Starting phenix.real_space_refine on Mon Mar 11 14:42:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbh_34632/03_2024/8hbh_34632_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbh_34632/03_2024/8hbh_34632.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbh_34632/03_2024/8hbh_34632.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbh_34632/03_2024/8hbh_34632.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbh_34632/03_2024/8hbh_34632_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbh_34632/03_2024/8hbh_34632_updated.pdb" } resolution = 3.1 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= 0.158 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: 7 Type Number sf(0) Gaussians Fe 1 7.16 5 P 3 5.49 5 Mg 2 5.21 5 S 58 5.16 5 C 5469 2.51 5 N 1455 2.21 5 O 1514 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 139": "OE1" <-> "OE2" Residue "A PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 321": "OE1" <-> "OE2" Residue "A PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 446": "OE1" <-> "OE2" Residue "B PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 175": "OD1" <-> "OD2" Residue "B GLU 183": "OE1" <-> "OE2" Residue "B TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 8502 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 3922 Classifications: {'peptide': 522} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 24, 'TRANS': 497} Chain breaks: 9 Unresolved non-hydrogen bonds: 211 Unresolved non-hydrogen angles: 262 Unresolved non-hydrogen dihedrals: 168 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 8, 'PHE:plan': 2, 'GLU:plan': 14, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 148 Chain: "B" Number of atoms: 4501 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 577, 4492 Classifications: {'peptide': 577} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 553} Chain breaks: 2 Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 90 Planarities with less than four sites: {'GLU:plan': 19, 'ARG:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 96 Conformer: "B" Number of residues, atoms: 577, 4492 Classifications: {'peptide': 577} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 553} Chain breaks: 2 Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 90 Planarities with less than four sites: {'GLU:plan': 19, 'ARG:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 96 bond proxies already assigned to first conformer: 4572 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 77 Unusual residues: {' NO': 1, 'G2P': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N LEU A 254 " occ=0.80 ... (3 atoms not shown) pdb=" CB LEU A 254 " occ=0.80 Time building chain proxies: 7.13, per 1000 atoms: 0.84 Number of scatterers: 8502 At special positions: 0 Unit cell: (71.06, 107.635, 150.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 1 26.01 S 58 16.00 P 3 15.00 Mg 2 11.99 O 1514 8.00 N 1455 7.00 C 5469 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.80 Conformation dependent library (CDL) restraints added in 2.7 seconds 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2070 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 39 helices and 10 sheets defined 43.4% alpha, 16.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.28 Creating SS restraints... Processing helix chain 'A' and resid 71 through 82 Processing helix chain 'A' and resid 86 through 98 Processing helix chain 'A' and resid 115 through 125 Processing helix chain 'A' and resid 131 through 148 removed outlier: 3.675A pdb=" N LEU A 136 " --> pdb=" O ILE A 132 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU A 147 " --> pdb=" O ILE A 143 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ASP A 148 " --> pdb=" O CYS A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 154 No H-bonds generated for 'chain 'A' and resid 152 through 154' Processing helix chain 'A' and resid 159 through 170 removed outlier: 3.548A pdb=" N PHE A 166 " --> pdb=" O PHE A 162 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N SER A 167 " --> pdb=" O LEU A 163 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N THR A 168 " --> pdb=" O ASN A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 226 removed outlier: 3.552A pdb=" N LEU A 215 " --> pdb=" O THR A 211 " (cutoff:3.500A) Proline residue: A 216 - end of helix removed outlier: 3.783A pdb=" N LYS A 220 " --> pdb=" O PRO A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 285 Processing helix chain 'A' and resid 303 through 308 Processing helix chain 'A' and resid 320 through 323 No H-bonds generated for 'chain 'A' and resid 320 through 323' Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 409 through 457 removed