start: 0.8016 (OUTLIER) cc_final: 0.7800 (t0) REVERT: D 236 PHE cc_start: 0.8650 (m-80) cc_final: 0.8282 (m-10) REVERT: D 304 PHE cc_start: 0.8667 (OUTLIER) cc_final: 0.8434 (p90) REVERT: D 372 TRP cc_start: 0.8555 (p-90) cc_final: 0.8321 (p-90) REVERT: D 464 LYS cc_start: 0.8294 (mmtt) cc_final: 0.8049 (mmmt) REVERT: B 213 ASN cc_start: 0.7904 (t0) cc_final: 0.7243 (t0) REVERT: B 216 LEU cc_start: 0.9508 (mt) cc_final: 0.9113 (mt) REVERT: B 226 ASP cc_start: 0.8448 (t0) cc_final: 0.7826 (t0) REVERT: B 491 ARG cc_start: 0.9046 (mmm160) cc_final: 0.8335 (ttp-170) REVERT: B 631 TYR cc_start: 0.8314 (t80) cc_final: 0.8021 (t80) REVERT: B 687 ASN cc_start: 0.9070 (t0) cc_final: 0.8856 (t0) REVERT: C 198 TYR cc_start: 0.7626 (t80) cc_final: 0.7280 (t80) REVERT: C 323 LEU cc_start: 0.8260 (tp) cc_final: 0.7975 (tp) REVERT: C 378 HIS cc_start: 0.7072 (OUTLIER) cc_final: 0.6667 (p-80) REVERT: C 460 LEU cc_start: 0.8030 (mt) cc_final: 0.7802 (tp) REVERT: C 491 ARG cc_start: 0.9014 (mmm160) cc_final: 0.8532 (mtp-110) outliers start: 55 outliers final: 36 residues processed: 513 average time/residue: 0.2678 time to fit residues: 213.9053 Evaluate side-chains 503 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 464 time to evaluate : 2.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 541 MET Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 358 HIS Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 514 ILE Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 681 LEU Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 378 HIS Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 512 SER Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 660 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 70 optimal weight: 0.7980 chunk 188 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 208 optimal weight: 0.0270 chunk 173 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 109 optimal weight: 9.9990 overall best weight: 0.7638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 652 ASN C 378 HIS C 560 GLN ** C 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 18340 Z= 0.151 Angle : 0.531 13.919 24884 Z= 0.272 Chirality : 0.038 0.160 2792 Planarity : 0.003 0.051 3064 Dihedral : 6.370 57.533 2776 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.49 % Allowed : 17.27 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.19), residues: 2172 helix: 1.73 (0.14), residues: 1360 sheet: -0.26 (0.58), residues: 76 loop : -1.32 (0.24), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 372 HIS 0.021 0.001 HIS C 378 PHE 0.013 0.001 PHE A 304 TYR 0.014 0.001 TYR A 309 ARG 0.005 0.000 ARG B 420 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 495 time to evaluate : 1.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 SER cc_start: 0.9145 (m) cc_final: 0.8895 (m) REVERT: A 372 TRP cc_start: 0.8219 (p-90) cc_final: 0.7678 (p-90) REVERT: A 394 SER cc_start: 0.8805 (m) cc_final: 0.8258 (p) REVERT: A 420 ARG cc_start: 0.8429 (mtp85) cc_final: 0.8124 (mtp85) REVERT: A 562 MET cc_start: 0.8665 (mmm) cc_final: 0.8205 (mmt) REVERT: A 746 GLU cc_start: 0.7990 (tp30) cc_final: 0.7727 (tm-30) REVERT: D 220 LEU cc_start: 0.9008 (mm) cc_final: 0.8806 (mm) REVERT: D 236 PHE cc_start: 0.8656 (m-80) cc_final: 0.8248 (m-10) REVERT: D 304 PHE cc_start: 0.8614 (OUTLIER) cc_final: 0.8389 (p90) REVERT: D 372 TRP cc_start: 0.8513 (p-90) cc_final: 0.8306 (p-90) REVERT: D 445 MET cc_start: 0.9486 (mmm) cc_final: 0.9224 (mmm) REVERT: D 464 LYS cc_start: 0.8289 (mmtt) cc_final: 0.8052 (mmmt) REVERT: D 491 ARG cc_start: 0.9010 (mmm160) cc_final: 0.8587 (mtp85) REVERT: B 213 ASN cc_start: 0.7844 (t0) cc_final: 0.7176 (t0) REVERT: B 216 LEU cc_start: 0.9509 (mt) cc_final: 0.9115 (mt) REVERT: B 226 ASP cc_start: 0.8447 (t0) cc_final: 0.7819 (t0) REVERT: B 445 MET