Starting phenix.real_space_refine on Sun Mar 17 00:05:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jyl_9718/03_2024/6jyl_9718_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jyl_9718/03_2024/6jyl_9718.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jyl_9718/03_2024/6jyl_9718.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jyl_9718/03_2024/6jyl_9718.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jyl_9718/03_2024/6jyl_9718_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jyl_9718/03_2024/6jyl_9718_updated.pdb" } resolution = 3.37 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= 0.005 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: 8 Type Number sf(0) Gaussians P 294 5.49 5 Mg 1 5.21 5 S 25 5.16 5 Be 1 3.05 5 C 9259 2.51 5 N 2959 2.21 5 O 3594 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 19": "NH1" <-> "NH2" Residue "B ARG 23": "NH1" <-> "NH2" Residue "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 266": "NH1" <-> "NH2" Residue "K ARG 308": "NH1" <-> "NH2" Residue "K ARG 341": "NH1" <-> "NH2" Residue "K ARG 473": "NH1" <-> "NH2" Residue "K TYR 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 611": "NH1" <-> "NH2" Residue "K ARG 614": "NH1" <-> "NH2" Residue "K ARG 639": "NH1" <-> "NH2" Residue "K ARG 645": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16136 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 707 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "C" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 718 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 632 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "K" Number of atoms: 4161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 4161 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'peptide': 504, 'undetermined': 3} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 485, None: 3} Not linked: pdbres="SER K 657 " pdbres="ADP K1201 " Not linked: pdbres="ADP K1201 " pdbres="BEF K1202 " Not linked: pdbres="BEF K1202 " pdbres=" MG K1203 " Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 8.77, per 1000 atoms: 0.54 Number of scatterers: 16136 At special positions: 0 Unit cell: (146.59, 130.54, 123.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 25 16.00 P 294 15.00 Mg 1 11.99 F 3 9.00 O 3594 8.00 N 2959 7.00 C 9259 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.89 Conformation dependent library (CDL) restraints added in 2.0 seconds 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2392 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 56 helices and 3 sheets defined 55.9% alpha, 2.5% beta 145 base pairs and 254 stacking pairs defined. Time for finding SS restraints: 8.85 Creating SS restraints... Processing helix chain 'A' and resid 45 through 56 Processing helix chain 'A' and resid 64 through 77 removed outlier: 4.333A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 113 Processing helix chain 'A' and resid 121 through 131 removed outlier: 3.748A pdb=" N ARG A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 28 Processing helix chain 'B' and resid 31 through 41 Processing helix chain 'B' and resid 50 through 75 Processing helix chain 'B' and resid 83 through 92 Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 28 through 37 Processing helix chain 'C' and resid 47 through 72 Processing helix chain 'C' and resid 80 through 89 Processing helix chain 'C' and resid 91 through 96 Processing helix chain 'D' and resid 35 through 45 Processing helix chain 'D' and resid 53 through 80 Processing helix chain 'D' and resid 88 through 98 Processing helix chain 'D' and resid 101 through 120 removed outlier: 3.629A pdb=" N LYS D 105 " --> pdb=" O GLU D 102 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS D 106 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR D 119 " --> pdb=" O THR D 116 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER D 120 " --> pdb=" O LYS D 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 56 Processing helix chain 'E' and resid 64 through 77 removed outlier: 4.113A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 113 Processing helix chain 'E' and resid 121 through 131 removed outlier: 3.580A pdb=" N ARG E 131 " --> pdb=" O ALA E 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 28 No H-bonds generated for 'chain 'F' and resid 26 through 28' Processing helix chain 'F' and resid 31 through 41 Processing helix chain 'F' and resid 50 through 75 Processing helix chain 'F' and resid 83 through 93 Processing helix chain 'G' and resid 17 through 21 Processing helix chain 'G' and resid 27 through 35 Processing helix chain 'G' and resid 47 through 73 removed outlier: 3.808A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 89 Processing helix chain 'G' and resid 92 through 96 Processing helix chain 'H' and resid 35 through 45 Processing helix chain 'H' and resid 53 through 80 Processing helix chain 'H' and resid 88 through 98 Processing helix chain 'H' and resid 101 through 120 removed outlier: 3.592A pdb=" N HIS H 106 " --> pdb=" O LEU H 103 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR H 119 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER H 120 " --> pdb=" O LYS H 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 102 through 112 removed outlier: 3.526A pdb=" N THR K 106 " --> pdb=" O LEU K 102 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N HIS K 111 " --> pdb=" O LYS K 107 " (cutoff:3.500A) Processing helix chain 'K' and resid 118 through 123 Processing helix chain 'K' and resid 132 through 142 removed outlier: 3.639A pdb=" N LEU K 137 " --> pdb=" O ARG K 134 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP K 138 " --> pdb=" O GLN K 135 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL K 139 " --> pdb=" O VAL K 136 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU K 141 " --> pdb=" O ASP K 138 " (cutoff:3.500A) Processing helix chain 'K' and resid 198 through 212 removed outlier: 3.733A pdb=" N GLN K 202 " --> pdb=" O PRO K 198 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU K 207 " --> pdb=" O GLY K 203 " (cutoff:3.500A) Processing helix chain 'K' and resid 227 through 240 Processing helix chain 'K' and resid 254 through 267 removed outlier: 3.507A pdb=" N LEU K 257 " --> pdb=" O LYS K 254 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N ASN K 258 " --> pdb=" O SER K 255 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TRP K 260 " --> pdb=" O LEU K 257 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG K 262 " --> pdb=" O ASN K 259 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE K 264 " --> pdb=" O LEU K 261 " (cutoff:3.500A) Processing helix chain 'K' and resid 282 through 289 removed outlier: 3.887A pdb=" N LEU K 286 " --> pdb=" O GLU K 282 " (cutoff:3.500A) Processing helix chain 'K' and resid 305 through 308 No H-bonds generated for 'chain 'K' and resid 305 through 308' Processing helix chain 'K' and resid 328 through 330 No H-bonds generated for 'chain 'K' and resid 328 through 330' Processing helix chain 'K' and resid 335 through 340 Processing helix chain 'K' and resid 360 through 368 removed outlier: 3.578A pdb=" N TRP K 364 " --> pdb=" O LEU K 360 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA K 365 " --> pdb=" O HIS K 361 " (cutoff:3.500A) Processing helix chain 'K' and resid 379 through 389 removed outlier: 3.527A pdb=" N PHE K 385 " --> pdb=" O PHE K 381 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N SER K 387 " --> pdb=" O ASP K 383 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N GLU K 388 " --> pdb=" O TRP K 384 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N SER K 389 " --> pdb=" O PHE K 385 " (cutoff:3.500A) Processing helix chain 'K' and resid 398 through 406 Processing helix chain 'K' and resid 435 through 445 removed outlier: 4.126A pdb=" N LYS K 439 " --> pdb=" O SER K 435 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TRP K 440 " --> pdb=" O MET K 436 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE K 444 " --> pdb=" O TRP K 440 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU K 445 " --> pdb=" O TYR K 441 " (cutoff:3.500A) Processing helix chain 'K' and resid 468 through 477 removed outlier: 3.649A pdb=" N ARG K 473 " --> pdb=" O MET K 469 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N CYS K 475 " --> pdb=" O GLN K 471 " (cutoff:3.500A) Processing helix chain 'K' and resid 479 through 481 No H-bonds generated for 'chain 'K' and resid 479 through 481' Processing helix chain 'K' and resid 496 through 500 Processing helix chain 'K' and resid 503 through 517 removed outlier: 3.921A pdb=" N GLU K 516 " --> pdb=" O LYS K 512 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU K 517 " --> pdb=" O LYS K 513 " (cutoff:3.500A) Processing helix chain 'K' and resid 528 through 540 removed outlier: 3.778A pdb=" N ASP K 532 " --> pdb=" O SER K 528 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE K 533 " --> pdb=" O ARG K 529 " (cutoff:3.500A) Processing helix chain 'K' and resid 555 through 564 Processing helix chain 'K' and resid 602 through 611 removed outlier: 3.703A pdb=" N ASP K 610 " --> pdb=" O LEU K 606 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ARG K 611 " --> pdb=" O GLN K 607 " (cutoff:3.500A) Processing helix chain 'K' and resid 632 through 656 removed outlier: 3.781A pdb=" N LEU K 646 " --> pdb=" O GLN K 642 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASP K 647 " --> pdb=" O LYS K 643 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU K 649 " --> pdb=" O ARG K 645 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N VAL K 650 " --> pdb=" O LEU K 646 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLN K 653 " --> pdb=" O LEU K 649 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN K 654 " --> pdb=" O VAL K 650 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ARG K 655 " --> pdb=" O ILE K 651 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N THR K 656 " --> pdb=" O GLN K 652 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'K' and resid 217 through 219 removed outlier: 3.504A pdb=" N LEU K 350 " --> pdb=" O GLY K 217 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'K' and resid 298 through 301 removed outlier: 6.896A pdb=" N PHE K 248 " --> pdb=" O VAL K 299 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ALA K 301 " --> pdb=" O PHE K 248 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL K 250 " --> pdb=" O ALA K 301 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N TYR K 320 " --> pdb=" O LEU K 249 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N ILE K 251 " --> pdb=" O TYR K 320 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE K 322 " --> pdb=" O ILE K 251 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'K' and resid 425 through 431 removed outlier: 3.550A pdb=" N VAL K 593 " --> pdb=" O LYS K 622 " (cutoff:3.500A) 452 hydrogen bonds defined for protein. 