outlier: 4.026A pdb=" N GLN A 441 " --> pdb=" O GLU A 437 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU A 444 " --> pdb=" O HIS A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 467 Processing helix chain 'A' and resid 490 through 496 Processing helix chain 'A' and resid 499 through 520 removed outlier: 3.585A pdb=" N GLN A 516 " --> pdb=" O ARG A 512 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLY A 518 " --> pdb=" O ASP A 514 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLU A 519 " --> pdb=" O GLN A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 559 Processing helix chain 'A' and resid 599 through 609 Processing helix chain 'A' and resid 620 through 626 Processing helix chain 'B' and resid 3 through 17 Processing helix chain 'B' and resid 19 through 28 Processing helix chain 'B' and resid 45 through 58 Processing helix chain 'B' and resid 63 through 81 Processing helix chain 'B' and resid 84 through 90 removed outlier: 3.696A pdb=" N LEU B 90 " --> pdb=" O ILE B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 111 removed outlier: 4.764A pdb=" N ASP B 102 " --> pdb=" O LEU B 98 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ALA B 103 " --> pdb=" O GLN B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 156 Processing helix chain 'B' and resid 210 through 216 Processing helix chain 'B' and resid 234 through 239 Processing helix chain 'B' and resid 241 through 243 No H-bonds generated for 'chain 'B' and resid 241 through 243' Processing helix chain 'B' and resid 250 through 252 No H-bonds generated for 'chain 'B' and resid 250 through 252' Processing helix chain 'B' and resid 265 through 271 removed outlier: 3.828A pdb=" N HIS B 271 " --> pdb=" O GLY B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 336 Processing helix chain 'B' and resid 349 through 397 removed outlier: 4.005A pdb=" N LEU B 354 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 407 Processing helix chain 'B' and resid 430 through 436 Processing helix chain 'B' and resid 443 through 462 removed outlier: 3.938A pdb=" N VAL B 447 " --> pdb=" O ALA B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 508 removed outlier: 3.822A pdb=" N ILE B 496 " --> pdb=" O HIS B 492 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N CYS B 497 " --> pdb=" O ALA B 493 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N GLY B 508 " --> pdb=" O MET B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 555 Processing helix chain 'B' and resid 566 through 572 Processing sheet with id= A, first strand: chain 'A' and resid 202 through 204 Processing sheet with id= B, first strand: chain 'A' and resid 232 through 234 Processing sheet with id= C, first strand: chain 'A' and resid 324 through 326 removed outlier: 3.757A pdb=" N GLN A 300 " --> pdb=" O MET A 291 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 475 through 477 Processing sheet with id= E, first strand: chain 'A' and resid 523 through 528 removed outlier: 7.199A pdb=" N CYS A 533 " --> pdb=" O VAL A 525 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N THR A 527 " --> pdb=" O ALA A 531 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ALA A 531 " --> pdb=" O THR A 527 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LYS A 615 " --> pdb=" O ILE A 575 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N LEU A 577 " --> pdb=" O LYS A 615 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ASN A 617 " --> pdb=" O LEU A 577 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N SER A 579 " --> pdb=" O ASN A 617 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ILE A 616 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N CYS A 654 " --> pdb=" O SER A 638 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N SER A 638 " --> pdb=" O CYS A 654 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N PHE A 656 " --> pdb=" O PRO A 636 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ASP A 658 " --> pdb=" O PHE A 634 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N PHE A 634 " --> pdb=" O ASP A 658 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 119 through 123 removed outlier: 6.323A pdb=" N LEU B 180 " --> pdb=" O VAL B 166 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N VAL B 166 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N GLU B 182 " --> pdb=" O MET B 164 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N MET B 164 " --> pdb=" O GLU B 182 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 309 through 313 removed outlier: 3.612A pdb=" N SER B 318 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ASP B 224 " --> pdb=" O VAL B 229 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL B 229 " --> pdb=" O