Starting phenix.real_space_refine on Sun Mar 17 11:44:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mze_24091/03_2024/7mze_24091_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mze_24091/03_2024/7mze_24091.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mze_24091/03_2024/7mze_24091_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mze_24091/03_2024/7mze_24091_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mze_24091/03_2024/7mze_24091_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mze_24091/03_2024/7mze_24091.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mze_24091/03_2024/7mze_24091.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mze_24091/03_2024/7mze_24091_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mze_24091/03_2024/7mze_24091_updated.pdb" } resolution = 3.42 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: 6 Type Number sf(0) Gaussians P 2 5.49 5 S 100 5.16 5 Na 1 4.78 5 C 11555 2.51 5 N 2819 2.21 5 O 3141 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 557": "NH1" <-> "NH2" Residue "A PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 557": "NH1" <-> "NH2" Residue "B PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 557": "NH1" <-> "NH2" Residue "B PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 557": "NH1" <-> "NH2" Residue "C GLU 570": "OE1" <-> "OE2" Residue "C PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17618 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4363 Classifications: {'peptide': 537} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 522} Chain: "D" Number of atoms: 4357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4357 Classifications: {'peptide': 536} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 521} Chain: "B" Number of atoms: 4357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4357 Classifications: {'peptide': 536} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 521} Chain: "C" Number of atoms: 4368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4368 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 523} Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {' NA': 1, 'XJ7': 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: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'XJ7': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.55, per 1000 atoms: 0.66 Number of scatterers: 17618 At special positions: 0 Unit cell: (123.432, 124.266, 112.59, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 100 16.00 P 2 15.00 Na 1 11.00 O 3141 8.00 N 2819 7.00 C 11555 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: 7.70 Conformation dependent library (CDL) restraints added in 3.2 seconds 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4062 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 89 helices and 4 sheets defined 58.4% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.83 Creating SS restraints... 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 269 Processing helix chain 'A' and resid 287 through 294 Processing helix chain 'A' and resid 299 through 319 removed outlier: 3.514A 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 342 Processing helix chain 'A' and resid 346 through 354 removed outlier: 3.842A 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: 5.287A pdb=" N LYS A 431 " --> pdb=" O ASP A 427 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ARG A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) removed outlier: 4.394A 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: 3.588A pdb=" N SER A 540 " --> pdb=" O TYR A 537 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL A 542 " --> pdb=" O ALA A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 598 removed outlier: 3.776A pdb=" N ILE A 564 " --> pdb=" O GLN A 560 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N CYS A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 641 removed outlier: 4.008A pdb=" N PHE A 640 " --> pdb=" O GLU A 636 " (cutoff:3.500A) removed outlier: 4.148A 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 673 through 688 removed outlier: 3.594A pdb=" N LYS A 688 " --> pdb=" O GLU A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 711 Processing helix chain 'D' and resid 204 through 211 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 268 Processing helix chain 'D' and resid 287 through 294 Processing helix chain 'D' and resid 299 through 319 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: 5.080A pdb=" N LYS D 431 " --> pdb=" O ASP D 427 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ARG D 432 " --> pdb=" O ARG D 428 " (cutoff:3.500A) removed outlier: 4.200A 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: 4.105A pdb=" N VAL D 542 " --> pdb=" O ALA D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 598 removed outlier: 3.695A pdb=" N ILE D 564 " --> pdb=" O GLN D 560 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LEU D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N CYS D 578 " --> pdb=" O LEU D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 641 removed outlier: 4.001A pdb=" N PHE D 640 " --> pdb=" O GLU D 636 " (cutoff:3.500A) removed outlier: 4.008A 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 673 through 688 Processing helix chain 'D' and resid 690 through 711 removed outlier: 3.639A pdb=" N LYS D 698 " --> pdb=" O LYS D 694 " (cutoff:3.500A) 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: 3.625A 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: 3.517A 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 409 through 414 removed outlier: 4.394A pdb=" N LEU B 413 " --> pdb=" O ARG B 409 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N LEU B 414 " --> pdb=" O HIS B 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 409 through 414' Processing helix chain 'B' and resid 416 through 428 Processing helix chain 'B' and resid 430 through 453 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: 4.185A pdb=" N VAL B 542 " --> pdb=" O ALA B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 598 removed outlier: 3.739A pdb=" N ILE B 564 " --> pdb=" O GLN B 560 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR B 565 " --> pdb=" O GLN B 561 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LEU B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N CYS B 578 " --> pdb=" O LEU B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 641 removed outlier: 4.018A pdb=" N PHE B 640 " --> pdb=" O GLU B 636 " (cutoff:3.500A) removed outlier: 4.039A 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 673 through 711 removed outlier: 6.163A pdb=" N GLN B 691 " --> pdb=" O ASN B 687 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N GLU B 692 " --> pdb=" O LYS B 688 " (cutoff:3.500A) 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 268 Processing helix chain 'C' and resid 287 through 294 Processing helix chain 'C' and resid 299 through 319 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 354 removed outlier: 4.014A pdb=" N GLN C 354 " --> pdb=" O ALA C 350 " (cutoff:3.500A) 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: 5.359A pdb=" N LYS C 431 " --> pdb=" O ASP C 427 