Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 22:01:07 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dcp_27327/04_2023/8dcp_27327.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dcp_27327/04_2023/8dcp_27327.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dcp_27327/04_2023/8dcp_27327.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dcp_27327/04_2023/8dcp_27327.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dcp_27327/04_2023/8dcp_27327.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dcp_27327/04_2023/8dcp_27327.pdb" } resolution = 2.41 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 75 5.16 5 C 6724 2.51 5 N 1835 2.21 5 O 1961 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 35": "OE1" <-> "OE2" Residue "A GLU 85": "OE1" <-> "OE2" Residue "A GLU 109": "OE1" <-> "OE2" Residue "A PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 149": "OE1" <-> "OE2" Residue "A GLU 218": "OE1" <-> "OE2" Residue "A TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 259": "OE1" <-> "OE2" Residue "A GLU 417": "OE1" <-> "OE2" Residue "A GLU 493": "OE1" <-> "OE2" Residue "A ASP 538": "OD1" <-> "OD2" Residue "A GLU 542": "OE1" <-> "OE2" Residue "A GLU 596": "OE1" <-> "OE2" Residue "A ASP 626": "OD1" <-> "OD2" Residue "A TYR 631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 707": "OE1" <-> "OE2" Residue "A PHE 744": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 768": "OE1" <-> "OE2" Residue "A ASP 843": "OD1" <-> "OD2" Residue "A ASP 925": "OD1" <-> "OD2" Residue "A ASP 959": "OD1" <-> "OD2" Residue "A PHE 1016": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1018": "OD1" <-> "OD2" Residue "A GLU 1032": "OE1" <-> "OE2" Residue "B TYR 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 496": "OE1" <-> "OE2" Residue "B GLU 555": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 10595 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8233 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1005, 8222 Classifications: {'peptide': 1005} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 959} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 1005, 8222 Classifications: {'peptide': 1005} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 959} Chain breaks: 4 bond proxies already assigned to first conformer: 8389 Chain: "B" Number of atoms: 2341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2341 Classifications: {'peptide': 276} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 271} Chain breaks: 1 Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG A 704 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 704 " occ=0.50 Time building chain proxies: 9.53, per 1000 atoms: 0.90 Number of scatterers: 10595 At special positions: 0 Unit cell: (89.88, 130.54, 119.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 75 16.00 O 1961 8.00 N 1835 7.00 C 6724 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.62 Conformation dependent library (CDL) restraints added in 2.8 seconds 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2454 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 11 sheets defined 52.1% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 41 through 52 Processing helix chain 'A' and resid 64 through 68 removed outlier: 3.705A pdb=" N SER A 67 " --> pdb=" O ASP A 64 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TYR A 68 " --> pdb=" O GLU A 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 64 through 68' Processing helix chain 'A' and resid 89 through 93 removed outlier: 3.564A pdb=" N LEU A 92 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG A 93 " --> pdb=" O CYS A 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 89 through 93' Processing helix chain 'A' and resid 107 through 122 removed outlier: 3.509A pdb=" N LYS A 111 " --> pdb=" O ASN A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 130 removed outlier: 3.684A pdb=" N ASP A 129 " --> pdb=" O VAL A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 155 removed outlier: 4.309A pdb=" N LEU A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ASN A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N VAL A 146 " --> pdb=" O ASN A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 167 Processing helix chain 'A' and resid 178 through 183 removed outlier: 3.544A pdb=" N ASN A 183 " --> pdb=" O LYS A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 232 removed outlier: 3.866A pdb=" N SER A 231 " --> pdb=" O LYS A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 269 Processing helix chain 'A' and resid 270 through 280 Processing helix chain 'A' and resid 