ASP B 224 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 305 through 308 removed outlier: 5.963A pdb=" N ARG B 279 " --> pdb=" O LEU B 256 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N LEU B 256 " --> pdb=" O ARG B 279 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 415 through 417 Processing sheet with id= J, first strand: chain 'B' and resid 469 through 475 removed outlier: 7.097A pdb=" N MET B 480 " --> pdb=" O VAL B 472 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N THR B 474 " --> pdb=" O LYS B 478 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LYS B 478 " --> pdb=" O THR B 474 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR B 421 " --> pdb=" O SER B 483 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N THR B 525 " --> pdb=" O SER B 565 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ILE B 562 " --> pdb=" O LEU B 604 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N PHE B 603 " --> pdb=" O HIS B 586 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N HIS B 586 " --> pdb=" O PHE B 603 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N SER B 605 " --> pdb=" O LEU B 584 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N LEU B 584 " --> pdb=" O SER B 605 " (cutoff:3.500A) 421 hydrogen bonds defined for protein. 1199 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: 3.10 Time building geometry restraints manager: 3.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.38: 3346 1.38 - 1.56: 5227 1.56 - 1.74: 5 1.74 - 1.92: 92 1.92 - 2.09: 3 Bond restraints: 8673 Sorted by residual: bond pdb=" O3B G2P B1001 " pdb=" PG G2P B1001 " ideal model delta sigma weight residual 1.716 1.604 0.112 2.00e-02 2.50e+03 3.15e+01 bond pdb=" O1A G2P B1001 " pdb=" PA G2P B1001 " ideal model delta sigma weight residual 1.507 1.606 -0.099 2.00e-02 2.50e+03 2.44e+01 bond pdb=" O1B G2P B1001 " pdb=" PB G2P B1001 " ideal model delta sigma weight residual 1.510 1.607 -0.097 2.00e-02 2.50e+03 2.34e+01 bond pdb=" C3C HEM B1002 " pdb=" CAC HEM B1002 " ideal model delta sigma weight residual 1.544 1.456 0.088 2.00e-02 2.50e+03 1.92e+01 bond pdb=" C3B HEM B1002 " pdb=" CAB HEM B1002 " ideal model delta sigma weight residual 1.544 1.462 0.082 2.00e-02 2.50e+03 1.67e+01 ... (remaining 8668 not shown) Histogram of bond angle deviations from ideal: 85.90 - 103.97: 140 103.97 - 122.04: 10086 122.04 - 140.11: 1542 140.11 - 158.18: 0 158.18 - 176.25: 2 Bond angle restraints: 11770 Sorted by residual: angle pdb=" N VAL A 363 " pdb=" CA VAL A 363 " pdb=" C VAL A 363 " ideal model delta sigma weight residual 110.42 118.52 -8.10 9.60e-01 1.09e+00 7.11e+01 angle pdb=" N PHE A 682 " pdb=" CA PHE A 682 " pdb=" C PHE A 682 " ideal model delta sigma weight residual 114.31 122.19 -7.88 1.29e+00 6.01e-01 3.74e+01 angle pdb=" N MET A 364 " pdb=" CA MET A 364 " pdb=" C MET A 364 " ideal model delta sigma weight residual 108.60 116.86 -8.26 1.46e+00 4.69e-01 3.20e+01 angle pdb=" PA G2P B1001 " pdb=" C3A G2P B1001 " pdb=" PB G2P B1001 " ideal model delta sigma weight residual 120.83 106.89 13.94 3.00e+00 1.11e-01 2.16e+01 angle pdb=" N MET B 164 " pdb=" CA MET B 164 " pdb=" C MET B 164 " ideal model delta sigma weight residual 107.41 116.09 -8.68 2.02e+00 2.45e-01 1.85e+01 ... (remaining 11765 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 4582 17.76 - 35.53: 497 35.53 - 53.29: 104 53.29 - 71.06: 21 71.06 - 88.82: 4 Dihedral angle restraints: 5208 sinusoidal: 2014 harmonic: 3194 Sorted by residual: dihedral pdb=" CA ARG B 407 " pdb=" C ARG B 407 " pdb=" N HIS B 408 " pdb=" CA HIS B 408 " ideal model delta harmonic sigma weight residual 180.00 158.53 21.47 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA HIS A 406 " pdb=" C HIS A 406 " pdb=" N ASN A 407 " pdb=" CA ASN A 407 " ideal model delta harmonic sigma weight residual -180.00 -158.62 -21.38 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" C VAL A 363 " pdb=" N VAL A 363 " pdb=" CA VAL A 363 " pdb=" CB VAL A 363 " ideal model delta harmonic sigma weight residual -122.00 -132.68 10.68 0 2.50e+00 1.60e-01 1.82e+01 ... (remaining 5205 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1199 0.075 - 0.150: 159 0.150 - 0.226: 7 0.226 - 0.301: 2 0.301 - 0.376: 4 Chirality restraints: 1371 Sorted by residual: chirality pdb=" CA VAL A 363 " pdb=" N VAL A 363 " pdb=" C VAL A 363 " pdb=" CB VAL A 363 " both_signs ideal model delta sigma weight residual False 2.44 2.07 0.38 2.00e-01 2.50e+01 3.53e+00 chirality pdb=" CA MET A 364 " pdb=" N MET A 364 " pdb=" C MET A 364 " pdb=" CB MET A 364 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.93e+00 chirality pdb=" CA ASP A 521 " pdb=" N ASP A 521 " pdb=" C ASP A 521 " pdb=" CB ASP A 521 