1242 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 369 hydrogen bonds 730 hydrogen bond angles 0 basepair planarities 145 basepair parallelities 254 stacking parallelities Total time for adding SS restraints: 7.62 Time building geometry restraints manager: 7.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3268 1.33 - 1.45: 5062 1.45 - 1.57: 8060 1.57 - 1.69: 586 1.69 - 1.81: 45 Bond restraints: 17021 Sorted by residual: bond pdb=" BE BEF K1202 " pdb=" F2 BEF K1202 " ideal model delta sigma weight residual 1.476 1.709 -0.233 2.00e-02 2.50e+03 1.36e+02 bond pdb=" BE BEF K1202 " pdb=" F1 BEF K1202 " ideal model delta sigma weight residual 1.476 1.702 -0.226 2.00e-02 2.50e+03 1.28e+02 bond pdb=" BE BEF K1202 " pdb=" F3 BEF K1202 " ideal model delta sigma weight residual 1.476 1.688 -0.212 2.00e-02 2.50e+03 1.12e+02 bond pdb=" C3' DG J 94 " pdb=" O3' DG J 94 " ideal model delta sigma weight residual 1.422 1.486 -0.064 3.00e-02 1.11e+03 4.49e+00 bond pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " ideal model delta sigma weight residual 1.422 1.468 -0.046 3.00e-02 1.11e+03 2.34e+00 ... (remaining 17016 not shown) Histogram of bond angle deviations from ideal: 97.98 - 105.68: 1639 105.68 - 113.37: 9683 113.37 - 121.07: 8492 121.07 - 128.77: 4233 128.77 - 136.47: 207 Bond angle restraints: 24254 Sorted by residual: angle pdb=" F1 BEF K1202 " pdb=" BE BEF K1202 " pdb=" F3 BEF K1202 " ideal model delta sigma weight residual 120.12 98.86 21.26 3.00e+00 1.11e-01 5.02e+01 angle pdb=" F2 BEF K1202 " pdb=" BE BEF K1202 " pdb=" F3 BEF K1202 " ideal model delta sigma weight residual 119.96 105.49 14.47 3.00e+00 1.11e-01 2.33e+01 angle pdb=" N ILE K 329 " pdb=" CA ILE K 329 " pdb=" C ILE K 329 " ideal model delta sigma weight residual 111.91 108.14 3.77 8.90e-01 1.26e+00 1.79e+01 angle pdb=" C SER D 75 " pdb=" N ARG D 76 " pdb=" CA ARG D 76 " ideal model delta sigma weight residual 121.58 114.57 7.01 1.95e+00 2.63e-01 1.29e+01 angle pdb=" C SER H 75 " pdb=" N ARG H 76 " pdb=" CA ARG H 76 " ideal model delta sigma weight residual 121.58 114.72 6.86 1.95e+00 2.63e-01 1.24e+01 ... (remaining 24249 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.90: 7856 30.90 - 61.80: 1612 61.80 - 92.70: 35 92.70 - 123.60: 0 123.60 - 154.50: 6 Dihedral angle restraints: 9509 sinusoidal: 5817 harmonic: 3692 Sorted by residual: dihedral pdb=" O2A ADP K1201 " pdb=" O3A ADP K1201 " pdb=" PA ADP K1201 " pdb=" PB ADP K1201 " ideal model delta sinusoidal sigma weight residual -60.00 84.35 -144.34 1 2.00e+01 2.50e-03 4.35e+01 dihedral pdb=" O1B ADP K1201 " pdb=" O3A ADP K1201 " pdb=" PB ADP K1201 " pdb=" PA ADP K1201 " ideal model delta sinusoidal sigma weight residual -60.00 82.54 -142.54 1 2.00e+01 2.50e-03 4.31e+01 dihedral pdb=" C5' ADP K1201 " pdb=" O5' ADP K1201 " pdb=" PA ADP K1201 " pdb=" O2A ADP K1201 " ideal model delta sinusoidal sigma weight residual -60.00 82.45 -142.44 1 2.00e+01 2.50e-03 4.30e+01 ... (remaining 9506 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2206 0.059 - 0.119: 491 0.119 - 0.178: 52 0.178 - 0.238: 5 0.238 - 0.297: 1 Chirality restraints: 2755 Sorted by residual: chirality pdb=" CA THR K 492 " pdb=" N THR K 492 " pdb=" C THR K 492 " pdb=" CB THR K 492 " both_signs ideal model delta sigma weight residual False 2.53 2.23 0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CB ILE K 329 " pdb=" CA ILE K 329 " pdb=" CG1 ILE K 329 " pdb=" CG2 ILE K 329 " both_signs ideal model delta sigma weight residual False 2.64 2.87 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CB ILE D 51 " pdb=" CA ILE D 51 " pdb=" CG1 ILE D 51 " pdb=" CG2 ILE D 51 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 2752 not shown) Planarity restraints: 2063 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY K 488 " 0.062 5.00e-02 4.00e+02 9.43e-02 1.42e+01 pdb=" N PRO K 489 " -0.163 5.00e-02 4.00e+02 pdb=" CA PRO K 489 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO K 489 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN K 406 " -0.043 5.00e-02 4.00e+02 6.46e-02 6.68e+00 pdb=" N PRO K 407 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO K 407 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO K 407 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO K 489 " 0.042 5.00e-02 4.00e+02 6.32e-02 6.40e+00 pdb=" N PRO K 490 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO K 490 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO K 490 " 0.036 5.00e-02 4.00e+02 ... (remaining 2060 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 304 2.65 - 3.21: 12839 3.21 - 3.77: 28128 3.77 - 4.34: 37285 4.34 - 4.90: 54234 Nonbonded interactions: 132790 Sorted by model distance: nonbonded pdb=" O3B ADP K1201 " pdb="MG MG K1203 " model vdw 2.086 2.170 nonbonded pdb=" N2 DG I 13 " pdb=" O2 DC J 135 " model vdw 2.254 2.496 nonbonded pdb=" N2 DG I 83 " pdb=" O2 DC J 65 " model vdw 2.310 2.496 nonbonded pdb=" OD2 ASP D 65 " pdb=" OH TYR F 98 " model vdw 2.334 2.440 nonbonded pdb=" O THR K 492 " pdb=" OG1 THR K 493 " model vdw 2.354 2.440 ... (remaining 132785 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 40 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and ((resid 23 and (name N or name CA or name C or name O or name CB \ )) or resid 24 through 101)) selection = (chain 'F' and resid 23 through 101) } ncs_group { reference = (chain 'C' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 118)) selection = (chain 'G' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 118)) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 29 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 53 or (resid 54 through 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 through 121)) } 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: 0.690 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: 3.890 Check model and map are aligned: 0.230 Set scattering table: 0.160 Process input model: 53.710 Find NCS groups from input model: 0.610 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: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 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 : 0.008 0.233 17021 Z= 0.479 Angle : 0.848 21.257 24254 Z= 0.487 Chirality : 0.048 0.297 2755 Planarity : 0.007 0.094 2063 Dihedral : 24.561 154.504 7117 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.83 % Favored : 95.00 % Rotamer: Outliers : 0.28 % Allowed : 0.74 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.67 (0.19), residues: 1241 helix: -1.94 (0.14), residues: 740 sheet: -3.11 (0.63), residues: 61 loop : -2.98 (0.24), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP K 267 HIS 0.014 0.002 HIS K 402 PHE 0.029 0.003 PHE C 25 TYR 0.035 0.003 TYR B 51 ARG 0.009 0.001 ARG F 45 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 225 time to evaluate : 1.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 THR cc_start: 0.9247 (t) cc_final: 0.8959 (p) REVERT: A 125 GLN cc_start: 0.9102 (mt0) cc_final: 0.8842 (mt0) REVERT: C 90 ASP cc_start: 0.8648 (t70) cc_final: 0.7838 (t0) REVERT: D 65 ASP cc_start: 0.8617 (t0) cc_final: 0.8414 (t0) REVERT: D 73 GLU cc_start: 0.8266 (tp30) cc_final: 0.7550 (tp30) REVERT: G 92 GLU cc_start: 0.8335 (mt-10) cc_final: 0.7793 (mt-10) REVERT: H 39 TYR cc_start: 0.8230 (t80) cc_final: 0.7916 (t80) REVERT: H 65 ASP cc_start: 0.8791 (t0) cc_final: 0.8529 (t0) REVERT: H 102 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7486 (mm-30) REVERT: K 325 GLU cc_start: 0.9050 (mm-30) cc_final: 0.8265 (tm-30) REVERT: K 327 HIS cc_start: 0.7327 (m90) cc_final: 0.6792 (m-70) REVERT: K 349 LEU cc_start: 0.8971 (mt) cc_final: 0.8715 (tp) REVERT: K 470 MET cc_start: 0.9182 (tpt) cc_final: 0.8374 (tpp) REVERT: K 476 CYS cc_start: 0.9093 (m) cc_final: 0.8787 (m) outliers start: 3 outliers final: 3 residues processed: 228 average time/residue: 0.4039 time to fit residues: 121.5021 Evaluate side-chains 156 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 153 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain K residue 611 ARG Chi-restraints excluded: chain K residue 614 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 9.9990 chunk 113 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 chunk 117 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 87 optimal weight: 10.0000 chunk 136 optimal weight: 4.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN E 68 GLN H 81 ASN K 205 ASN K 230 GLN K 277 GLN K 437 GLN K 500 ASN K 526 GLN ** K 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17021 Z= 0.186 Angle : 0.564 6.939 24254 Z= 0.330 Chirality : 0.036 0.162 2755 Planarity : 0.005 0.071 2063 Dihedral : 28.752 171.552 4604 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.57 % Allowed : 5.19 % Favored : 93.