290 through 296 Processing helix chain 'A' and resid 305 through 309 removed outlier: 3.538A pdb=" N SER A 308 " --> pdb=" O PRO A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 330 No H-bonds generated for 'chain 'A' and resid 328 through 330' Processing helix chain 'A' and resid 394 through 396 No H-bonds generated for 'chain 'A' and resid 394 through 396' Processing helix chain 'A' and resid 488 through 496 Processing helix chain 'A' and resid 498 through 503 removed outlier: 3.683A pdb=" N ARG A 502 " --> pdb=" O TRP A 498 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU A 503 " --> pdb=" O SER A 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 498 through 503' Processing helix chain 'A' and resid 524 through 536 removed outlier: 3.517A pdb=" N GLN A 530 " --> pdb=" O ASN A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 554 Processing helix chain 'A' and resid 557 through 563 Proline residue: A 562 - end of helix Processing helix chain 'A' and resid 564 through 571 Processing helix chain 'A' and resid 576 through 589 removed outlier: 4.045A pdb=" N ASP A 589 " --> pdb=" O CYS A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 599 Processing helix chain 'A' and resid 600 through 603 Processing helix chain 'A' and resid 608 through 623 Processing helix chain 'A' and resid 624 through 631 Processing helix chain 'A' and resid 631 through 638 Processing helix chain 'A' and resid 639 through 642 Processing helix chain 'A' and resid 647 through 660 Processing helix chain 'A' and resid 660 through 674 removed outlier: 3.690A pdb=" N PHE A 666 " --> pdb=" O ARG A 662 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU A 674 " --> pdb=" O HIS A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 695 Processing helix chain 'A' and resid 697 through 722 removed outlier: 4.058A pdb=" N HIS A 701 " --> pdb=" O MET A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 739 Processing helix chain 'A' and resid 741 through 748 Processing helix chain 'A' and resid 765 through 769 Processing helix chain 'A' and resid 789 through 794 removed outlier: 4.330A pdb=" N LEU A 793 " --> pdb=" O MET A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 828 Processing helix chain 'A' and resid 857 through 864 Processing helix chain 'A' and resid 871 through 874 Processing helix chain 'A' and resid 875 through 885 Processing helix chain 'A' and resid 888 through 912 removed outlier: 4.245A pdb=" N ALA A 892 " --> pdb=" O GLU A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 965 removed outlier: 3.541A pdb=" N VAL A 963 " --> pdb=" O ASP A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 974 through 993 Processing helix chain 'A' and resid 994 through 1004 removed outlier: 3.787A pdb=" N PHE A 998 " --> pdb=" O HIS A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1026 removed outlier: 3.889A pdb=" N ILE A1019 " --> pdb=" O SER A1015 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N TYR A1021 " --> pdb=" O ASP A1017 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ILE A1022 " --> pdb=" O ASP A1018 " (cutoff:3.500A) Processing helix chain 'A' and resid 1031 through 1048 removed outlier: 3.561A pdb=" N ALA A1046 " --> pdb=" O GLN A1042 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 347 Processing helix chain 'B' and resid 400 through 411 removed outlier: 3.815A pdb=" N LEU B 404 " --> pdb=" O SER B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 416 removed outlier: 3.550A pdb=" N GLN B 415 " --> pdb=" O SER B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 509 removed outlier: 3.858A pdb=" N LYS B 506 " --> pdb=" O GLU B 502 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N GLU B 507 " --> pdb=" O ARG B 503 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N TYR B 508 " --> pdb=" O TYR B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 514 removed outlier: 3.863A pdb=" N LYS B 513 " --> pdb=" O GLU B 510 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG B 514 " --> pdb=" O LYS B 511 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 510 through 514' Processing helix chain 'B' and resid 517 through 588 removed outlier: 4.136A pdb=" N ILE B 521 " --> pdb=" O ASN B 517 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASN B 527 " --> pdb=" O ARG B 523 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR B 528 " --> pdb=" O ILE B 524 " (cutoff:3.500A) Proline residue: B 568 - end of helix removed outlier: 3.999A pdb=" N GLY B 588 " --> pdb=" O LEU B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 596 removed outlier: 4.054A pdb=" N LEU B 594 " --> pdb=" O ARG B 