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.72e+00 ... (remaining 1368 not shown) Planarity restraints: 1477 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 467 " 0.021 2.00e-02 2.50e+03 1.63e-02 6.62e+00 pdb=" CG TRP A 467 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP A 467 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP A 467 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 467 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 467 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 467 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 467 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 467 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 467 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 161 " -0.011 2.00e-02 2.50e+03 2.13e-02 4.53e+00 pdb=" C GLU B 161 " 0.037 2.00e-02 2.50e+03 pdb=" O GLU B 161 " -0.014 2.00e-02 2.50e+03 pdb=" N ILE B 162 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 519 " 0.009 2.00e-02 2.50e+03 1.81e-02 3.27e+00 pdb=" C GLU A 519 " -0.031 2.00e-02 2.50e+03 pdb=" O GLU A 519 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU A 520 " 0.011 2.00e-02 2.50e+03 ... (remaining 1474 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 72 2.59 - 3.16: 6979 3.16 - 3.74: 13007 3.74 - 4.32: 18356 4.32 - 4.90: 31286 Nonbonded interactions: 69700 Sorted by model distance: nonbonded pdb=" OD2 ASP A 530 " pdb="MG MG A 701 " model vdw 2.007 2.170 nonbonded pdb=" O ILE A 487 " pdb="MG MG A 702 " model vdw 2.221 2.170 nonbonded pdb=" O ILE A 82 " pdb=" OG1 THR A 211 " model vdw 2.241 2.440 nonbonded pdb=" OH TYR B 395 " pdb=" OD1 ASN B 404 " model vdw 2.244 2.440 nonbonded pdb=" O LEU B 251 " pdb=" NZ LYS B 281 " model vdw 2.250 2.520 ... (remaining 69695 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 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: 4.110 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 32.230 Find NCS groups from input model: 0.310 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 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 0.219 8673 Z= 0.499 Angle : 0.840 13.942 11770 Z= 0.423 Chirality : 0.052 0.376 1371 Planarity : 0.005 0.061 1477 Dihedral : 15.288 88.820 3138 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.90 % Allowed : 20.43 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -0.10 (0.25), residues: 1074 helix: 0.57 (0.23), residues: 501 sheet: 0.10 (0.34), residues: 221 loop : -0.95 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP A 467 HIS 0.008 0.001 HIS A 539 PHE 0.021 0.002 PHE A 682 TYR 0.017 0.002 TYR B 237 ARG 0.014 0.001 ARG B 335 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 102 time to evaluate : 1.091 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 107 average time/residue: 0.2152 time to fit residues: 32.2038 Evaluate side-chains 104 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 100 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain B residue 331 ASP Chi-restraints excluded: chain B residue 425 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.0770 chunk 82 optimal weight: 0.0980 chunk 45 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 55 optimal weight: 0.3980 chunk 44 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 33 optimal weight: 0.0870 chunk 51 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 98 optimal weight: 0.9980 overall best weight: 0.2716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 600 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.0669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8673 Z= 0.170 Angle : 0.557 7.836 11770 Z= 0.279 Chirality : 0.041 0.152 1371 Planarity : 0.004 0.041 1477 Dihedral : 6.650 72.561 1220 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.47 % Allowed : 19.75 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.35 (0.25), residues: 1074 helix: 1.10 (0.23), residues: 500 sheet: 0.21 (0.34), residues: 222 loop : -0.91 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 467 HIS 0.005 0.001 HIS B 437 PHE 0.013 0.001 PHE B 75 TYR 0.013 0.001 TYR B 479 ARG 0.011 0.000 ARG B 335 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 114 time to evaluate : 0.997 Fit side-chains REVERT: A 370 MET cc_start: 0.8403 (mtt) cc_final: 0.7848 (mmt) REVERT: B 247 ASN cc_start: 0.7351 (m-40) cc_final: 0.6827 (p0) REVERT: B 328 MET cc_start: 0.7717 (ttp) cc_final: 0.7511 (mmm) REVERT: B 335 ARG cc_start: 0.7801 (mtm110) cc_final: 0.7486 (mtm110) REVERT: B 473 GLU cc_start: 0.7790 (tt0) cc_final: 0.7551 (tt0) REVERT: B 552 ARG cc_start: 0.6740 (tpp-160) cc_final: 0.6467 (tpp-160) outliers start: 22 outliers final: 14 residues processed: 130 average time/residue: 0.1839 