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.66 (0.22), residues: 1241 helix: -0.11 (0.18), residues: 767 sheet: -2.76 (0.63), residues: 61 loop : -2.67 (0.27), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K 364 HIS 0.004 0.001 HIS K 613 PHE 0.015 0.001 PHE K 274 TYR 0.014 0.001 TYR F 51 ARG 0.006 0.000 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 175 time to evaluate : 1.449 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 90 ASP cc_start: 0.8404 (t70) cc_final: 0.7908 (t0) REVERT: D 65 ASP cc_start: 0.8590 (t0) cc_final: 0.8358 (t0) REVERT: D 73 GLU cc_start: 0.8377 (tp30) cc_final: 0.7734 (tp30) REVERT: E 120 MET cc_start: 0.8449 (mtp) cc_final: 0.8221 (mtp) REVERT: H 39 TYR cc_start: 0.8011 (t80) cc_final: 0.7689 (t80) REVERT: K 325 GLU cc_start: 0.9136 (mm-30) cc_final: 0.8709 (mm-30) REVERT: K 349 LEU cc_start: 0.9017 (mt) cc_final: 0.8659 (tp) REVERT: K 469 MET cc_start: 0.7994 (tmm) cc_final: 0.7792 (tmm) REVERT: K 470 MET cc_start: 0.9174 (tpt) cc_final: 0.8926 (mmp) REVERT: K 476 CYS cc_start: 0.8830 (m) cc_final: 0.8525 (m) REVERT: K 610 ASP cc_start: 0.8825 (m-30) cc_final: 0.8557 (m-30) outliers start: 17 outliers final: 11 residues processed: 183 average time/residue: 0.3294 time to fit residues: 84.8565 Evaluate side-chains 161 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 150 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain K residue 306 ILE Chi-restraints excluded: chain K residue 347 ASN Chi-restraints excluded: chain K residue 364 TRP Chi-restraints excluded: chain K residue 611 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 8.9990 chunk 42 optimal weight: 0.6980 chunk 113 optimal weight: 5.9990 chunk 92 optimal weight: 7.9990 chunk 37 optimal weight: 0.9990 chunk 136 optimal weight: 5.9990 chunk 147 optimal weight: 7.9990 chunk 121 optimal weight: 0.5980 chunk 135 optimal weight: 2.9990 chunk 46 optimal weight: 0.0030 chunk 109 optimal weight: 5.9990 overall best weight: 1.0594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 44 GLN ** K 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 613 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17021 Z= 0.163 Angle : 0.522 6.108 24254 Z= 0.307 Chirality : 0.034 0.154 2755 Planarity : 0.004 0.057 2063 Dihedral : 28.399 178.846 4600 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.67 % Allowed : 7.04 % Favored : 91.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.60 (0.24), residues: 1241 helix: 0.82 (0.19), residues: 757 sheet: -2.36 (0.64), residues: 61 loop : -2.35 (0.27), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 364 HIS 0.002 0.001 HIS D 106 PHE 0.012 0.001 PHE K 574 TYR 0.012 0.001 TYR F 51 ARG 0.006 0.000 ARG C 99 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 164 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 90 ASP cc_start: 0.8484 (t70) cc_final: 0.8187 (t0) REVERT: D 65 ASP cc_start: 0.8570 (t0) cc_final: 0.8313 (t0) REVERT: D 69 ARG cc_start: 0.9022 (mtt180) cc_final: 0.8750 (mtt180) REVERT: D 73 GLU cc_start: 0.8489 (tp30) cc_final: 0.7877 (tp30) REVERT: D 83 ARG cc_start: 0.8764 (mmt90) cc_final: 0.8458 (mmt-90) REVERT: E 120 MET cc_start: 0.8370 (mtp) cc_final: 0.8111 (mtp) REVERT: F 84 MET cc_start: 0.8394 (mmm) cc_final: 0.7704 (mmm) REVERT: G 104 GLN cc_start: 0.8887 (mt0) cc_final: 0.8639 (mt0) REVERT: H 39 TYR cc_start: 0.7922 (t80) cc_final: 0.7604 (t80) REVERT: K 276 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8786 (tt) REVERT: K 325 GLU cc_start: 0.9159 (mm-30) cc_final: 0.8767 (mm-30) REVERT: K 349 LEU cc_start: 0.9012 (mt) cc_final: 0.8681 (tp) REVERT: K 469 MET cc_start: 0.8006 (tmm) cc_final: 0.7754 (tmm) REVERT: K 470 MET cc_start: 0.9202 (tpt) cc_final: 0.8729 (mmp) REVERT: K 476 CYS cc_start: 0.8909 (m) cc_final: 0.8617 (m) REVERT: K 609 MET cc_start: 0.9085 (OUTLIER) cc_final: 0.8864 (mmm) outliers start: 18 outliers final: 12 residues processed: 175 average time/residue: 0.3287 time to fit residues: 80.7664 Evaluate side-chains 156 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 142 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 276 LEU Chi-restraints excluded: chain K residue 347 ASN Chi-restraints excluded: chain K residue 364 TRP Chi-restraints excluded: chain K residue 609 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 6.9990 chunk 102 optimal weight: 0.0370 chunk 70 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 chunk 136 optimal weight: 2.9990 chunk 144 optimal weight: 9.9990 chunk 71 optimal weight: 4.9990 chunk 129 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 overall best weight: 2.3864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN D 44 GLN F 75 HIS H 81 ASN K 402 HIS ** K 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17021 Z= 0.237 Angle : 0.545 6.133 24254 Z= 0.317 Chirality : 0.035 0.146 2755 Planarity : 0.004 0.049 2063 Dihedral : 28.317 168.451 4596 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.39 % Allowed : 8.70 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.03 (0.25), residues: 1241 helix: 1.30 (0.20), residues: 763 sheet: -1.85 (0.69), residues: 57 loop : -2.18 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K 364 HIS 0.007 0.001 HIS K 402 PHE 0.012 0.001 PHE G 25 TYR 0.013 0.001 TYR F 51 ARG 0.007 0.000 ARG D 76 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 144 time to evaluate : 1.561 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 92 ARG cc_start: 0.8968 (OUTLIER) cc_final: 0.8658 (ttp80) REVERT: C 56 GLU cc_start: 0.8466 (tm-30) cc_final: 0.8246 (tm-30) REVERT: C 90 ASP cc_start: 0.8589 (t70) cc_final: 0.8352 (t0) REVERT: D 65 ASP cc_start: 0.8658 (t0) cc_final: 0.8404 (t0) REVERT: D 73 GLU cc_start: 0.8544 (tp30) cc_final: 0.7924 (tp30) REVERT: E 77 ASP cc_start: 0.8825 (t0) cc_final: 