590 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 35 removed outlier: 3.601A pdb=" N VAL A 22 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 8.421A pdb=" N LEU A 99 " --> pdb=" O LEU A 21 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLU A 23 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N VAL A 101 " --> pdb=" O GLU A 23 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N LEU A 25 " --> pdb=" O VAL A 101 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N PHE A 98 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N VAL A 73 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N PHE A 70 " --> pdb=" O PHE A 82 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER A 72 " --> pdb=" O GLU A 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 205 through 212 removed outlier: 4.457A pdb=" N LEU A 252 " --> pdb=" O PHE A 261 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 325 through 326 removed outlier: 6.751A pdb=" N LYS A 325 " --> pdb=" O LYS A 485 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 382 through 392 removed outlier: 6.788A pdb=" N TRP A 383 " --> pdb=" O CYS A 340 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N CYS A 340 " --> pdb=" O TRP A 383 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LEU A 334 " --> pdb=" O TYR A 389 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLU A 474 " --> pdb=" O LEU A 339 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ALA A 341 " --> pdb=" O CYS A 472 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N CYS A 472 " --> pdb=" O ALA A 341 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY A 439 " --> pdb=" O PHE A 477 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 365 through 366 Processing sheet with id=AA6, first strand: chain 'A' and resid 371 through 372 removed outlier: 3.794A pdb=" N LYS A 353 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU A 402 " --> pdb=" O ASN A 426 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ASN A 426 " --> pdb=" O LEU A 402 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N LEU A 404 " --> pdb=" O TRP A 424 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N TRP A 424 " --> pdb=" O LEU A 404 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE A 406 " --> pdb=" O LEU A 422 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 751 through 752 Processing sheet with id=AA8, first strand: chain 'A' and resid 770 through 771 removed outlier: 6.924A pdb=" N VAL A 845 " --> pdb=" O ILE A 841 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 854 through 856 Processing sheet with id=AB1, first strand: chain 'B' and resid 377 through 382 removed outlier: 4.434A pdb=" N THR B 354 " --> pdb=" O ARG B 373 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 384 through 386 521 hydrogen bonds defined for protein. 1492 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: 3.73 Time building geometry restraints manager: 4.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3480 1.34 - 1.46: 2355 1.46 - 1.58: 4841 1.58 - 1.70: 0 1.70 - 1.82: 117 Bond restraints: 10793 Sorted by residual: bond pdb=" CG1 ILE A 121 " pdb=" CD1 ILE A 121 " ideal model delta sigma weight residual 1.513 1.445 0.068 3.90e-02 6.57e+02 3.07e+00 bond pdb=" CG1 ILE A 894 " pdb=" CD1 ILE A 894 " ideal model delta sigma weight residual 1.513 1.450 0.063 3.90e-02 6.57e+02 2.58e+00 bond pdb=" CG LYS A 132 " pdb=" CD LYS A 132 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.02e+00 bond pdb=" CB LYS A 132 " pdb=" CG LYS A 132 " ideal model delta sigma weight residual 1.520 1.560 -0.040 3.00e-02 1.11e+03 1.75e+00 bond pdb=" CB MET B 322 " pdb=" CG MET B 322 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.70e+00 ... (remaining 10788 not shown) Histogram of bond angle deviations from ideal: 98.62 - 105.69: 193 105.69 - 112.77: 5614 112.77 - 119.84: 3697 119.84 - 126.91: 4912 126.91 - 133.98: 132 Bond angle restraints: 14548 Sorted by residual: angle pdb=" CB LYS A 132 " pdb=" CG LYS A 132 " pdb=" CD LYS A 132 " ideal model delta sigma weight residual 111.30 121.47 -10.17 2.30e+00 1.89e-01 1.96e+01 angle pdb=" CA MET B 322 " pdb=" CB MET B 322 " pdb=" CG MET B 322 " ideal model delta sigma weight residual 114.10 122.17 -8.07 2.00e+00 2.50e-01 1.63e+01 angle pdb=" CB MET B 563 " pdb=" CG MET B 563 " pdb=" SD MET B 563 " ideal model delta sigma weight residual 112.70 102.26 10.44 3.00e+00 1.11e-01 1.21e+01 angle pdb=" CB MET A 299 " pdb=" CG MET A 299 " pdb=" SD MET A 299 " ideal model delta sigma weight residual 112.70 123.07 -10.37 3.00e+00 1.11e-01 1.20e+01 angle pdb=" CA GLU A 493 " pdb=" CB GLU A 493 " pdb=" CG GLU A 493 " ideal model delta sigma weight residual 114.10 120.77 -6.67 2.00e+00 2.50e-01 1.11e+01 ... (remaining 14543 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 5413 17.83 - 35.66: 823 35.66 - 53.48: 284 53.48 - 71.31: 63 71.31 - 89.14: 29 Dihedral angle restraints: 6612 sinusoidal: 2829 harmonic: 3783 Sorted by residual: dihedral pdb=" CA PRO A 200 " pdb=" C PRO A 200 " pdb=" N ASN A 201 " pdb=" CA ASN A 201 " ideal model delta harmonic sigma weight residual 180.00 161.75 18.25 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA HIS A 940 " pdb=" C HIS A 940 " pdb=" N LYS A 941 " pdb=" CA LYS A 941 " ideal model delta harmonic sigma weight residual 180.00 162.02 17.98 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA SER A 199 " pdb=" C SER A 199 " pdb=" N PRO A 200 " pdb=" CA PRO A 200 " ideal model delta harmonic sigma weight residual 180.00 162.14 17.86 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 6609 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 971 0.031 - 0.061: 392 0.061 - 0.092: 128 0.092 - 0.123: 71 0.123 - 0.154: 8 Chirality restraints: 1570 Sorted by residual: chirality pdb=" CB ILE A 197 " pdb=" CA ILE A 197 " pdb=" CG1 ILE A 197 " pdb=" CG2 ILE A 197 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.90e-01 chirality pdb=" CA ILE A 191 " pdb=" N ILE A 191 " pdb=" C ILE A 191 " pdb=" CB ILE A 191 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.81e-01 chirality pdb=" CA ILE A 561 " pdb=" N ILE A 561 " pdb=" C ILE A 561 " pdb=" CB ILE A 561 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.52e-01 ... (remaining 1567 not shown) Planarity restraints: 1871 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 282 " 0.029 5.00e-02 4.00e+02 4.38e-02 3.07e+00 pdb=" N PRO A 283 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 283 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 283 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 420 " 0.024 5.00e-02 4.00e+02 3.65e-02 2.14e+00 pdb=" N PRO A 421 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 421 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 421 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 216 " -0.022 5.00e-02 4.00e+02 3.28e-02 1.73e+00 pdb=" N PRO A 217 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 217 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 217 " -0.018 5.00e-02 4.00e+02 ... (remaining 1868 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2293 2.78 - 3.31: 9871 3.31 - 3.84: 18197 3.84 - 4.37: 20893 4.37 - 4.90: 35063 Nonbonded interactions: 86317 Sorted by model distance: nonbonded pdb=" NZ LYS A 884 " pdb=" OD1 ASP A 925 " model vdw 2.253 2.520 nonbonded pdb=" O GLY B 321 " pdb=" ND2 ASN B 323 " model vdw 2.263 2.520 nonbonded pdb=" N ASN B 319 " pdb=" ND2 ASN B 319 " model vdw 2.293 3.200 nonbonded pdb=" ND2 ASN A 782 " pdb=" OD1 ASN A 796 " model vdw 2.296 2.520 nonbonded pdb=" NH2 ARG A 398 " pdb=" OD1 ASP A 434 " model vdw 2.296 2.520 ... (remaining 86312 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.50 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: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.560 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 36.930 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.060 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:10.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 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 : 0.003 0.068 10793 Z= 0.201 Angle : 0.641 10.437 14548 Z= 0.317 Chirality : 0.041 0.154 1570 Planarity : 0.004 0.047 1871 Dihedral : 20.067 89.140 4158 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer Outliers : 3.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.24), residues: 1270 helix: 1.62 (0.22), residues: 575 sheet: -0.03 (0.42), residues: 162 loop : -0.47 (0.27), residues: 533 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 239 time to evaluate : 1.317 Fit side-chains outliers start: 35 outliers final: 30 residues processed: 272 average time/residue: 1.3003 time to fit residues: 379.1307 Evaluate side-chains 258 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 228 time to evaluate : 1.387 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 29 residues processed: 1 average time/residue: 0.1711 time to fit residues: 2.2298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 0.7980 chunk 96 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 32 optimal weight: 8.9990 chunk 64 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 99 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 74 optimal weight: 7.9990 chunk 115 optimal weight: 10.0000 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 826 ASN A 958 GLN ** A1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 ASN B 478 GLN B 552 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.0684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 10793 Z= 0.210 Angle : 0.569 8.585 14548 Z= 0.290 Chirality : 0.041 0.153 1570 Planarity : 0.004 0.041 1871 Dihedral : 4.239 17.813 1408 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer Outliers : 6.