time to fit residues: 34.6057 Evaluate side-chains 118 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 104 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 332 ASN Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 377 GLN Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 496 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 99 optimal weight: 0.0980 chunk 107 optimal weight: 0.8980 chunk 88 optimal weight: 0.0010 chunk 98 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.0845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8673 Z= 0.193 Angle : 0.546 7.847 11770 Z= 0.273 Chirality : 0.041 0.144 1371 Planarity : 0.004 0.039 1477 Dihedral : 6.369 66.605 1215 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.25 % Allowed : 21.44 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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 (0.26), residues: 1074 helix: 1.28 (0.23), residues: 501 sheet: 0.21 (0.34), residues: 223 loop : -0.86 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 467 HIS 0.005 0.001 HIS B 437 PHE 0.012 0.001 PHE B 75 TYR 0.012 0.001 TYR B 136 ARG 0.006 0.000 ARG B 335 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 111 time to evaluate : 0.947 Fit side-chains REVERT: B 247 ASN cc_start: 0.7323 (m-40) cc_final: 0.6814 (p0) REVERT: B 473 GLU cc_start: 0.7846 (tt0) cc_final: 0.7628 (tt0) REVERT: B 505 GLU cc_start: 0.6862 (mm-30) cc_final: 0.6500 (mm-30) outliers start: 29 outliers final: 20 residues processed: 131 average time/residue: 0.1889 time to fit residues: 35.6180 Evaluate side-chains 125 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 105 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 332 ASN Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 331 ASP Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 377 GLN Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain B residue 525 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 10 optimal weight: 10.0000 chunk 47 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 87 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.0903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8673 Z= 0.236 Angle : 0.554 8.334 11770 Z= 0.278 Chirality : 0.042 0.149 1371 Planarity : 0.004 0.040 1477 Dihedral : 6.315 67.240 1215 Min Nonbonded Distance : 1.703 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 4.15 % Allowed : 20.54 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.46 (0.25), residues: 1074 helix: 1.22 (0.23), residues: 503 sheet: 0.20 (0.34), residues: 224 loop : -0.87 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 467 HIS 0.005 0.001 HIS B 437 PHE 0.013 0.001 PHE B 75 TYR 0.013 0.001 TYR B 136 ARG 0.006 0.000 ARG B 335 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 108 time to evaluate : 1.159 Fit side-chains REVERT: A 364 MET cc_start: 0.7620 (ptp) cc_final: 0.7405 (ptt) REVERT: B 9 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7488 (tt) REVERT: B 247 ASN cc_start: 0.7280 (m-40) cc_final: 0.6813 (p0) REVERT: B 473 GLU cc_start: 0.7874 (tt0) cc_final: 0.7640 (tt0) REVERT: B 505 GLU cc_start: 0.6855 (mm-30) cc_final: 0.6509 (mm-30) REVERT: B 559 LYS cc_start: 0.7682 (OUTLIER) cc_final: 0.6591 (mptp) outliers start: 37 outliers final: 28 residues processed: 136 average time/residue: 0.1855 time to fit residues: 36.7561 Evaluate side-chains 133 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 103 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 332 ASN Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 654 CYS Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 331 ASP Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 377 GLN Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 559 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 53 optimal weight: 0.0570 chunk 94 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 overall best weight: 0.8702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.0955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8673 Z= 0.237 Angle : 0.553 8.432 11770 Z= 0.276 Chirality : 0.042 0.155 1371 Planarity : 0.004 0.040 1477 Dihedral : 6.280 68.774 1215 Min Nonbonded Distance : 1.386 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.82 % Allowed : 21.44 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.44 (0.25), residues: 1074 helix: 1.20 (0.23), residues: 503 sheet: 0.19 (0.34), residues: 224 loop : -0.88 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 467 HIS 0.006 0.001 HIS B 437 PHE 0.014 0.001 PHE B 75 TYR 0.014 0.001 TYR B 237 ARG 0.007 0.000 ARG B 335 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 109 time to evaluate : 0.964 Fit side-chains REVERT: B 9 