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ARG C 432 " --> pdb=" O ARG C 428 " (cutoff:3.500A) removed outlier: 4.371A 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: 4.071A pdb=" N VAL C 542 " --> pdb=" O ALA C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 598 removed outlier: 3.759A pdb=" N ILE C 564 " --> pdb=" O GLN C 560 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR C 565 " --> pdb=" O GLN C 561 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU C 577 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N CYS C 578 " --> pdb=" O LEU C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 641 removed outlier: 4.026A pdb=" N PHE C 640 " --> pdb=" O GLU C 636 " (cutoff:3.500A) removed outlier: 4.234A 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 673 through 686 Processing helix chain 'C' and resid 690 through 711 Processing sheet with id= A, first strand: chain 'A' and resid 742 through 747 removed outlier: 3.944A pdb=" N TRP A 372 " --> pdb=" O SER A 379 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LEU A 381 " --> pdb=" O THR A 370 " (cutoff:3.500A) removed outlier: 5.527A 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: 4.027A pdb=" N TRP D 372 " --> pdb=" O SER D 379 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LEU D 381 " --> pdb=" O THR D 370 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N THR D 370 " --> pdb=" O LEU D 381 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 742 through 747 removed outlier: 4.050A pdb=" N TRP B 372 " --> pdb=" O SER B 379 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LEU B 381 " --> pdb=" O THR B 370 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N THR B 370 " --> pdb=" O LEU B 381 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 742 through 747 removed outlier: 3.921A pdb=" N TRP C 372 " --> pdb=" O SER C 379 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LEU C 381 " --> pdb=" O THR C 370 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N THR C 370 " --> pdb=" O LEU C 381 " (cutoff:3.500A) 894 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: 5.83 Time building geometry restraints manager: 8.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2720 1.30 - 1.43: 5153 1.43 - 1.56: 10003 1.56 - 1.69: 13 1.69 - 1.82: 164 Bond restraints: 18053 Sorted by residual: bond pdb=" CAM 6EU B 901 " pdb=" OAC 6EU B 901 " ideal model delta sigma weight residual 1.422 1.193 0.229 2.00e-02 2.50e+03 1.32e+02 bond pdb=" CAM 6EU D 901 " pdb=" OAC 6EU D 901 " ideal model delta sigma weight residual 1.422 1.193 0.229 2.00e-02 2.50e+03 1.31e+02 bond pdb=" CAV 6EU D 901 " pdb=" CBB 6EU D 901 " ideal model delta sigma weight residual 1.330 1.522 -0.192 2.00e-02 2.50e+03 9.22e+01 bond pdb=" CAV 6EU B 901 " pdb=" CBB 6EU B 901 " ideal model delta sigma weight residual 1.330 1.521 -0.191 2.00e-02 2.50e+03 9.12e+01 bond pdb=" CAL 6EU B 901 " pdb=" OAB 6EU B 901 " ideal model delta sigma weight residual 1.415 1.239 0.176 2.00e-02 2.50e+03 7.76e+01 ... (remaining 18048 not shown) Histogram of bond angle deviations from ideal: 96.43 - 103.96: 202 103.96 - 111.50: 8096 111.50 - 119.03: 6364 119.03 - 126.57: 9596 126.57 - 134.10: 211 Bond angle restraints: 24469 Sorted by residual: angle pdb=" C ARG D 557 " pdb=" CA ARG D 557 " pdb=" CB ARG D 557 " ideal model delta sigma weight residual 109.54 119.33 -9.79 1.84e+00 2.95e-01 2.83e+01 angle pdb=" N ILE A 387 " pdb=" CA ILE A 387 " pdb=" C ILE A 387 " ideal model delta sigma weight residual 111.67 106.68 4.99 9.50e-01 1.11e+00 2.76e+01 angle pdb=" CAN 6EU B 901 " pdb=" CAJ 6EU B 901 " pdb=" CAO 6EU B 901 " ideal model delta sigma weight residual 115.38 129.54 -14.16 3.00e+00 1.11e-01 2.23e+01 angle pdb=" CAN 6EU D 901 " pdb=" CAJ 6EU D 901 " pdb=" CAO 6EU D 901 " ideal model delta sigma weight residual 115.38 129.41 -14.03 3.00e+00 1.11e-01 2.19e+01 angle pdb=" C ARG B 557 " pdb=" CA ARG B 557 " pdb=" CB ARG B 557 " ideal model delta sigma weight residual 109.54 118.08 -8.54 1.84e+00 2.95e-01 2.16e+01 ... (remaining 24464 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.96: 10231 18.96 - 37.92: 406 37.92 - 56.88: 73 56.88 - 75.84: 23 75.84 - 94.80: 13 Dihedral angle restraints: 10746 sinusoidal: 4417 harmonic: 6329 Sorted by residual: dihedral pdb=" CA PHE D 429 " pdb=" C PHE D 429 " pdb=" N VAL D 430 " pdb=" CA VAL D 430 " ideal model delta harmonic sigma weight residual 180.00 -157.95 -22.05 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA PHE C 429 " pdb=" C PHE C 429 " pdb=" N VAL C 430 " pdb=" CA VAL C 430 " ideal model delta harmonic sigma weight residual -180.00 -158.35 -21.65 0 5.00e+00 4.00e-02 1.87e+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 180.00 158.51 21.49 0 5.00e+00 4.00e-02 1.85e+01 ... (remaining 10743 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.011: 2745 1.011 - 2.022: 0 2.022 - 3.033: 0 3.033 - 4.043: 0 4.043 - 5.054: 4 Chirality restraints: 2749 Sorted by residual: chirality pdb=" C3 XJ7 A 801 " pdb=" C2 XJ7 A 801 " pdb=" C24 XJ7 A 801 " pdb=" O3 XJ7 A 801 " both_signs ideal model delta sigma weight residual False -2.50 2.55 -5.05 2.00e-01 2.50e+01 6.39e+02 chirality pdb=" C3 XJ7 C 801 " pdb=" C2 XJ7 C 801 " pdb=" C24 XJ7 C 801 " pdb=" O3 XJ7 C 801 " both_signs ideal model delta sigma weight residual False -2.50 2.53 -5.04 2.00e-01 2.50e+01 6.34e+02 chirality pdb=" C XJ7 C 801 " pdb=" O XJ7 C 801 " pdb=" C1 XJ7 C 801 " pdb=" C25 XJ7 C 801 " both_signs ideal model delta sigma weight residual False 2.51 -2.45 4.95 2.00e-01 2.50e+01 6.13e+02 ... (remaining 2746 not shown) Planarity restraints: 3013 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAM 6EU D 901 " 0.097 2.00e-02 2.50e+03 1.68e-01 2.82e+02 pdb=" CAV 6EU D 901 " -0.291 2.00e-02 2.50e+03 pdb=" CBB 6EU D 901 " 0.098 2.00e-02 2.50e+03 pdb=" CBD 6EU D 901 " 0.096 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAM 6EU B 901 " -0.096 2.00e-02 2.50e+03 1.66e-01 2.75e+02 pdb=" CAV 6EU B 901 " 0.287 2.00e-02 2.50e+03 pdb=" CBB 6EU B 901 " -0.097 2.00e-02 2.50e+03 pdb=" CBD 6EU B 901 " -0.095 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 548 " -0.014 2.00e-02 2.50e+03 2.81e-02 7.90e+00 pdb=" C GLY C 548 " 0.049 2.00e-02 2.50e+03 pdb=" O GLY C 548 " -0.018 2.00e-02 2.50e+03 pdb=" N TRP C 549 " -0.016 2.00e-02 2.50e+03 ... (remaining 3010 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 459 2.69 - 3.24: 18665 3.24 - 3.80: 28466 3.80 - 4.35: 36961 4.35 - 4.90: 61340 Nonbonded interactions: 145891 Sorted by model distance: nonbonded pdb=" OE2 GLU A 570 " pdb=" O11 XJ7 A 801 " model vdw 2.138 2.440 nonbonded pdb=" OE2 GLU A 416 " pdb=" NE ARG A 420 " model vdw 2.196 2.520 nonbonded pdb=" OG1 THR C 731 " pdb=" OD1 ASP C 733 " model vdw 2.228 2.440 nonbonded pdb=" OG1 THR A 731 " pdb=" OD1 ASP A 733 " model vdw 2.260 2.440 nonbonded pdb=" O VAL A 528 " pdb=" OG SER A 532 " model vdw 2.261 2.440 ... (remaining 145886 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 194 through 752) selection = (chain 'B' and resid 194 through 752) selection = (chain 'C' and resid 194 through 752) selection = (chain 'D' and resid 194 through 752) } 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: 1.