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.24), residues: 1270 helix: 1.80 (0.22), residues: 596 sheet: 0.02 (0.40), residues: 162 loop : -0.51 (0.27), residues: 512 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 250 time to evaluate : 1.196 Fit side-chains outliers start: 78 outliers final: 41 residues processed: 299 average time/residue: 1.2698 time to fit residues: 407.7925 Evaluate side-chains 283 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 242 time to evaluate : 1.256 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 29 residues processed: 12 average time/residue: 0.5843 time to fit residues: 9.9387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 64 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 95 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 31 optimal weight: 7.9990 chunk 115 optimal weight: 10.0000 chunk 124 optimal weight: 8.9990 chunk 102 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 92 optimal weight: 9.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 826 ASN A 958 GLN ** A1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 ASN B 488 ASN ** B 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.0807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.045 10793 Z= 0.154 Angle : 0.536 7.648 14548 Z= 0.271 Chirality : 0.040 0.150 1570 Planarity : 0.003 0.044 1871 Dihedral : 4.094 18.343 1408 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer Outliers : 5.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 1.14 (0.24), residues: 1270 helix: 1.95 (0.22), residues: 599 sheet: 0.01 (0.40), residues: 160 loop : -0.39 (0.28), residues: 511 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 239 time to evaluate : 1.285 Fit side-chains outliers start: 64 outliers final: 38 residues processed: 282 average time/residue: 1.2956 time to fit residues: 391.9191 Evaluate side-chains 273 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 235 time to evaluate : 1.310 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 28 residues processed: 10 average time/residue: 0.4107 time to fit residues: 6.7958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 114 optimal weight: 3.9990 chunk 86 optimal weight: 0.6980 chunk 59 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 55 optimal weight: 9.9990 chunk 77 optimal weight: 7.9990 chunk 115 optimal weight: 9.9990 chunk 122 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 33 optimal weight: 9.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS A 107 ASN ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 822 ASN A 826 ASN A 958 GLN ** A1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 ASN B 488 ASN ** B 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.0918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.073 10793 Z= 0.263 Angle : 0.595 8.738 14548 Z= 0.302 Chirality : 0.043 0.175 1570 Planarity : 0.004 0.053 1871 Dihedral : 4.321 18.354 1408 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer Outliers : 6.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 1.05 (0.24), residues: 1270 helix: 1.86 (0.21), residues: 597 sheet: 0.00 (0.40), residues: 161 loop : -0.43 (0.28), residues: 512 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 246 time to evaluate : 1.290 Fit side-chains outliers start: 71 outliers final: 43 residues processed: 292 average time/residue: 1.2853 time to fit residues: 402.4669 Evaluate side-chains 282 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 239 time to evaluate : 1.279 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 30 residues processed: 13 average time/residue: 0.5089 time to fit residues: 9.5702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 102 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 chunk 50 optimal weight: 8.9990 chunk 104 optimal weight: 10.0000 chunk 84 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 110 optimal weight: 9.9990 chunk 30 optimal weight: 6.