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7486 (tt) REVERT: B 247 ASN cc_start: 0.7278 (m-40) cc_final: 0.6820 (p0) REVERT: B 368 GLU cc_start: 0.7362 (mt-10) cc_final: 0.6630 (mm-30) REVERT: B 473 GLU cc_start: 0.7843 (tt0) cc_final: 0.7599 (tt0) REVERT: B 505 GLU cc_start: 0.6875 (mm-30) cc_final: 0.6514 (mm-30) REVERT: B 559 LYS cc_start: 0.7681 (OUTLIER) cc_final: 0.6547 (mptp) outliers start: 34 outliers final: 27 residues processed: 136 average time/residue: 0.1832 time to fit residues: 35.8859 Evaluate side-chains 133 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 104 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 332 ASN Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 331 ASP Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 377 GLN Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 559 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 2.9990 chunk 20 optimal weight: 0.1980 chunk 61 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 48 optimal weight: 0.0170 chunk 8 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 overall best weight: 0.7220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.1050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8673 Z= 0.213 Angle : 0.540 8.285 11770 Z= 0.269 Chirality : 0.042 0.152 1371 Planarity : 0.004 0.039 1477 Dihedral : 6.243 68.855 1215 Min Nonbonded Distance : 1.119 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 4.04 % Allowed : 21.66 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.55 (0.25), residues: 1074 helix: 1.34 (0.23), residues: 501 sheet: 0.19 (0.34), residues: 224 loop : -0.87 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 467 HIS 0.006 0.001 HIS B 437 PHE 0.013 0.001 PHE A 166 TYR 0.013 0.001 TYR B 136 ARG 0.005 0.000 ARG B 335 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 107 time to evaluate : 1.051 Fit side-chains REVERT: A 370 MET cc_start: 0.8513 (mtt) cc_final: 0.7799 (mtt) REVERT: B 9 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7474 (tt) REVERT: B 247 ASN cc_start: 0.7250 (m-40) cc_final: 0.6890 (p0) REVERT: B 368 GLU cc_start: 0.7360 (mt-10) cc_final: 0.6628 (mm-30) REVERT: B 473 GLU cc_start: 0.7819 (tt0) cc_final: 0.7604 (tt0) REVERT: B 505 GLU cc_start: 0.6857 (mm-30) cc_final: 0.6498 (mm-30) outliers start: 36 outliers final: 27 residues processed: 131 average time/residue: 0.1787 time to fit residues: 34.0967 Evaluate side-chains 132 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 104 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 332 ASN Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 654 CYS Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 331 ASP Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 377 GLN Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 496 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 8.9990 chunk 60 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 58 optimal weight: 0.5980 chunk 105 optimal weight: 3.9990 chunk 65 optimal weight: 0.5980 chunk 64 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8673 Z= 0.206 Angle : 0.539 8.273 11770 Z= 0.268 Chirality : 0.042 0.150 1371 Planarity : 0.004 0.040 1477 Dihedral : 6.222 68.820 1215 Min Nonbonded Distance : 1.102 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.93 % Allowed : 21.66 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.59 (0.25), residues: 1074 helix: 1.38 (0.23), residues: 501 sheet: 0.24 (0.34), residues: 223 loop : -0.89 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 467 HIS 0.005 0.001 HIS B 437 PHE 0.013 0.001 PHE B 75 TYR 0.014 0.001 TYR B 237 ARG 0.006 0.000 ARG B 335 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 108 time to evaluate : 0.951 Fit side-chains REVERT: A 370 MET cc_start: 0.8535 (mtt) cc_final: 0.7879 (mmt) REVERT: B 9 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7471 (tt) REVERT: B 36 GLN cc_start: 0.7378 (tp40) cc_final: 0.7049 (tp40) REVERT: B 247 ASN cc_start: 0.7235 (m-40) cc_final: 0.6894 (p0) REVERT: B 310 MET cc_start: 0.9253 (mmt) cc_final: 0.8288 (mmt) REVERT: B 368 GLU cc_start: 0.7357 (mt-10) cc_final: 0.6627 (mm-30) REVERT: B 473 GLU cc_start: 0.7831 (tt0) cc_final: 0.7587 (tt0) REVERT: B 505 GLU cc_start: 0.6887 (mm-30) cc_final: 0.6516 (mm-30) REVERT: B 559 LYS cc_start: 0.7669 (OUTLIER) cc_final: 0.6583 (mptp) outliers start: 35 outliers final: 29 residues processed: 135 average time/residue: 0.1991 time to fit residues: 38.6157 Evaluate side-chains 138 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 107 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 332 ASN Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 467 TRP Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 654 