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.020 Check model and map are aligned: 0.260 Set scattering table: 0.160 Process input model: 50.000 Find NCS groups from input model: 1.290 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 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 : 0.010 0.229 18053 Z= 0.619 Angle : 0.866 14.159 24469 Z= 0.453 Chirality : 0.196 5.054 2749 Planarity : 0.006 0.168 3013 Dihedral : 11.933 94.795 6681 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.84 % Favored : 93.92 % Rotamer: Outliers : 0.42 % Allowed : 2.16 % Favored : 97.42 % 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: 0.74 (0.18), residues: 2139 helix: 1.52 (0.14), residues: 1342 sheet: -1.48 (0.54), residues: 66 loop : -1.29 (0.24), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 749 HIS 0.004 0.001 HIS D 378 PHE 0.024 0.002 PHE C 304 TYR 0.033 0.002 TYR D 511 ARG 0.006 0.001 ARG D 557 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 871 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 863 time to evaluate : 2.115 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 PHE cc_start: 0.8883 (t80) cc_final: 0.8279 (t80) REVERT: A 310 ASN cc_start: 0.9008 (t0) cc_final: 0.8677 (t0) REVERT: A 320 HIS cc_start: 0.8699 (m-70) cc_final: 0.8458 (m-70) REVERT: A 369 PHE cc_start: 0.6430 (t80) cc_final: 0.6207 (t80) REVERT: A 394 SER cc_start: 0.8803 (m) cc_final: 0.6796 (p) REVERT: A 419 ASN cc_start: 0.9037 (t0) cc_final: 0.8757 (t0) REVERT: A 438 PHE cc_start: 0.9416 (t80) cc_final: 0.9179 (t80) REVERT: A 656 LYS cc_start: 0.8705 (mttt) cc_final: 0.8501 (mmmt) REVERT: D 213 ASN cc_start: 0.8960 (t0) cc_final: 0.8505 (t0) REVERT: D 216 LEU cc_start: 0.9165 (mt) cc_final: 0.8696 (mt) REVERT: D 219 LEU cc_start: 0.9303 (mt) cc_final: 0.9047 (mt) REVERT: D 309 TYR cc_start: 0.9298 (t80) cc_final: 0.8865 (t80) REVERT: D 320 HIS cc_start: 0.8201 (m-70) cc_final: 0.7934 (m90) REVERT: D 369 PHE cc_start: 0.8482 (m-80) cc_final: 0.8170 (m-80) REVERT: D 394 SER cc_start: 0.8216 (m) cc_final: 0.7761 (t) REVERT: D 409 ARG cc_start: 0.8257 (ptm-80) cc_final: 0.7714 (ttm170) REVERT: D 420 ARG cc_start: 0.8362 (mtt-85) cc_final: 0.8160 (ttm110) REVERT: D 431 LYS cc_start: 0.8758 (tttt) cc_final: 0.8486 (tptm) REVERT: D 474 ARG cc_start: 0.8795 (ttp80) cc_final: 0.8254 (tmm-80) REVERT: D 478 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7476 (mt-10) REVERT: D 576 ASP cc_start: 0.8716 (m-30) cc_final: 0.8347 (m-30) REVERT: B 213 ASN cc_start: 0.9017 (t0) cc_final: 0.8480 (t0) REVERT: B 215 THR cc_start: 0.9238 (m) cc_final: 0.8972 (p) REVERT: B 216 LEU cc_start: 0.8991 (mt) cc_final: 0.8427 (mt) REVERT: B 309 TYR cc_start: 0.9129 (t80) cc_final: 0.8724 (t80) REVERT: B 320 HIS cc_start: 0.8605 (m-70) cc_final: 0.8343 (m90) REVERT: B 378 HIS cc_start: 0.8491 (p-80) cc_final: 0.7068 (p90) REVERT: B 394 SER cc_start: 0.8127 (m) cc_final: 0.7133 (p) REVERT: B 406 THR cc_start: 0.8082 (m) cc_final: 0.7875 (m) REVERT: B 478 GLU cc_start: 0.7717 (mt-10) cc_final: 0.7504 (mt-10) REVERT: B 628 ASN cc_start: 0.8374 (t0) cc_final: 0.8093 (t0) REVERT: B 636 GLU cc_start: 0.8746 (tp30) cc_final: 0.8445 (tp30) REVERT: B 639 LYS cc_start: 0.9172 (mttt) cc_final: 0.8821 (mttt) REVERT: B 687 ASN cc_start: 0.8864 (t0) cc_final: 0.8657 (t0) REVERT: B 721 ARG cc_start: 0.6992 (mmm160) cc_final: 0.6718 (mmt-90) REVERT: C 311 GLU cc_start: 0.9206 (mm-30) cc_final: 0.8946 (mm-30) REVERT: C 343 SER cc_start: 0.9251 (m) cc_final: 0.9050 (m) REVERT: C 419 ASN cc_start: 0.8912 (t0) cc_final: 0.8621 (t0) REVERT: C 439 PHE cc_start: 0.9157 (t80) cc_final: 0.8950 (t80) REVERT: C 561 GLN cc_start: 0.7675 (mp-120) cc_final: 0.7471 (pm20) REVERT: C 688 LYS cc_start: 0.8827 (mmtm) cc_final: 0.8396 (mmtp) outliers start: 8 outliers final: 2 residues processed: 866 average time/residue: 0.3262 time to fit residues: 405.3907 Evaluate side-chains 606 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 604 time to evaluate : 2.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 570 GLU Chi-restraints excluded: chain C residue 722 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 5.9990 chunk 160 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 108 optimal weight: 9.9990 chunk 85 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 123 optimal weight: 9.9990 chunk 192 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 HIS A 676 ASN D 259 ASN ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 285 ASN D 393 ASN ** D 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 GLN ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 ASN B 378 HIS B 419 ASN B 748 ASN C 223 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 18053 Z= 0.278 Angle : 0.672 11.431 24469 Z= 0.343 Chirality : 0.041 0.272 2749 Planarity : 0.005 0.048 3013 Dihedral : 7.453 85.052 2607 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.84 % Favored : 93.92 % Rotamer: Outliers : 3.37 % Allowed : 11.80 % Favored : 84.83 % 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: 0.85 (0.18), residues: 2139 helix: 1.64 (0.14), residues: 1341 sheet: -1.21 (0.56), residues: 76 loop : -1.32 (0.24), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 372 HIS 0.010 0.001 HIS D 410 PHE 0.036 0.002 PHE D 304 TYR 0.029 0.002 TYR D 511 ARG 0.006 0.001 ARG D 579 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 706 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 642 time to evaluate : 1.722 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 GLU cc_start: 0.8939 (mm-30) cc_final: 0.8653 (mm-30) REVERT: A 320 HIS cc_start: 0.8689 (m-70) cc_final: 0.8431 (m-70) REVERT: A 425 LYS cc_start: 0.8966 (mttm) cc_final: 0.8744 (tttm) REVERT: A 427 ASP cc_start: 0.8692 (m-30) cc_final: 0.8456 (m-30) REVERT: A 472 TYR cc_start: 0.8477 (m-10) cc_final: 0.8193 (m-80) REVERT: A 562 MET cc_start: 0.9062 (mmm) cc_final: 0.8217 (mmt) REVERT: A 656 LYS cc_start: 0.8705 (mttt) cc_final: 0.8298 (ttmm) REVERT: D 309 TYR cc_start: 0.9343 (t80) cc_final: 0.8828 (t80) REVERT: D 320 HIS cc_start: 0.8224 (m-70) cc_final: 0.7963 (m90) REVERT: D 369 PHE cc_start: 0.8225 (m-80) cc_final: 0.7807 (m-80) REVERT: D 380 SER cc_start: 0.8891 (OUTLIER) cc_final: 0.8365 (t) REVERT: D 409 ARG cc_start: 0.7843 (ptm-80) cc_final: 0.7228 (ttm110) REVERT: D 419 ASN cc_start: 0.8813 (OUTLIER) cc_final: 0.8520 (m-40) REVERT: D 474 ARG cc_start: 0.8802 (ttp80) cc_final: 0.8215 (tmm-80) REVERT: D 478 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7433 (mt-10) REVERT: D 536 GLU cc_start: 0.8578 (mp0) cc_final: 0.7976 (mp0) REVERT: D 570 GLU cc_start: 0.8398 (tt0) cc_final: 0.8138 (tt0) REVERT: B 213 ASN cc_start: 0.9032 (t0) cc_final: 0.8461 (t0) REVERT: B 215 THR cc_start: 0.9263 (m) cc_final: 0.8972 (p) REVERT: B 216 LEU cc_start: 0.8967 (mt) cc_final: 0.8331 (mt) REVERT: B 304 PHE cc_start: 0.8399 (OUTLIER) cc_final: 0.8092 (p90) REVERT: B 320 HIS cc_start: 0.8580 (m-70) cc_final: 0.8351 (m90) REVERT: B 361 GLU cc_start: 0.8689 (mp0) cc_final: 0.8464 (mp0) REVERT: B 392 LYS cc_start: 0.8893 (mtmt) cc_final: 0.8675 (mtmt) REVERT: C 246 TYR cc_start: 0.7540 (t80) cc_final: 0.7300 (t80) REVERT: C 304 PHE cc_start: 0.8878 (OUTLIER) cc_final: 0.8360 (p90) REVERT: C 311 GLU cc_start: 0.9160 (mm-30) cc_final: 0.8889 (mm-30) REVERT: C 419 ASN cc_start: 0.8872 (t0) cc_final: 0.8582 (t0) REVERT: C 428 ARG cc_start: 0.8264 (mmt-90) cc_final: 0.8025 (mtp85) REVERT: C 438 PHE cc_start: 0.9380 (t80) cc_final: 0.9120 (t80) REVERT: C 439 PHE cc_start: 0.9132 (t80) cc_final: 0.8921 (t80) REVERT: C 472 TYR cc_start: 0.8620 (m-80) cc_final: 0.8329 (m-80) REVERT: C 498 GLN cc_start: 0.8712 (mm-40) cc_final: 0.8391 (mt0) REVERT: C 684 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7459 (tp30) REVERT: C 688 LYS cc_start: 0.8513 (mmtm) cc_final: 0.8173 (mmtp) outliers start: 64 outliers final: 40 residues processed: 674 average time/residue: 0.3061 time to fit residues: 310.2321 Evaluate side-chains 610 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 566 time to evaluate : 2.