cc_start: 0.9495 (mmm) cc_final: 0.9237 (mmm) REVERT: B 491 ARG cc_start: 0.9026 (mmm160) cc_final: 0.8262 (ttp-170) REVERT: B 631 TYR cc_start: 0.8287 (t80) cc_final: 0.7982 (t80) REVERT: B 687 ASN cc_start: 0.9081 (t0) cc_final: 0.8873 (t0) REVERT: B 733 ASP cc_start: 0.8468 (p0) cc_final: 0.8259 (p0) REVERT: C 198 TYR cc_start: 0.7661 (t80) cc_final: 0.7364 (t80) REVERT: C 378 HIS cc_start: 0.7183 (OUTLIER) cc_final: 0.6840 (p-80) REVERT: C 491 ARG cc_start: 0.8987 (mmm160) cc_final: 0.8610 (mtp85) REVERT: C 524 LEU cc_start: 0.9086 (mt) cc_final: 0.8842 (mt) REVERT: C 562 MET cc_start: 0.8542 (mmt) cc_final: 0.7686 (mmt) outliers start: 48 outliers final: 35 residues processed: 519 average time/residue: 0.2687 time to fit residues: 217.1580 Evaluate side-chains 505 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 468 time to evaluate : 2.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 358 HIS Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 514 ILE Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 378 HIS Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 660 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 201 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 119 optimal weight: 0.8980 chunk 152 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 175 optimal weight: 7.9990 chunk 116 optimal weight: 5.9990 chunk 208 optimal weight: 0.8980 chunk 130 optimal weight: 0.0570 chunk 126 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 overall best weight: 1.1700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 378 HIS C 652 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18340 Z= 0.180 Angle : 0.546 17.110 24884 Z= 0.276 Chirality : 0.038 0.232 2792 Planarity : 0.003 0.051 3064 Dihedral : 6.081 55.454 2776 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 3.01 % Allowed : 17.32 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.98 (0.19), residues: 2172 helix: 1.70 (0.14), residues: 1360 sheet: -0.21 (0.58), residues: 76 loop : -1.30 (0.24), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 749 HIS 0.011 0.001 HIS C 378 PHE 0.014 0.001 PHE A 304 TYR 0.025 0.001 TYR B 309 ARG 0.004 0.000 ARG C 420 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 466 time to evaluate : 2.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 GLU cc_start: 0.8724 (mt-10) cc_final: 0.8373 (mt-10) REVERT: A 304 PHE cc_start: 0.8406 (OUTLIER) cc_final: 0.8047 (p90) REVERT: A 343 SER cc_start: 0.9153 (m) cc_final: 0.8901 (m) REVERT: A 372 TRP cc_start: 0.8229 (p-90) cc_final: 0.7765 (p-90) REVERT: A 394 SER cc_start: 0.8776 (m) cc_final: 0.8242 (p) REVERT: A 562 MET cc_start: 0.8693 (mmm) cc_final: 0.8245 (mmt) REVERT: A 682 MET cc_start: 0.8568 (mmm) cc_final: 0.8148 (mtt) REVERT: D 220 LEU cc_start: 0.9011 (mm) cc_final: 0.8805 (mm) REVERT: D 236 PHE cc_start: 0.8659 (m-80) cc_final: 0.8227 (m-10) REVERT: D 304 PHE cc_start: 0.8593 (OUTLIER) cc_final: 0.8338 (p90) REVERT: D 372 TRP cc_start: 0.8528 (p-90) cc_final: 0.8298 (p-90) REVERT: D 464 LYS cc_start: 0.8281 (mmtt) cc_final: 0.8040 (mmmt) REVERT: D 491 ARG cc_start: 0.9017 (mmm160) cc_final: 0.8597 (mtp85) REVERT: B 213 ASN cc_start: 0.7892 (t0) cc_final: 0.7200 (t0) REVERT: B 214 MET cc_start: 0.8611 (ttt) cc_final: 0.8393 (tpp) REVERT: B 216 LEU cc_start: 0.9509 (mt) cc_final: 0.9107 (mt) REVERT: B 226 ASP cc_start: 0.8478 (t0) cc_final: 0.7861 (t0) REVERT: B 445 MET cc_start: 0.9505 (mmm) cc_final: 0.9257 (mmm) REVERT: B 491 ARG cc_start: 0.9023 (mmm160) cc_final: 0.8339 (ttp-170) REVERT: B 631 TYR cc_start: 0.8309 (t80) cc_final: 0.7997 (t80) REVERT: C 198 TYR cc_start: 0.7637 (t80) cc_final: 0.7327 (t80) REVERT: C 378 HIS cc_start: 0.7281 (OUTLIER) cc_final: 0.6874 (p-80) REVERT: C 491 ARG cc_start: 0.8997 (mmm160) cc_final: 0.8528 (mtp-110) REVERT: C 524 LEU cc_start: 0.9104 (mt) cc_final: 0.8866 (mt) outliers start: 58 outliers final: 50 residues processed: 498 average time/residue: 0.2681 time to fit residues: 209.6944 Evaluate side-chains 510 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 457 time to evaluate : 1.