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 826 ASN A 958 GLN ** A1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 ASN ** B 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.0943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 10793 Z= 0.227 Angle : 0.592 10.485 14548 Z= 0.297 Chirality : 0.042 0.162 1570 Planarity : 0.004 0.052 1871 Dihedral : 4.313 18.577 1408 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer Outliers : 5.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 1.04 (0.24), residues: 1270 helix: 1.86 (0.21), residues: 598 sheet: -0.01 (0.40), residues: 161 loop : -0.44 (0.28), residues: 511 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 242 time to evaluate : 1.334 Fit side-chains outliers start: 66 outliers final: 43 residues processed: 285 average time/residue: 1.2918 time to fit residues: 395.0306 Evaluate side-chains 282 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 239 time to evaluate : 1.283 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 33 residues processed: 10 average time/residue: 0.4236 time to fit residues: 6.9914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 41 optimal weight: 7.9990 chunk 110 optimal weight: 7.9990 chunk 24 optimal weight: 9.9990 chunk 72 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 122 optimal weight: 10.0000 chunk 102 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 40 optimal weight: 6.9990 chunk 64 optimal weight: 0.6980 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 ASN A 444 ASN A 822 ASN A 826 ASN A 958 GLN ** A1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 ASN ** B 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.091 10793 Z= 0.402 Angle : 0.711 10.589 14548 Z= 0.358 Chirality : 0.048 0.200 1570 Planarity : 0.005 0.072 1871 Dihedral : 4.714 18.843 1408 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer Outliers : 5.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.63 (0.23), residues: 1270 helix: 1.48 (0.21), residues: 597 sheet: -0.09 (0.39), residues: 163 loop : -0.64 (0.27), residues: 510 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 243 time to evaluate : 1.322 Fit side-chains outliers start: 65 outliers final: 42 residues processed: 288 average time/residue: 1.3039 time to fit residues: 403.5690 Evaluate side-chains 277 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 235 time to evaluate : 1.323 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 33 residues processed: 9 average time/residue: 0.7621 time to fit residues: 9.6372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 118 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 70 optimal weight: 0.2980 chunk 89 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 122 optimal weight: 10.0000 chunk 76 optimal weight: 8.9990 chunk 74 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 826 ASN A 958 GLN ** A1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 ASN B 552 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 10793 Z= 0.167 Angle : 0.589 9.894 14548 Z= 0.291 Chirality : 0.041 0.175 1570 Planarity : 0.003 0.043 1871 Dihedral : 4.303 19.972 1408 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer Outliers : 4.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 1.03 (0.24), residues: 1270 helix: 1.87 (0.21), residues: 598 sheet: 0.06 (0.38), residues: 166 loop : -0.50 (0.28), residues: 506 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 249 time to evaluate : 1.479 Fit side-chains outliers start: 55 outliers final: 41 residues processed: 286 average time/residue: 1.3126 time to fit residues: 403.4092 Evaluate side-chains 284 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 243 time to evaluate : 1.277 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 32 residues processed: 10 average time/residue: 0.6179 time to fit residues: 8.9465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 75 optimal weight: 10.0000 chunk 48 optimal weight: 9.9990 chunk 73 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 83 optimal weight: 0.0060 chunk 60 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 96 optimal weight: 9.9990 overall best weight: 2.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 826 ASN A 918 ASN A 958 GLN ** A1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.071 10793 Z= 0.225 Angle : 0.622 10.880 14548 Z= 0.307 Chirality : 0.042 0.182 1570 Planarity : 0.004 0.054 1871 Dihedral : 4.325 19.872 1408 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer Outliers : 4.