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 735 LYS Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 419 ASN Chi-restraints excluded: chain D residue 467 ASN Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 578 CYS Chi-restraints excluded: chain D residue 664 LEU Chi-restraints excluded: chain D residue 696 ILE Chi-restraints excluded: chain D residue 722 SER Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 419 ASN Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain B residue 696 ILE Chi-restraints excluded: chain B residue 703 ILE Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 404 SER Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 654 ASP Chi-restraints excluded: chain C residue 735 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 106 optimal weight: 20.0000 chunk 59 optimal weight: 2.9990 chunk 160 optimal weight: 0.7980 chunk 131 optimal weight: 4.9990 chunk 53 optimal weight: 0.0670 chunk 192 optimal weight: 1.9990 chunk 208 optimal weight: 0.9990 chunk 171 optimal weight: 3.9990 chunk 191 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 154 optimal weight: 3.9990 overall best weight: 0.9724 ------------------------------------------------------------------------------- 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 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 498 GLN B 206 HIS ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 ASN C 301 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18053 Z= 0.180 Angle : 0.597 14.145 24469 Z= 0.308 Chirality : 0.039 0.252 2749 Planarity : 0.004 0.052 3013 Dihedral : 6.429 66.094 2603 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.45 % Favored : 93.22 % Rotamer: Outliers : 2.63 % Allowed : 14.81 % Favored : 82.56 % 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: 2139 helix: 1.87 (0.14), residues: 1315 sheet: -0.94 (0.57), residues: 76 loop : -1.38 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 372 HIS 0.011 0.001 HIS D 410 PHE 0.028 0.001 PHE D 304 TYR 0.022 0.001 TYR B 511 ARG 0.005 0.000 ARG D 579 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 606 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 ASP cc_start: 0.8588 (m-30) cc_final: 0.8360 (m-30) REVERT: A 577 LEU cc_start: 0.9347 (tp) cc_final: 0.9070 (tp) REVERT: A 656 LYS cc_start: 0.8663 (mttt) cc_final: 0.8264 (ttmm) REVERT: D 210 GLU cc_start: 0.8178 (tm-30) cc_final: 0.7568 (tm-30) REVERT: D 309 TYR cc_start: 0.9376 (t80) cc_final: 0.8987 (t80) REVERT: D 320 HIS cc_start: 0.8202 (m-70) cc_final: 0.7943 (m90) REVERT: D 359 GLU cc_start: 0.7570 (tm-30) cc_final: 0.7226 (tm-30) REVERT: D 369 PHE cc_start: 0.8072 (m-80) cc_final: 0.7682 (m-80) REVERT: D 380 SER cc_start: 0.8865 (OUTLIER) cc_final: 0.8368 (t) REVERT: D 409 ARG cc_start: 0.7812 (ptm-80) cc_final: 0.6895 (ttm110) REVERT: D 478 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7307 (mt-10) REVERT: D 509 ASP cc_start: 0.8416 (t0) cc_final: 0.8147 (t0) REVERT: D 536 GLU cc_start: 0.8516 (mp0) cc_final: 0.7893 (mp0) REVERT: B 213 ASN cc_start: 0.9002 (t0) cc_final: 0.8674 (t0) REVERT: B 215 THR cc_start: 0.9281 (m) cc_final: 0.9045 (p) REVERT: B 272 TRP cc_start: 0.6972 (m-90) cc_final: 0.6628 (m-90) REVERT: B 320 HIS cc_start: 0.8541 (m-70) cc_final: 0.8337 (m90) REVERT: B 431 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8323 (tptp) REVERT: B 478 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7487 (mt-10) REVERT: C 246 TYR cc_start: 0.7543 (t80) cc_final: 0.7299 (t80) REVERT: C 304 PHE cc_start: 0.8885 (OUTLIER) cc_final: 0.8220 (p90) REVERT: C 310 ASN cc_start: 0.8903 (t0) cc_final: 0.8702 (t0) REVERT: C 311 GLU cc_start: 0.9123 (mm-30) cc_final: 0.8760 (mm-30) REVERT: C 419 ASN cc_start: 0.8840 (t0) cc_final: 0.8544 (t0) REVERT: C 427 ASP cc_start: 0.8451 (m-30) cc_final: 0.8089 (m-30) REVERT: C 428 ARG cc_start: 0.8318 (mmt-90) cc_final: 0.8022 (mtt-85) REVERT: C 438 PHE cc_start: 0.9358 (t80) cc_final: 0.9109 (t80) REVERT: C 687 ASN cc_start: 0.9108 (t0) cc_final: 0.8781 (t0) REVERT: C 688 LYS cc_start: 0.8564 (mmtm) cc_final: 0.7994 (mmtp) outliers start: 50 outliers final: 28 residues processed: 632 average time/residue: 0.2904 time to fit residues: 278.9095 Evaluate side-chains 587 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 556 time to evaluate : 2.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 735 LYS Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 419 ASN Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 514 ILE Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 578 CYS Chi-restraints excluded: chain D residue 664 LEU Chi-restraints excluded: chain D residue 703 ILE Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 703 ILE Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 654 ASP Chi-restraints excluded: chain C residue 735 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 190 optimal weight: 7.9990 chunk 145 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 21 optimal weight: 9.9990 chunk 92 optimal weight: 3.9990 chunk 129 optimal weight: 0.9980 chunk 193 optimal weight: 0.8980 chunk 204 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 183 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 ASN A 494 GLN A 561 GLN ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 560 GLN B 206 HIS ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 419 ASN C 206 HIS C 358 HIS C 410 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 18053 Z= 0.180 Angle : 0.580 12.234 24469 Z= 0.300 Chirality : 0.039 0.183 2749 Planarity : 0.004 0.047 3013 Dihedral : 6.026 62.040 2603 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.12 % Favored : 93.60 % Rotamer: Outliers : 3.21 % Allowed : 16.49 % Favored : 80.30 % 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: 1.07 (0.19), residues: 2139 helix: 1.90 (0.14), residues: 1316 sheet: -0.63 (0.58), residues: 76 loop : -1.37 (0.23), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 372 HIS 0.014 0.001 HIS D 410 PHE 0.043 0.001 PHE D 304 TYR 0.020 0.001 TYR B 511 ARG 0.006 0.000 ARG C 363 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 603 time to evaluate : 2.043 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 MET cc_start: 0.8848 (ttm) cc_final: 0.8641 (ttm) REVERT: A 419 ASN cc_start: 0.8968 (t0) cc_final: 0.8696 (t0) REVERT: A 427 ASP cc_start: 0.8489 (m-30) cc_final: 