0.8589 (t0) REVERT: G 72 ASP cc_start: 0.8779 (t0) cc_final: 0.8525 (t0) REVERT: H 39 TYR cc_start: 0.7907 (t80) cc_final: 0.7638 (t80) REVERT: K 325 GLU cc_start: 0.9177 (mm-30) cc_final: 0.8856 (mm-30) REVERT: K 349 LEU cc_start: 0.8971 (mt) cc_final: 0.8541 (tt) REVERT: K 436 MET cc_start: 0.8622 (tmm) cc_final: 0.8359 (tmm) REVERT: K 469 MET cc_start: 0.8158 (tmm) cc_final: 0.7875 (tmm) REVERT: K 470 MET cc_start: 0.9262 (tpt) cc_final: 0.8780 (mmp) REVERT: K 476 CYS cc_start: 0.8995 (m) cc_final: 0.8687 (m) REVERT: K 609 MET cc_start: 0.9069 (OUTLIER) cc_final: 0.8772 (mmm) outliers start: 15 outliers final: 9 residues processed: 155 average time/residue: 0.3149 time to fit residues: 70.4594 Evaluate side-chains 148 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 137 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 347 ASN Chi-restraints excluded: chain K residue 364 TRP Chi-restraints excluded: chain K residue 609 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 9.9990 chunk 82 optimal weight: 7.9990 chunk 2 optimal weight: 9.9990 chunk 107 optimal weight: 8.9990 chunk 59 optimal weight: 7.9990 chunk 123 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 chunk 130 optimal weight: 8.9990 chunk 36 optimal weight: 0.0050 overall best weight: 4.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** K 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 17021 Z= 0.366 Angle : 0.598 6.860 24254 Z= 0.343 Chirality : 0.038 0.141 2755 Planarity : 0.004 0.048 2063 Dihedral : 28.395 149.997 4596 Min Nonbonded Distance : 1.491 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 1.57 % Allowed : 9.54 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.20 (0.25), residues: 1241 helix: 1.43 (0.20), residues: 760 sheet: -1.82 (0.70), residues: 57 loop : -2.04 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP K 364 HIS 0.004 0.001 HIS F 75 PHE 0.020 0.002 PHE G 25 TYR 0.016 0.002 TYR G 50 ARG 0.004 0.001 ARG D 76 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 137 time to evaluate : 1.467 Fit side-chains REVERT: B 92 ARG cc_start: 0.8977 (OUTLIER) cc_final: 0.8051 (ttp80) REVERT: C 90 ASP cc_start: 0.8623 (t70) cc_final: 0.7915 (t0) REVERT: C 91 GLU cc_start: 0.8064 (pm20) cc_final: 0.7647 (pm20) REVERT: D 65 ASP cc_start: 0.8758 (t0) cc_final: 0.8498 (t0) REVERT: D 73 GLU cc_start: 0.8586 (tp30) cc_final: 0.7977 (tp30) REVERT: D 102 GLU cc_start: 0.8063 (tm-30) cc_final: 0.7781 (tm-30) REVERT: G 72 ASP cc_start: 0.8851 (t0) cc_final: 0.8615 (t0) REVERT: H 39 TYR cc_start: 0.8238 (t80) cc_final: 0.7917 (t80) REVERT: K 325 GLU cc_start: 0.9177 (mm-30) cc_final: 0.8836 (mm-30) REVERT: K 349 LEU cc_start: 0.8955 (mt) cc_final: 0.8742 (tt) REVERT: K 470 MET cc_start: 0.9304 (tpt) cc_final: 0.8872 (mmp) REVERT: K 476 CYS cc_start: 0.9050 (m) cc_final: 0.8766 (m) REVERT: K 609 MET cc_start: 0.9039 (OUTLIER) cc_final: 0.8809 (mmm) outliers start: 17 outliers final: 13 residues processed: 150 average time/residue: 0.3192 time to fit residues: 68.7339 Evaluate side-chains 147 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 132 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 347 ASN Chi-restraints excluded: chain K residue 364 TRP Chi-restraints excluded: chain K residue 568 ASP Chi-restraints excluded: chain K residue 609 MET Chi-restraints excluded: chain K residue 610 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 0.9980 chunk 130 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 35 optimal weight: 0.9980 chunk 145 optimal weight: 10.0000 chunk 120 optimal weight: 8.9990 chunk 67 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 139 optimal weight: 6.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** K 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17021 Z= 0.194 Angle : 0.533 6.331 24254 Z= 0.310 Chirality : 0.034 0.148 2755 Planarity : 0.004 0.046 2063 Dihedral : 28.036 149.718 4596 Min Nonbonded Distance : 1.387 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.30 % Allowed : 10.56 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.58 (0.25), residues: 1241 helix: 1.77 (0.20), residues: 758 sheet: -1.61 (0.70), residues: 57 loop : -1.98 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 364 HIS 0.004 0.001 HIS F 75 PHE 0.012 0.001 PHE E 78 TYR 0.011 0.001 TYR F 51 ARG 0.007 0.000 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 147 time to evaluate : 1.409 Fit side-chains REVERT: B 92 ARG cc_start: 0.8951 (OUTLIER) cc_final: 0.8071 (ttp80) REVERT: D 65 ASP cc_start: 0.8695 (t0) cc_final: 0.8445 (t0) REVERT: D 73 GLU cc_start: 0.8530 (tp30) cc_final: 0.7908 (tp30) REVERT: D 83 ARG cc_start: 0.8761 (mmt90) cc_final: 0.8441 (mmt-90) REVERT: G 72 ASP cc_start: 0.8804 (t0) cc_final: 0.8559 (t0) REVERT: H 39 TYR cc_start: 0.7922 (t80) cc_final: 0.7655 (t80) REVERT: K 325 GLU cc_start: 0.9187 (mm-30) cc_final: 0.8902 (mm-30) REVERT: K 349 LEU cc_start: 0.8947 (mt) cc_final: 0.8672 (tp) REVERT: K 476 CYS cc_start: 0.8994 (m) cc_final: 0.8710 (m) REVERT: K 609 MET cc_start: 0.9021 (OUTLIER) cc_final: 0.8784 (mmm) outliers start: 14 