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 541 MET Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 358 HIS Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 514 ILE Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 378 HIS Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 660 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 128 optimal weight: 0.2980 chunk 83 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 141 optimal weight: 1.9990 chunk 102 optimal weight: 0.5980 chunk 19 optimal weight: 6.9990 chunk 163 optimal weight: 10.0000 chunk 189 optimal weight: 0.7980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 260 GLN ** D 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 676 ASN B 260 GLN C 378 HIS C 652 ASN ** C 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18340 Z= 0.149 Angle : 0.547 15.035 24884 Z= 0.276 Chirality : 0.038 0.248 2792 Planarity : 0.003 0.051 3064 Dihedral : 5.711 51.862 2776 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.54 % Allowed : 18.31 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.96 (0.19), residues: 2172 helix: 1.68 (0.14), residues: 1364 sheet: -0.32 (0.57), residues: 76 loop : -1.29 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 372 HIS 0.013 0.001 HIS C 378 PHE 0.014 0.001 PHE B 582 TYR 0.019 0.001 TYR B 309 ARG 0.005 0.000 ARG A 420 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 471 time to evaluate : 2.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8335 (mt-10) REVERT: A 343 SER cc_start: 0.9133 (m) cc_final: 0.8883 (m) REVERT: A 372 TRP cc_start: 0.8222 (p-90) cc_final: 0.7708 (p-90) REVERT: A 394 SER cc_start: 0.8768 (m) cc_final: 0.8225 (p) REVERT: A 481 SER cc_start: 0.9165 (m) cc_final: 0.8917 (t) REVERT: A 562 MET cc_start: 0.8695 (mmm) cc_final: 0.8237 (mmt) REVERT: D 236 PHE cc_start: 0.8637 (m-80) cc_final: 0.8185 (m-10) REVERT: D 372 TRP cc_start: 0.8517 (p-90) cc_final: 0.8259 (p-90) REVERT: D 464 LYS cc_start: 0.8272 (mmtt) cc_final: 0.8033 (mmmt) REVERT: D 491 ARG cc_start: 0.9011 (mmm160) cc_final: 0.8592 (mtp85) REVERT: B 213 ASN cc_start: 0.7865 (t0) cc_final: 0.7187 (t0) REVERT: B 214 MET cc_start: 0.8623 (ttt) cc_final: 0.8404 (tpp) REVERT: B 216 LEU cc_start: 0.9502 (mt) cc_final: 0.9095 (mt) REVERT: B 226 ASP cc_start: 0.8495 (t0) cc_final: 0.7899 (t0) REVERT: B 491 ARG cc_start: 0.9013 (mmm160) cc_final: 0.8246 (ttp-170) REVERT: B 631 TYR cc_start: 0.8275 (t80) cc_final: 0.7934 (t80) REVERT: C 198 TYR cc_start: 0.7732 (t80) cc_final: 0.7410 (t80) REVERT: C 378 HIS cc_start: 0.7250 (OUTLIER) cc_final: 0.6771 (p-80) REVERT: C 491 ARG cc_start: 0.8972 (mmm160) cc_final: 0.8498 (mtp-110) REVERT: C 524 LEU cc_start: 0.9085 (mt) cc_final: 0.8847 (mt) outliers start: 49 outliers final: 39 residues processed: 497 average time/residue: 0.2638 time to fit residues: 203.9322 Evaluate side-chains 500 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 460 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 358 HIS Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 514 ILE Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 378 HIS Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 660 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 199 optimal weight: 0.8980 chunk 181 optimal weight: 6.9990 chunk 194 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 chunk 59 optimal weight: 9.9990 chunk 175 optimal weight: 10.0000 chunk 183 optimal weight: 4.9990 chunk 193 optimal weight: 0.6980 chunk 127 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 