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.94 (0.24), residues: 1270 helix: 1.80 (0.21), residues: 598 sheet: -0.05 (0.38), residues: 169 loop : -0.54 (0.28), residues: 503 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 243 time to evaluate : 1.171 Fit side-chains outliers start: 49 outliers final: 37 residues processed: 278 average time/residue: 1.3422 time to fit residues: 400.0215 Evaluate side-chains 278 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 241 time to evaluate : 1.188 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 30 residues processed: 7 average time/residue: 0.1715 time to fit residues: 3.7125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 111 optimal weight: 2.9990 chunk 117 optimal weight: 9.9990 chunk 106 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 chunk 68 optimal weight: 20.0000 chunk 49 optimal weight: 9.9990 chunk 89 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 826 ASN A 958 GLN ** A1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.076 10793 Z= 0.260 Angle : 0.664 11.569 14548 Z= 0.326 Chirality : 0.044 0.182 1570 Planarity : 0.004 0.059 1871 Dihedral : 4.442 22.798 1408 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer Outliers : 4.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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 (0.24), residues: 1270 helix: 1.67 (0.21), residues: 599 sheet: -0.06 (0.39), residues: 163 loop : -0.52 (0.28), residues: 508 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 240 time to evaluate : 1.329 Fit side-chains outliers start: 48 outliers final: 36 residues processed: 274 average time/residue: 1.3397 time to fit residues: 394.9389 Evaluate side-chains 273 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 237 time to evaluate : 1.386 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 29 residues processed: 7 average time/residue: 0.7327 time to fit residues: 7.8272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 74 optimal weight: 0.9990 chunk 120 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 126 optimal weight: 20.0000 chunk 116 optimal weight: 9.9990 chunk 100 optimal weight: 4.9990 chunk 10 optimal weight: 0.2980 chunk 77 optimal weight: 8.9990 chunk 61 optimal weight: 9.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN A 826 ASN A 958 GLN ** A1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 10793 Z= 0.202 Angle : 0.635 11.884 14548 Z= 0.312 Chirality : 0.042 0.170 1570 Planarity : 0.004 0.053 1871 Dihedral : 4.328 23.844 1408 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer Outliers : 3.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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 (0.24), residues: 1270 helix: 1.73 (0.21), residues: 599 sheet: -0.05 (0.39), residues: 161 loop : -0.45 (0.28), residues: 510 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 235 time to evaluate : 1.524 Fit side-chains outliers start: 40 outliers final: 33 residues processed: 269 average time/residue: 1.4108 time to fit residues: 407.4684 Evaluate side-chains 267 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 234 time to evaluate : 1.345 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 29 residues processed: 4 average time/residue: 0.5188 time to fit residues: 4.4820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 80 optimal weight: 5.9990 chunk 107 optimal weight: 8.9990 chunk 30 optimal weight: 6.9990 chunk 92 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 27 optimal weight: 0.1980 chunk 100 optimal weight: 20.0000 chunk 42 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN A 826 ASN A 958 GLN ** A1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.187992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.148637 restraints weight = 23205.026| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 2.42 r_work: 0.3446 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3298 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3298 r_free = 0.3298 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3298 r_free = 0.3298 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3298 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.067 10793 Z= 0.210 Angle : 0.634 11.909 14548 Z= 0.312 Chirality : 0.042 0.230 1570 Planarity : 0.004 0.054 1871 Dihedral : 4.292 18.252 1408 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer Outliers : 3.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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 (0.24), residues: 1270 helix: 1.75 (0.21), residues: 598 sheet: -0.09 (0.38), residues: 167 loop : -0.48 (0.28), residues: 505 =============================================================================== Job complete usr+sys time: 6008.94 seconds wall clock time: 106 minutes 16.61 seconds (6376.61 seconds total)