outliers final: 10 residues processed: 156 average time/residue: 0.3116 time to fit residues: 70.1154 Evaluate side-chains 150 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 138 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 347 ASN Chi-restraints excluded: chain K residue 364 TRP Chi-restraints excluded: chain K residue 609 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 0.9990 chunk 82 optimal weight: 7.9990 chunk 105 optimal weight: 9.9990 chunk 122 optimal weight: 9.9990 chunk 81 optimal weight: 6.9990 chunk 144 optimal weight: 9.9990 chunk 90 optimal weight: 6.9990 chunk 88 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN H 81 ASN ** K 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 17021 Z= 0.371 Angle : 0.606 6.904 24254 Z= 0.346 Chirality : 0.038 0.143 2755 Planarity : 0.004 0.044 2063 Dihedral : 28.273 149.416 4596 Min Nonbonded Distance : 1.260 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.57 % Allowed : 10.83 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.49 (0.25), residues: 1241 helix: 1.67 (0.20), residues: 757 sheet: -1.62 (0.71), residues: 57 loop : -1.94 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K 364 HIS 0.005 0.001 HIS F 75 PHE 0.017 0.002 PHE G 25 TYR 0.014 0.002 TYR G 50 ARG 0.005 0.000 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 132 time to evaluate : 1.504 Fit side-chains REVERT: B 92 ARG cc_start: 0.8982 (OUTLIER) cc_final: 0.8648 (ttp80) REVERT: D 65 ASP cc_start: 0.8773 (t0) cc_final: 0.8504 (t0) REVERT: D 73 GLU cc_start: 0.8590 (tp30) cc_final: 0.7953 (tp30) REVERT: F 84 MET cc_start: 0.8563 (mmm) cc_final: 0.8107 (mmm) REVERT: G 72 ASP cc_start: 0.8890 (t0) cc_final: 0.8626 (t0) REVERT: H 39 TYR cc_start: 0.8183 (t80) cc_final: 0.7828 (t80) REVERT: H 56 MET cc_start: 0.8875 (tpp) cc_final: 0.8588 (mmm) REVERT: K 325 GLU cc_start: 0.9156 (mm-30) cc_final: 0.8913 (mm-30) REVERT: K 349 LEU cc_start: 0.8970 (mt) cc_final: 0.8706 (tp) REVERT: K 476 CYS cc_start: 0.9049 (m) cc_final: 0.8785 (m) outliers start: 17 outliers final: 11 residues processed: 144 average time/residue: 0.3252 time to fit residues: 67.4233 Evaluate side-chains 143 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 131 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 347 ASN Chi-restraints excluded: chain K residue 364 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 chunk 91 optimal weight: 6.9990 chunk 98 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 113 optimal weight: 6.9990 chunk 131 optimal weight: 10.0000 chunk 138 optimal weight: 8.9990 chunk 126 optimal weight: 10.0000 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** K 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 17021 Z= 0.311 Angle : 0.584 7.641 24254 Z= 0.335 Chirality : 0.037 0.147 2755 Planarity : 0.004 0.044 2063 Dihedral : 28.173 149.478 4596 Min Nonbonded Distance : 1.281 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.39 % Allowed : 10.93 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.51 (0.25), residues: 1241 helix: 1.65 (0.20), residues: 765 sheet: -1.65 (0.70), residues: 57 loop : -1.92 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K 364 HIS 0.006 0.001 HIS F 75 PHE 0.012 0.001 PHE G 25 TYR 0.013 0.001 TYR G 50 ARG 0.008 0.000 ARG D 76 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 133 time to evaluate : 1.455 Fit side-chains REVERT: B 92 ARG cc_start: 0.8980 (OUTLIER) cc_final: 0.8062 (ttp80) REVERT: C 64 GLU cc_start: 0.8572 (tm-30) cc_final: 0.8283 (tm-30) REVERT: D 65 ASP cc_start: 0.8762 (t0) cc_final: 0.8496 (t0) REVERT: D 73 GLU cc_start: 0.8573 (tp30) cc_final: 0.7958 (tp30) REVERT: F 84 MET cc_start: 0.8554 (mmm) cc_final: 0.8074 (mmm) REVERT: G 64 GLU cc_start: 0.8237 (tm-30) cc_final: 0.8005 (tm-30) REVERT: G 72 ASP cc_start: 0.8896 (t0) cc_final: 0.8639 (t0) REVERT: H 39 TYR cc_start: 0.8104 (t80) cc_final: 0.7794 (t80) REVERT: K 325 GLU cc_start: 0.9174 (mm-30) cc_final: 0.8948 (mm-30) REVERT: K 349 LEU cc_start: 0.8949 (mt) cc_final: 0.8691 (tp) REVERT: K 476 CYS cc_start: 0.9048 (m) cc_final: 0.8758 (m) REVERT: K 609 MET cc_start: 0.9087 (tpp) cc_final: 0.8833 (mmm) outliers start: 15 outliers final: 13 residues processed: 143 average time/residue: 0.3174 time to fit residues: 64.9982 Evaluate side-chains 145 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 131 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 347 ASN Chi-restraints excluded: chain K residue 364 TRP Chi-restraints excluded: chain K residue 610 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 8.9990 chunk 138 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 105 optimal weight: 7.9990 chunk 41 optimal weight: 0.9980 chunk 121 optimal weight: 7.9990 chunk 127 optimal weight: 20.0000 chunk 88 optimal weight: 8.9990 chunk 142 optimal weight: 0.9990 chunk 86 optimal weight: 10.