GLN ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 560 GLN ** D 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 310 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 18340 Z= 0.229 Angle : 0.575 15.311 24884 Z= 0.291 Chirality : 0.039 0.247 2792 Planarity : 0.004 0.051 3064 Dihedral : 5.598 48.901 2776 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.65 % Allowed : 18.62 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.00 (0.19), residues: 2172 helix: 1.76 (0.14), residues: 1328 sheet: -0.44 (0.55), residues: 76 loop : -1.21 (0.24), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 372 HIS 0.014 0.001 HIS C 378 PHE 0.019 0.001 PHE B 582 TYR 0.029 0.001 TYR B 309 ARG 0.004 0.000 ARG A 420 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 460 time to evaluate : 2.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 GLN cc_start: 0.8580 (mt0) cc_final: 0.8362 (mt0) REVERT: A 293 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8344 (mt-10) REVERT: A 343 SER cc_start: 0.9128 (m) cc_final: 0.8880 (m) REVERT: A 372 TRP cc_start: 0.8224 (p-90) cc_final: 0.7790 (p-90) REVERT: A 394 SER cc_start: 0.8778 (m) cc_final: 0.8224 (p) REVERT: A 562 MET cc_start: 0.8784 (mmm) cc_final: 0.8474 (mmt) REVERT: A 572 MET cc_start: 0.8433 (tpp) cc_final: 0.8112 (mmm) REVERT: D 236 PHE cc_start: 0.8670 (m-80) cc_final: 0.8204 (m-10) REVERT: D 372 TRP cc_start: 0.8534 (p-90) cc_final: 0.8290 (p-90) REVERT: D 445 MET cc_start: 0.9482 (mmm) cc_final: 0.9237 (mmm) REVERT: D 464 LYS cc_start: 0.8260 (mmtt) cc_final: 0.8048 (mmmt) REVERT: B 213 ASN cc_start: 0.7887 (t0) cc_final: 0.7190 (t0) REVERT: B 214 MET cc_start: 0.8645 (ttt) cc_final: 0.8427 (tpp) REVERT: B 216 LEU cc_start: 0.9498 (mt) cc_final: 0.9034 (mt) REVERT: B 226 ASP cc_start: 0.8506 (t0) cc_final: 0.7891 (t0) REVERT: B 236 PHE cc_start: 0.8849 (m-80) cc_final: 0.8268 (m-80) REVERT: B 445 MET cc_start: 0.9525 (mmm) cc_final: 0.9284 (mmm) REVERT: B 491 ARG cc_start: 0.9015 (mmm160) cc_final: 0.8319 (ttp-170) REVERT: B 631 TYR cc_start: 0.8353 (t80) cc_final: 0.8025 (t80) REVERT: C 198 TYR cc_start: 0.7734 (t80) cc_final: 0.7395 (t80) REVERT: C 378 HIS cc_start: 0.7151 (OUTLIER) cc_final: 0.6803 (p90) REVERT: C 478 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7897 (tt0) REVERT: C 491 ARG cc_start: 0.8987 (mmm160) cc_final: 0.8494 (mtp-110) outliers start: 51 outliers final: 47 residues processed: 490 average time/residue: 0.2563 time to fit residues: 196.7310 Evaluate side-chains 503 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 455 time to evaluate : 1.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain A residue 390 CYS Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 358 HIS Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 514 ILE Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 378 HIS Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 660 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 205 optimal weight: 1.9990 chunk 125 optimal weight: 6.9990 chunk 97 optimal weight: 0.0770 chunk 142 optimal weight: 4.9990 chunk 215 optimal weight: 8.9990 chunk 198 optimal weight: 1.9990 chunk 171 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 132 optimal weight: 0.6980 chunk 105 optimal weight: 0.0060 chunk 136 optimal weight: 5.9990 overall best weight: 0.9558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 GLN D 560 GLN ** D 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 378 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18340 Z= 0.169 Angle : 0.578 17.906 24884 Z= 0.286 Chirality : 0.039 0.253 2792 Planarity : 0.004 0.051 3064 Dihedral : 5.277 43.064 2776 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.39 % Allowed : 19.50 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.19), residues: 2172 helix: 1.77 (0.14), residues: 1328 sheet: -0.36 (0.56), residues: 76 loop : -1.19 (0.24), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 372 HIS 0.002 0.001 HIS B 289 PHE 0.021 0.001 PHE A 304 TYR 0.019 0.001 TYR B 309 ARG 0.007 0.000 ARG B 721 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 466 time to evaluate : 2.