0.8224 (m-30) REVERT: A 653 TYR cc_start: 0.8444 (p90) cc_final: 0.7969 (p90) REVERT: A 656 LYS cc_start: 0.8641 (mttt) cc_final: 0.8252 (ttmm) REVERT: D 309 TYR cc_start: 0.9420 (t80) cc_final: 0.8913 (t80) REVERT: D 320 HIS cc_start: 0.8222 (m-70) cc_final: 0.7958 (m90) REVERT: D 412 MET cc_start: 0.7891 (mtt) cc_final: 0.7413 (mtt) REVERT: D 509 ASP cc_start: 0.8425 (t0) cc_final: 0.8161 (t0) REVERT: D 536 GLU cc_start: 0.8514 (mp0) cc_final: 0.7864 (mt-10) REVERT: D 746 GLU cc_start: 0.6726 (tm-30) cc_final: 0.6365 (tm-30) REVERT: B 213 ASN cc_start: 0.9022 (t0) cc_final: 0.8644 (t0) REVERT: B 215 THR cc_start: 0.9319 (m) cc_final: 0.9103 (p) REVERT: B 247 PHE cc_start: 0.8171 (p90) cc_final: 0.7956 (p90) REVERT: B 272 TRP cc_start: 0.6991 (m-90) cc_final: 0.6664 (m-90) REVERT: B 369 PHE cc_start: 0.7849 (m-80) cc_final: 0.7621 (m-80) REVERT: B 419 ASN cc_start: 0.8797 (OUTLIER) cc_final: 0.8432 (m110) REVERT: B 431 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8289 (tptp) REVERT: B 478 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7527 (mt-10) REVERT: C 246 TYR cc_start: 0.7603 (t80) cc_final: 0.7323 (t80) REVERT: C 304 PHE cc_start: 0.8957 (OUTLIER) cc_final: 0.8324 (p90) REVERT: C 310 ASN cc_start: 0.8917 (t0) cc_final: 0.8661 (t0) REVERT: C 311 GLU cc_start: 0.9123 (mm-30) cc_final: 0.8805 (mm-30) REVERT: C 419 ASN cc_start: 0.8855 (t0) cc_final: 0.8534 (t0) REVERT: C 427 ASP cc_start: 0.8380 (m-30) cc_final: 0.8091 (m-30) REVERT: C 428 ARG cc_start: 0.8301 (mmt-90) cc_final: 0.8071 (mtt-85) REVERT: C 438 PHE cc_start: 0.9357 (t80) cc_final: 0.9047 (t80) REVERT: C 687 ASN cc_start: 0.9075 (t0) cc_final: 0.8748 (t0) REVERT: C 688 LYS cc_start: 0.8558 (mmtm) cc_final: 0.8224 (mmtp) outliers start: 61 outliers final: 42 residues processed: 628 average time/residue: 0.2788 time to fit residues: 264.5511 Evaluate side-chains 603 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 558 time to evaluate : 2.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 735 LYS Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 419 ASN Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 514 ILE Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 578 CYS Chi-restraints excluded: chain D residue 630 LEU Chi-restraints excluded: chain D residue 703 ILE Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 392 LYS Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 419 ASN Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 634 CYS Chi-restraints excluded: chain B residue 741 CYS Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 654 ASP Chi-restraints excluded: chain C residue 735 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 170 optimal weight: 0.6980 chunk 116 optimal weight: 0.0970 chunk 2 optimal weight: 8.9990 chunk 152 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 174 optimal weight: 6.9990 chunk 141 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 104 optimal weight: 0.7980 chunk 183 optimal weight: 0.8980 chunk 51 optimal weight: 0.0980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 494 GLN ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 628 ASN ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 HIS ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 419 ASN B 551 ASN ** B 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 18053 Z= 0.156 Angle : 0.570 11.474 24469 Z= 0.292 Chirality : 0.038 0.198 2749 Planarity : 0.004 0.047 3013 Dihedral : 5.780 59.194 2603 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.73 % Favored : 93.03 % Rotamer: Outliers : 2.42 % Allowed : 18.70 % Favored : 78.87 % 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: 1.10 (0.19), residues: 2139 helix: 1.93 (0.14), residues: 1301 sheet: -0.47 (0.59), residues: 76 loop : -1.32 (0.23), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP C 372 HIS 0.014 0.001 HIS D 410 PHE 0.033 0.001 PHE D 304 TYR 0.027 0.001 TYR D 511 ARG 0.006 0.000 ARG B 579 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 596 time to evaluate : 2.008 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 THR cc_start: 0.9006 (p) cc_final: 0.8755 (p) REVERT: A 419 ASN cc_start: 0.8953 (t0) cc_final: 0.8712 (t0) REVERT: A 427 ASP cc_start: 0.8432 (m-30) cc_final: 0.8227 (m-30) REVERT: A 656 LYS cc_start: 0.8616 (mttt) cc_final: 0.8388 (mmmm) REVERT: D 309 TYR cc_start: 0.9402 (t80) cc_final: 0.8956 (t80) REVERT: D 320 HIS cc_start: 0.8211 (m-70) cc_final: 0.7955 (m90) REVERT: D 536 GLU cc_start: 0.8447 (mp0) cc_final: 0.7829 (mt-10) REVERT: D 677 MET cc_start: 0.8451 (ttp) cc_final: 0.8019 (ttt) REVERT: D 746 GLU cc_start: 0.6867 (tm-30) cc_final: 0.6659 (tm-30) REVERT: B 213 ASN cc_start: 0.9013 (t0) cc_final: 0.8667 (t0) REVERT: B 215 THR cc_start: 0.9309 (m) cc_final: 0.9108 (p) REVERT: B 247 PHE cc_start: 0.8195 (p90) cc_final: 0.7956 (p90) REVERT: B 272 TRP cc_start: 0.6975 (m-90) cc_final: 0.6665 (m-90) REVERT: B 308 MET cc_start: 0.9106 (ttm) cc_final: 0.8833 (ttm) REVERT: B 369 PHE cc_start: 0.7721 (m-80) cc_final: 0.7519 (m-80) REVERT: B 431 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8577 (ttmm) REVERT: B 478 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7403 (mt-10) REVERT: B 551 ASN cc_start: 0.9314 (m-40) cc_final: 0.8941 (m-40) REVERT: B 716 MET cc_start: 0.6557 (mmm) cc_final: 0.6331 (mtt) REVERT: C 288 LEU cc_start: 0.9278 (mt) cc_final: 0.9011 (mt) REVERT: C 304 PHE cc_start: 0.8952 (OUTLIER) cc_final: 0.8234 (p90) REVERT: C 311 GLU cc_start: 0.9075 (mm-30) cc_final: 0.8866 (mm-30) REVERT: C 419 ASN cc_start: 0.8844 (t0) cc_final: 0.8534 (t0) REVERT: C 427 ASP cc_start: 0.8324 (m-30) cc_final: 0.8017 (m-30) REVERT: C 438 PHE cc_start: 0.9374 (t80) cc_final: 0.9131 (t80) REVERT: C 687 ASN cc_start: 0.8991 (t0) cc_final: 0.8730 (t0) REVERT: C 688 LYS cc_start: 0.8557 (mmtm) cc_final: 0.8222 (mmtp) outliers start: 46 outliers final: 36 residues processed: 617 average time/residue: 0.2691 time to fit residues: 253.7987 Evaluate side-chains 597 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 559 time to evaluate : 2.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 735 LYS Chi-restraints excluded: chain D residue 419 ASN Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 541 MET Chi-restraints excluded: chain D residue 630 LEU Chi-restraints excluded: chain D residue 664 LEU Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 392 LYS Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 419 ASN Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 634 CYS Chi-restraints excluded: chain B residue 703 ILE Chi-restraints excluded: chain B residue 741 CYS Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 654 ASP Chi-restraints excluded: chain C residue 735 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 68 optimal weight: 0.9990 chunk 184 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 120 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 205 optimal weight: 3.9990 chunk 170 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 107 optimal weight: 6.