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** K 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 17021 Z= 0.331 Angle : 0.596 8.292 24254 Z= 0.340 Chirality : 0.037 0.147 2755 Planarity : 0.004 0.042 2063 Dihedral : 28.190 149.353 4596 Min Nonbonded Distance : 1.276 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.39 % Allowed : 11.11 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.54 (0.25), residues: 1241 helix: 1.69 (0.20), residues: 761 sheet: -1.61 (0.70), residues: 57 loop : -1.91 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K 364 HIS 0.008 0.001 HIS K 402 PHE 0.014 0.002 PHE G 25 TYR 0.012 0.001 TYR G 50 ARG 0.009 0.000 ARG D 76 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 131 time to evaluate : 1.412 Fit side-chains REVERT: B 92 ARG cc_start: 0.8987 (OUTLIER) cc_final: 0.8078 (ttp80) REVERT: D 65 ASP cc_start: 0.8768 (t0) cc_final: 0.8496 (t0) REVERT: D 73 GLU cc_start: 0.8583 (tp30) cc_final: 0.7970 (tp30) REVERT: F 84 MET cc_start: 0.8609 (mmm) cc_final: 0.8140 (mmm) REVERT: G 72 ASP cc_start: 0.8871 (t0) cc_final: 0.8612 (t0) REVERT: H 39 TYR cc_start: 0.8089 (t80) cc_final: 0.7771 (t80) REVERT: K 325 GLU cc_start: 0.9175 (mm-30) cc_final: 0.8958 (mm-30) REVERT: K 349 LEU cc_start: 0.8945 (mt) cc_final: 0.8688 (tp) REVERT: K 476 CYS cc_start: 0.9056 (m) cc_final: 0.8771 (m) REVERT: K 609 MET cc_start: 0.9093 (tpp) cc_final: 0.8723 (mmm) outliers start: 15 outliers final: 13 residues processed: 140 average time/residue: 0.3186 time to fit residues: 63.9916 Evaluate side-chains 144 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 130 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 347 ASN Chi-restraints excluded: chain K residue 364 TRP Chi-restraints excluded: chain K residue 610 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 0.9980 chunk 99 optimal weight: 10.0000 chunk 149 optimal weight: 7.9990 chunk 137 optimal weight: 8.9990 chunk 118 optimal weight: 6.9990 chunk 12 optimal weight: 0.0270 chunk 91 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 chunk 94 optimal weight: 5.9990 chunk 126 optimal weight: 8.9990 chunk 36 optimal weight: 0.7980 overall best weight: 2.9642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** K 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 17021 Z= 0.275 Angle : 0.578 8.813 24254 Z= 0.331 Chirality : 0.036 0.147 2755 Planarity : 0.004 0.042 2063 Dihedral : 28.135 149.263 4596 Min Nonbonded Distance : 1.304 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.20 % Allowed : 11.20 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.60 (0.25), residues: 1241 helix: 1.70 (0.20), residues: 767 sheet: -1.52 (0.70), residues: 57 loop : -1.88 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 364 HIS 0.008 0.001 HIS K 402 PHE 0.012 0.001 PHE K 274 TYR 0.011 0.001 TYR G 50 ARG 0.009 0.000 ARG D 76 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 134 time to evaluate : 1.198 Fit side-chains REVERT: B 92 ARG cc_start: 0.8980 (OUTLIER) cc_final: 0.8656 (ttp80) REVERT: C 64 GLU cc_start: 0.8619 (tm-30) cc_final: 0.8334 (tm-30) REVERT: D 65 ASP cc_start: 0.8752 (t0) cc_final: 0.8488 (t0) REVERT: D 73 GLU cc_start: 0.8566 (tp30) cc_final: 0.7933 (tp30) REVERT: F 84 MET cc_start: 0.8576 (mmm) cc_final: 0.8088 (mmm) REVERT: G 72 ASP cc_start: 0.8863 (t0) cc_final: 0.8610 (t0) REVERT: H 39 TYR cc_start: 0.8016 (t80) cc_final: 0.7736 (t80) REVERT: K 349 LEU cc_start: 0.8979 (mt) cc_final: 0.8712 (tp) REVERT: K 470 MET cc_start: 0.9282 (mmm) cc_final: 0.8994 (mmm) REVERT: K 476 CYS cc_start: 0.9043 (m) cc_final: 0.8760 (m) REVERT: K 609 MET cc_start: 0.9091 (tpp) cc_final: 0.8834 (mmm) outliers start: 13 outliers final: 12 residues processed: 142 average time/residue: 0.3161 time to fit residues: 64.4364 Evaluate side-chains 145 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 132 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 347 ASN Chi-restraints excluded: chain K residue 364 TRP Chi-restraints excluded: chain K residue 610 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 119 optimal weight: 8.9990 chunk 49 optimal weight: 0.7980 chunk 122 optimal weight: 7.9990 chunk 15 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 86 optimal weight: 10.0000 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 68 GLN B 75 HIS D 46 HIS K 554 HIS K 601 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.069832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.046062 restraints weight = 63635.982| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 2.67 r_work: 0.2655 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17021 Z= 0.175 Angle : 0.542 9.175 24254 Z= 0.312 Chirality : 0.034 0.148 2755 Planarity : 0.004 0.041 2063 Dihedral : 27.864 148.816 4596 Min Nonbonded Distance : 1.441 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.65 % Allowed : 11.94 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.87 (0.25), residues: 1241 helix: 1.97 (0.20), residues: 761 sheet: -1.53 (0.63), residues: 67 loop : -1.79 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 364 HIS 0.008 0.001 HIS K 402 PHE 0.011 0.001 PHE K 274 TYR 0.010 0.001 TYR F 51 ARG 0.009 0.000 ARG D 76 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2840.77 seconds wall clock time: 52 minutes 7.47 seconds (3127.47 seconds total)