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 GLN cc_start: 0.8545 (mt0) cc_final: 0.8327 (mt0) REVERT: A 293 GLU cc_start: 0.8730 (mt-10) cc_final: 0.8330 (mt-10) REVERT: A 343 SER cc_start: 0.9110 (m) cc_final: 0.8865 (m) REVERT: A 372 TRP cc_start: 0.8196 (p-90) cc_final: 0.7712 (p-90) REVERT: A 394 SER cc_start: 0.8764 (m) cc_final: 0.8225 (p) REVERT: A 562 MET cc_start: 0.8731 (mmm) cc_final: 0.8413 (mmt) REVERT: D 220 LEU cc_start: 0.9015 (mm) cc_final: 0.8806 (mm) REVERT: D 236 PHE cc_start: 0.8654 (m-80) cc_final: 0.8168 (m-10) REVERT: D 372 TRP cc_start: 0.8522 (p-90) cc_final: 0.8276 (p-90) REVERT: D 491 ARG cc_start: 0.9002 (mmm160) cc_final: 0.8596 (mtp85) REVERT: B 213 ASN cc_start: 0.7875 (t0) cc_final: 0.7184 (t0) REVERT: B 214 MET cc_start: 0.8636 (ttt) cc_final: 0.8417 (tpp) REVERT: B 216 LEU cc_start: 0.9509 (mt) cc_final: 0.9055 (mt) REVERT: B 226 ASP cc_start: 0.8449 (t0) cc_final: 0.7851 (t0) REVERT: B 445 MET cc_start: 0.9517 (mmm) cc_final: 0.9272 (mmm) REVERT: B 491 ARG cc_start: 0.9020 (mmm160) cc_final: 0.8256 (ttp-170) REVERT: B 631 TYR cc_start: 0.8302 (t80) cc_final: 0.7964 (t80) REVERT: C 198 TYR cc_start: 0.7731 (t80) cc_final: 0.7358 (t80) REVERT: C 378 HIS cc_start: 0.7503 (OUTLIER) cc_final: 0.7116 (p-80) REVERT: C 478 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7895 (tt0) REVERT: C 491 ARG cc_start: 0.8978 (mmm160) cc_final: 0.8501 (mtp-110) REVERT: C 524 LEU cc_start: 0.9100 (mt) cc_final: 0.8877 (mt) REVERT: C 572 MET cc_start: 0.8157 (mtt) cc_final: 0.7804 (mtt) outliers start: 46 outliers final: 43 residues processed: 489 average time/residue: 0.2511 time to fit residues: 195.3583 Evaluate side-chains 496 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 452 time to evaluate : 2.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain A residue 390 CYS Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 358 HIS Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 514 ILE Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 600 GLU Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 378 HIS Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 660 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 0.2980 chunk 52 optimal weight: 8.9990 chunk 158 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 171 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 176 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 31 optimal weight: 0.0000 chunk 150 optimal weight: 4.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 GLN ** D 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.143216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.107709 restraints weight = 30536.761| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.91 r_work: 0.3124 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18340 Z= 0.170 Angle : 0.580 16.646 24884 Z= 0.287 Chirality : 0.039 0.235 2792 Planarity : 0.004 0.051 3064 Dihedral : 5.024 36.542 2776 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 2.59 % Allowed : 19.19 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.19), residues: 2172 helix: 1.76 (0.14), residues: 1332 sheet: -0.48 (0.55), residues: 76 loop : -1.18 (0.24), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP D 697 HIS 0.011 0.001 HIS C 378 PHE 0.020 0.001 PHE A 304 TYR 0.024 0.001 TYR A 309 ARG 0.010 0.000 ARG B 721 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4705.78 seconds wall clock time: 84 minutes 57.83 seconds (5097.83 seconds total)