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 494 GLN A 628 ASN ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 628 ASN ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 HIS ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 419 ASN ** B 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 393 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 18053 Z= 0.234 Angle : 0.592 10.849 24469 Z= 0.306 Chirality : 0.039 0.244 2749 Planarity : 0.004 0.047 3013 Dihedral : 5.797 58.939 2603 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.73 % Favored : 92.99 % Rotamer: Outliers : 3.64 % Allowed : 18.60 % Favored : 77.77 % 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: 1.01 (0.19), residues: 2139 helix: 1.86 (0.14), residues: 1311 sheet: -0.57 (0.58), residues: 76 loop : -1.40 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 372 HIS 0.013 0.001 HIS D 410 PHE 0.027 0.001 PHE D 304 TYR 0.034 0.001 TYR D 511 ARG 0.006 0.000 ARG B 428 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 571 time to evaluate : 2.175 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 THR cc_start: 0.9004 (p) cc_final: 0.8736 (p) REVERT: A 419 ASN cc_start: 0.8990 (t0) cc_final: 0.8774 (t0) REVERT: A 427 ASP cc_start: 0.8477 (m-30) cc_final: 0.8246 (m-30) REVERT: A 653 TYR cc_start: 0.8495 (p90) cc_final: 0.7866 (p90) REVERT: A 656 LYS cc_start: 0.8700 (mttt) cc_final: 0.8280 (ttmm) REVERT: A 741 CYS cc_start: 0.8366 (m) cc_final: 0.8141 (m) REVERT: D 309 TYR cc_start: 0.9454 (t80) cc_final: 0.8931 (t80) REVERT: D 320 HIS cc_start: 0.8203 (m-70) cc_final: 0.7992 (m90) REVERT: D 412 MET cc_start: 0.7769 (mtt) cc_final: 0.7264 (mtt) REVERT: D 572 MET cc_start: 0.8921 (mmt) cc_final: 0.8661 (mmp) REVERT: D 677 MET cc_start: 0.8504 (ttp) cc_final: 0.8059 (ttt) REVERT: D 746 GLU cc_start: 0.6896 (tm-30) cc_final: 0.6590 (tm-30) REVERT: B 213 ASN cc_start: 0.9034 (t0) cc_final: 0.8694 (t0) REVERT: B 247 PHE cc_start: 0.8278 (p90) cc_final: 0.8078 (p90) REVERT: B 272 TRP cc_start: 0.6996 (m-90) cc_final: 0.6689 (m-90) REVERT: B 369 PHE cc_start: 0.7684 (m-80) cc_final: 0.7470 (m-80) REVERT: B 384 LEU cc_start: 0.9110 (mp) cc_final: 0.8875 (tt) REVERT: B 419 ASN cc_start: 0.8936 (OUTLIER) cc_final: 0.8591 (m-40) REVERT: B 431 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8181 (ttmm) REVERT: B 478 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7347 (mt-10) REVERT: B 551 ASN cc_start: 0.9375 (m-40) cc_final: 0.8956 (m-40) REVERT: C 288 LEU cc_start: 0.9276 (mt) cc_final: 0.8993 (mt) REVERT: C 304 PHE cc_start: 0.8961 (OUTLIER) cc_final: 0.8221 (p90) REVERT: C 308 MET cc_start: 0.8920 (tpp) cc_final: 0.8702 (tpp) REVERT: C 412 MET cc_start: 0.9253 (mmm) cc_final: 0.8791 (mtt) REVERT: C 419 ASN cc_start: 0.8870 (t0) cc_final: 0.8545 (t0) REVERT: C 427 ASP cc_start: 0.8342 (m-30) cc_final: 0.8057 (m-30) REVERT: C 438 PHE cc_start: 0.9411 (t80) cc_final: 0.9170 (t80) REVERT: C 687 ASN cc_start: 0.9037 (t0) cc_final: 0.8741 (t0) REVERT: C 688 LYS cc_start: 0.8596 (mmtm) cc_final: 0.8254 (mmtp) outliers start: 69 outliers final: 51 residues processed: 599 average time/residue: 0.2688 time to fit residues: 246.5827 Evaluate side-chains 603 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 549 time to evaluate : 2.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 346 ILE Chi-restraints excluded: chain D residue 419 ASN Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 541 MET Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 578 CYS Chi-restraints excluded: chain D residue 630 LEU Chi-restraints excluded: chain D residue 664 LEU Chi-restraints excluded: chain D residue 703 ILE Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 392 LYS Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 419 ASN Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 634 CYS Chi-restraints excluded: chain B residue 696 ILE Chi-restraints excluded: chain B residue 703 ILE Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 654 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 197 optimal weight: 0.6980 chunk 23 optimal weight: 6.9990 chunk 116 optimal weight: 8.9990 chunk 149 optimal weight: 2.9990 chunk 172 optimal weight: 7.9990 chunk 114 optimal weight: 0.0770 chunk 204 optimal weight: 0.8980 chunk 127 optimal weight: 9.9990 chunk 124 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 126 optimal weight: 0.9980 overall best weight: 1.1340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 494 GLN ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 285 ASN ** D 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 628 ASN ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 HIS ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 ASN B 419 ASN ** B 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 18053 Z= 0.191 Angle : 0.588 11.187 24469 Z= 0.300 Chirality : 0.039 0.173 2749 Planarity : 0.004 0.047 3013 Dihedral : 5.671 58.191 2603 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.78 % Favored : 92.89 % Rotamer: Outliers : 3.42 % Allowed : 19.65 % Favored : 76.92 % 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: 0.93 (0.19), residues: 2139 helix: 1.81 (0.14), residues: 1323 sheet: -0.50 (0.59), residues: 76 loop : -1.53 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 372 HIS 0.013 0.001 HIS D 410 PHE 0.028 0.001 PHE B 266 TYR 0.029 0.001 TYR D 511 ARG 0.007 0.000 ARG C 428 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 567 time to evaluate : 2.285 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 THR cc_start: 0.8985 (p) cc_final: 0.8701 (p) REVERT: A 419 ASN cc_start: 0.8986 (t0) cc_final: 0.8763 (t0) REVERT: A 427 ASP cc_start: 0.8436 (m-30) cc_final: 0.8211 (m-30) REVERT: A 653 TYR cc_start: 0.8461 (p90) cc_final: 0.7852 (p90) REVERT: A 656 LYS cc_start: 0.8690 (mttt) cc_final: 0.8203 (ttmm) REVERT: A 741 CYS cc_start: 0.8351 (m) cc_final: 0.8133 (m) REVERT: D 309 TYR cc_start: 0.9482 (t80) cc_final: 0.8906 (t80) REVERT: D 320 HIS cc_start: 0.8156 (m-70) cc_final: 0.7920 (m90) REVERT: D 409 ARG cc_start: 0.7177 (ptm-80) cc_final: 0.6785 (tmm160) REVERT: D 412 MET cc_start: 0.7800 (mtt) cc_final: 0.7335 (mtt) REVERT: D 572 MET cc_start: 0.8939 (mmt) cc_final: 0.8688 (mmp) REVERT: D 746 GLU cc_start: 0.6968 (tm-30) cc_final: 0.6655 (tm-30) REVERT: B 247 PHE cc_start: 0.8320 (p90) cc_final: 0.8098 (p90) REVERT: B 272 TRP cc_start: 0.6993 (m-90) cc_final: 0.6687 (m-90) REVERT: B 369 PHE cc_start: 0.7620 (m-80) cc_final: 0.7150 (m-80) REVERT: B 384 LEU cc_start: 0.9111 (mp) cc_final: 0.8880 (tt) REVERT: B 419 ASN cc_start: 0.8889 (OUTLIER) cc_final: 0.8596 (m-40) REVERT: B 431 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8238 (ttmm) REVERT: B 478 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7344 (mt-10) REVERT: C 288 LEU cc_start: 0.9272 (mt) cc_final: 0.8952 (mt) REVERT: C 304 PHE cc_start: 0.8940 (OUTLIER) cc_final: 0.8170 (p90) REVERT: C 412 MET cc_start: 0.9176 (mmm) cc_final: 0.8835 (mtt) REVERT: C 419 ASN cc_start: 0.8849 (t0) cc_final: 0.8537 (t0) REVERT: C 427 ASP cc_start: 0.8337 (m-30) cc_final: 0.8042 (m-30) REVERT: C 438 PHE cc_start: 0.9399 (t80) cc_final: 0.9154 (t80) REVERT: C 684 GLU cc_start: 0.7807 (tp30) cc_final: 0.7518 (tp30) REVERT: C 687 ASN cc_start: 0.8998 (t0) cc_final: 0.8759 (t0) REVERT: C 688 LYS cc_start: 0.8598 (mmtm) cc_final: 0.8220 (mmtp) REVERT: C 721 ARG cc_start: 0.7178 (mmt180) cc_final: 0.6728 (mmm160) outliers start: 65 outliers final: 50 residues processed: 597 average time/residue: 0.2753 time to fit residues: 250.1861 Evaluate side-chains 600 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 547 time to evaluate : 2.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 324 LYS Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain D residue 346 ILE Chi-restraints excluded: chain D residue 419 ASN Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 541 MET Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 578 CYS Chi-restraints excluded: chain D residue 630 LEU Chi-restraints excluded: chain D residue 664 LEU Chi-restraints excluded: chain D residue 703 ILE Chi-restraints excluded: chain D residue 706 LEU Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 392 LYS Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 419 ASN Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 634 CYS Chi-restraints excluded: chain B residue 660 ILE Chi-restraints excluded: chain B residue 696 ILE Chi-restraints excluded: chain B residue 703 ILE Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 663 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 81 optimal weight: 0.9990 chunk 122 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 129 optimal weight: 0.8980 chunk 139 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 19 optimal weight: 0.0770 chunk 160 optimal weight: 0.9980 chunk 185 optimal weight: 0.0980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 494 GLN A 676 ASN ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 628 ASN D 676 ASN B 206 HIS ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 18053 Z= 0.161 Angle : 0.588 13.770 24469 Z= 0.299 Chirality : 0.039 0.217 2749 Planarity : 0.004 0.047 3013 Dihedral : 5.523 58.997 2603 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.78 % Favored : 92.94 % Rotamer: Outliers : 3.00 % Allowed : 20.71 % Favored : 76.29 % 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: 2139 helix: 1.80 (0.14), residues: 1310 sheet: -0.42 (0.59), residues: 76 loop : -1.49 (0.23), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 372 HIS 0.013 0.001 HIS D 410 PHE 0.032 0.001 PHE D 496 TYR 0.027 0.001 TYR D 511 ARG 0.011 0.000 ARG B 739 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 572 time to evaluate : 2.022 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 THR cc_start: 0.8939 (p) cc_final: 0.8634 (p) REVERT: A 419 ASN cc_start: 0.8970 (t0) cc_final: 0.8693 (t0) REVERT: A 427 ASP cc_start: 0.8382 (m-30) cc_final: 0.8173 (m-30) REVERT: A 494 GLN cc_start: 0.8529 (tt0) cc_final: 0.8193 (tt0) REVERT: A 499 ARG cc_start: 0.8434 (mmp80) cc_final: 0.8096 (mmp-170) REVERT: A 653 TYR cc_start: 0.8417 (p90) cc_final: 0.7873 (p90) REVERT: A 656 LYS cc_start: 0.8676 (mttt) cc_final: 0.8228 (ttmm) REVERT: A 716 MET cc_start: 0.6831 (mtp) cc_final: 0.6404 (ttp) REVERT: A 741 CYS cc_start: 0.8295 (m) cc_final: 0.8056 (m) REVERT: D 309 TYR cc_start: 0.9490 (t80) cc_final: 0.8919 (t80) REVERT: D 320 HIS cc_start: 0.8143 (m-70) cc_final: 0.7911 (m90) REVERT: D 412 MET cc_start: 0.7819 (mtt) cc_final: 0.7408 (mtt) REVERT: D 572 MET cc_start: 0.8911 (mmt) cc_final: 0.8663 (mmp) REVERT: D 746 GLU cc_start: 0.6977 (tm-30) cc_final: 0.6652 (tm-30) REVERT: B 247 PHE cc_start: 0.8313 (p90) cc_final: 0.8071 (p90) REVERT: B 272 TRP cc_start: 0.6992 (m-90) cc_final: 0.6685 (m-90) REVERT: B 369 PHE cc_start: 0.7343 (m-80) cc_final: 0.7143 (m-80) REVERT: B 384 LEU cc_start: 0.9141 (mp) cc_final: 0.8922 (tt) REVERT: B 431 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8273 (ttmm) REVERT: B 478 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7336 (mt-10) REVERT: C 288 LEU cc_start: 0.9235 (mt) cc_final: 0.8911 (mt) REVERT: C 304 PHE cc_start: 0.8935 (OUTLIER) cc_final: 0.8161 (p90) REVERT: C 412 MET cc_start: 0.9102 (mmm) cc_final: 0.8815 (mtp) REVERT: C 419 ASN cc_start: 0.8795 (t0) cc_final: 0.8468 (t0) REVERT: C 427 ASP cc_start: 0.8309 (m-30) cc_final: 0.8034 (m-30) REVERT: C 438 PHE cc_start: 0.9378 (t80) cc_final: 0.9129 (t80) REVERT: C 684 GLU cc_start: 0.7775 (tp30) cc_final: 0.7513 (tp30) REVERT: C 687 ASN cc_start: 0.8955 (t0) cc_final: 0.8737 (t0) REVERT: C 688 LYS cc_start: 0.8588 (mmtm) cc_final: 0.8223 (mmtp) REVERT: C 721 ARG cc_start: 0.7149 (mmt180) cc_final: 0.6700 (mmm160) outliers start: 57 outliers final: 46 residues processed: 601 average time/residue: 0.2772 time to fit residues: 253.8726 Evaluate side-chains 588 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 540 time to evaluate : 2.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 324 LYS Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 735 LYS Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 346 ILE Chi-restraints excluded: chain D residue 419 ASN Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 541 MET Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 578 CYS Chi-restraints excluded: chain D residue 664 LEU Chi-restraints excluded: chain D residue 703 ILE Chi-restraints excluded: chain D residue 706 LEU Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 392 LYS Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 634 CYS Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 654 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 195 optimal weight: 3.9990 chunk 178 optimal weight: 4.9990 chunk 190 optimal weight: 0.0970 chunk 114 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 149 optimal weight: 6.9990 chunk 58 optimal weight: 9.9990 chunk 172 optimal weight: 0.0030 chunk 180 optimal weight: 0.9990 chunk 189 optimal weight: 1.9990 chunk 125 optimal weight: 0.0070 overall best weight: 0.4208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 628 ASN D 748 ASN B 206 HIS ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 419 ASN B 494 GLN ** B 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 18053 Z= 0.160 Angle : 0.591 12.186 24469 Z= 0.300 Chirality : 0.039 0.242 2749 Planarity : 0.004 0.047 3013 Dihedral : 5.415 59.244 2603 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.97 % Favored : 92.89 % Rotamer: Outliers : 2.42 % Allowed : 21.81 % Favored : 75.76 % 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: 0.89 (0.19), residues: 2139 helix: 1.77 (0.14), residues: 1310 sheet: -0.34 (0.58), residues: 76 loop : -1.48 (0.23), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP D 372 HIS 0.011 0.001 HIS D 410 PHE 0.049 0.001 PHE D 304 TYR 0.029 0.001 TYR D 511 ARG 0.007 0.000 ARG C 428 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 585 time to evaluate : 2.157 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: symmetry clash revert: symmetry clash REVERT: A 258 THR cc_start: 0.8904 (p) cc_final: 0.8589 (p) REVERT: A 494 GLN cc_start: 0.8562 (tt0) cc_final: 0.8207 (tt0) REVERT: A 499 ARG cc_start: 0.8476 (mmp80) cc_final: 0.8176 (mmp-170) REVERT: A 656 LYS cc_start: 0.8666 (mttt) cc_final: 0.8275 (ttmm) REVERT: A 716 MET cc_start: 0.6686 (mtp) cc_final: 0.6297 (ttp) REVERT: A 741 CYS cc_start: 0.8236 (m) cc_final: 0.8016 (m) REVERT: D 320 HIS cc_start: 0.8114 (m-70) cc_final: 0.7873 (m90) REVERT: D 369 PHE cc_start: 0.7948 (m-80) cc_final: 0.7532 (m-80) REVERT: D 412 MET cc_start: 0.7839 (mtt) cc_final: 0.7457 (mtt) REVERT: D 431 LYS cc_start: 0.8825 (tttt) cc_final: 0.8233 (ttmm) REVERT: D 572 MET cc_start: 0.8896 (mmt) cc_final: 0.8671 (mmp) REVERT: D 746 GLU cc_start: 0.6894 (tm-30) cc_final: 0.6538 (tm-30) REVERT: B 247 PHE cc_start: 0.8303 (p90) cc_final: 0.8011 (p90) REVERT: B 272 TRP cc_start: 0.6959 (m-90) cc_final: 0.5972 (m-90) REVERT: B 419 ASN cc_start: 0.8879 (OUTLIER) cc_final: 0.8639 (m-40) REVERT: B 431 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8768 (ttmm) REVERT: B 478 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7331 (mt-10) REVERT: B 721 ARG cc_start: 0.5787 (mmm-85) cc_final: 0.5565 (mmm-85) REVERT: C 288 LEU cc_start: 0.9199 (mt) cc_final: 0.8863 (mt) REVERT: C 304 PHE cc_start: 0.8922 (OUTLIER) cc_final: 0.8098 (p90) REVERT: C 419 ASN cc_start: 0.8730 (t0) cc_final: 0.8462 (t0) REVERT: C 438 PHE cc_start: 0.9368 (t80) cc_final: 0.9118 (t80) REVERT: C 684 GLU cc_start: 0.7770 (tp30) cc_final: 0.7569 (tp30) REVERT: C 721 ARG cc_start: 0.7125 (mmt180) cc_final: 0.6707 (mmm160) outliers start: 46 outliers final: 39 residues processed: 610 average time/residue: 0.2678 time to fit residues: 249.3539 Evaluate side-chains 602 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 560 time to evaluate : 1.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 324 LYS Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 735 LYS Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 346 ILE Chi-restraints excluded: chain D residue 419 ASN Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 578 CYS Chi-restraints excluded: chain D residue 664 LEU Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 419 ASN Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 634 CYS Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 324 LYS Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 654 ASP Chi-restraints excluded: chain C residue 663 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 201 optimal weight: 2.9990 chunk 122 optimal weight: 0.5980 chunk 95 optimal weight: 0.3980 chunk 139 optimal weight: 0.9980 chunk 211 optimal weight: 3.9990 chunk 194 optimal weight: 0.9980 chunk 168 optimal weight: 4.9990 chunk 17 optimal weight: 9.9990 chunk 129 optimal weight: 1.9990 chunk 103 optimal weight: 9.9990 chunk 133 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 628 ASN B 206 HIS ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.4092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.140 18053 Z= 0.233 Angle : 0.773 59.199 24469 Z= 0.435 Chirality : 0.040 0.327 2749 Planarity : 0.004 0.048 3013 Dihedral : 5.412 59.227 2603 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.06 % Favored : 92.85 % Rotamer: Outliers : 2.37 % Allowed : 22.97 % Favored : 74.66 % Cbeta Deviations : 0.05 % 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: 0.86 (0.19), residues: 2139 helix: 1.74 (0.14), residues: 1310 sheet: -0.32 (0.58), residues: 76 loop : -1.49 (0.23), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP D 372 HIS 0.009 0.001 HIS D 410 PHE 0.045 0.001 PHE D 304 TYR 0.030 0.001 TYR D 511 ARG 0.006 0.000 ARG C 428 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 557 time to evaluate : 2.083 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: symmetry clash revert: symmetry clash REVERT: A 258 THR cc_start: 0.8894 (p) cc_final: 0.8582 (p) REVERT: A 494 GLN cc_start: 0.8565 (tt0) cc_final: 0.8212 (tt0) REVERT: A 499 ARG cc_start: 0.8504 (mmp80) cc_final: 0.8173 (mmp-170) REVERT: A 656 LYS cc_start: 0.8670 (mttt) cc_final: 0.8278 (ttmm) REVERT: A 716 MET cc_start: 0.6687 (mtp) cc_final: 0.6303 (ttp) REVERT: A 741 CYS cc_start: 0.8246 (m) cc_final: 0.8022 (m) REVERT: D 320 HIS cc_start: 0.8114 (m-70) cc_final: 0.7874 (m90) REVERT: D 369 PHE cc_start: 0.7949 (m-80) cc_final: 0.7532 (m-80) REVERT: D 412 MET cc_start: 0.7860 (mtt) cc_final: 0.7482 (mtt) REVERT: D 431 LYS cc_start: 0.8826 (tttt) cc_final: 0.8233 (ttmm) REVERT: D 572 MET cc_start: 0.8905 (mmt) cc_final: 0.8680 (mmp) REVERT: D 746 GLU cc_start: 0.6888 (tm-30) cc_final: 0.6538 (tm-30) REVERT: B 247 PHE cc_start: 0.8305 (p90) cc_final: 0.8008 (p90) REVERT: B 272 TRP cc_start: 0.6959 (m-90) cc_final: 0.5972 (m-90) REVERT: B 431 LYS cc_start: 0.9018 (OUTLIER) cc_final: 0.8767 (ttmm) REVERT: B 478 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7363 (mt-10) REVERT: B 721 ARG cc_start: 0.5769 (mmm-85) cc_final: 0.5566 (mmm-85) REVERT: C 288 LEU cc_start: 0.9196 (mt) cc_final: 0.8863 (mt) REVERT: C 304 PHE cc_start: 0.8923 (OUTLIER) cc_final: 0.8099 (p90) REVERT: C 419 ASN cc_start: 0.8744 (t0) cc_final: 0.8461 (t0) REVERT: C 438 PHE cc_start: 0.9366 (t80) cc_final: 0.9120 (t80) REVERT: C 721 ARG cc_start: 0.7132 (mmt180) cc_final: 0.6711 (mmm160) outliers start: 45 outliers final: 40 residues processed: 582 average time/residue: 0.2709 time to fit residues: 240.3256 Evaluate side-chains 600 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 558 time to evaluate : 2.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 324 LYS Chi-restraints excluded: chain A residue 735 LYS Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 346 ILE Chi-restraints excluded: chain D residue 392 LYS Chi-restraints excluded: chain D residue 419 ASN Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 541 MET Chi-restraints excluded: chain D residue 578 CYS Chi-restraints excluded: chain D residue 664 LEU Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 634 CYS Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 324 LYS Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 654 ASP Chi-restraints excluded: chain C residue 663 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 0.0970 chunk 51 optimal weight: 8.9990 chunk 155 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 168 optimal weight: 4.9990 chunk 70 optimal weight: 10.0000 chunk 172 optimal weight: 0.9990 chunk 21 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 chunk 147 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 628 ASN B 206 HIS ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.125009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.097595 restraints weight = 34486.150| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 3.12 r_work: 0.3042 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.140 18053 Z= 0.233 Angle : 0.773 59.199 24469 Z= 0.435 Chirality : 0.040 0.327 2749 Planarity : 0.004 0.048 3013 Dihedral : 5.412 59.227 2603 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.06 % Favored : 92.85 % Rotamer: Outliers : 2.27 % Allowed : 22.87 % Favored : 74.87 % Cbeta Deviations : 0.05 % 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: 0.86 (0.19), residues: 2139 helix: 1.74 (0.14), residues: 1310 sheet: -0.32 (0.58), residues: 76 loop : -1.49 (0.23), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP D 372 HIS 0.009 0.001 HIS D 410 PHE 0.045 0.001 PHE D 304 TYR 0.030 0.001 TYR D 511 ARG 0.006 0.000 ARG C 428 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5133.35 seconds wall clock time: 92 minutes 51.64 seconds (5571.64 seconds total)