CYS Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 331 ASP Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 377 GLN Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 559 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 20 optimal weight: 0.4980 chunk 66 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 82 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 100 optimal weight: 0.0770 chunk 91 optimal weight: 0.6980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8673 Z= 0.188 Angle : 0.535 8.109 11770 Z= 0.265 Chirality : 0.041 0.149 1371 Planarity : 0.004 0.039 1477 Dihedral : 6.203 68.530 1215 Min Nonbonded Distance : 1.122 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.70 % Allowed : 22.11 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.66 (0.25), residues: 1074 helix: 1.47 (0.23), residues: 501 sheet: 0.24 (0.34), residues: 223 loop : -0.86 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 467 HIS 0.005 0.001 HIS B 437 PHE 0.013 0.001 PHE B 75 TYR 0.015 0.001 TYR A 372 ARG 0.006 0.000 ARG B 335 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 105 time to evaluate : 1.011 Fit side-chains REVERT: A 370 MET cc_start: 0.8534 (mtt) cc_final: 0.7957 (mmt) REVERT: B 9 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.7481 (tt) REVERT: B 247 ASN cc_start: 0.7223 (m-40) cc_final: 0.6878 (p0) REVERT: B 301 ILE cc_start: 0.6919 (OUTLIER) cc_final: 0.6502 (pt) REVERT: B 368 GLU cc_start: 0.7285 (mt-10) cc_final: 0.6526 (mm-30) REVERT: B 473 GLU cc_start: 0.7816 (tt0) cc_final: 0.7612 (tt0) REVERT: B 505 GLU cc_start: 0.6845 (mm-30) cc_final: 0.6479 (mm-30) outliers start: 33 outliers final: 26 residues processed: 129 average time/residue: 0.1812 time to fit residues: 33.9450 Evaluate side-chains 131 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 103 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 332 ASN Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 341 MET Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 467 TRP Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 331 ASP Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 377 GLN Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 423 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 chunk 92 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8673 Z= 0.237 Angle : 0.556 8.441 11770 Z= 0.276 Chirality : 0.042 0.153 1371 Planarity : 0.004 0.040 1477 Dihedral : 6.249 69.498 1215 Min Nonbonded Distance : 1.081 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.59 % Allowed : 21.77 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 1074 helix: 1.37 (0.23), residues: 503 sheet: 0.26 (0.34), residues: 223 loop : -0.86 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 467 HIS 0.004 0.001 HIS B 105 PHE 0.014 0.001 PHE B 75 TYR 0.016 0.001 TYR A 372 ARG 0.006 0.000 ARG B 335 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 105 time to evaluate : 1.099 Fit side-chains REVERT: A 370 MET cc_start: 0.8537 (mtt) cc_final: 0.7992 (mmt) REVERT: B 9 LEU cc_start: 0.7736 (OUTLIER) cc_final: 0.7484 (tt) REVERT: B 247 ASN cc_start: 0.7217 (m-40) cc_final: 0.6889 (p0) REVERT: B 368 GLU cc_start: 0.7276 (mt-10) cc_final: 0.6517 (mm-30) REVERT: B 473 GLU cc_start: 0.7823 (tt0) cc_final: 0.7595 (tt0) REVERT: B 505 GLU cc_start: 0.6843 (mm-30) cc_final: 0.6498 (mm-30) REVERT: B 559 LYS cc_start: 0.7669 (OUTLIER) cc_final: 0.6581 (mptp) outliers start: 32 outliers final: 29 residues processed: 128 average time/residue: 0.1886 time to fit residues: 34.9394 Evaluate side-chains 134 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 103 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 332 ASN Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 467 TRP Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 654 CYS Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 331 ASP Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 377 GLN Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain B residue 559 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 108 optimal weight: 7.9990 chunk 99 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 68 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8673 Z= 0.273 Angle : 0.582 8.647 11770 Z= 0.289 Chirality : 0.043 0.155 1371 Planarity : 0.004 0.041 1477 Dihedral : 6.333 71.106 1215 Min Nonbonded Distance : 1.077 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.82 % Allowed : 21.77 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.50 (0.25), residues: 1074 helix: 1.25 (0.23), residues: 505 sheet: 0.19 (0.34), residues: 227 loop : -0.86 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 467 HIS 0.005 0.001 HIS B 105 PHE 0.015 0.001 PHE B 75 TYR 0.020 0.002 TYR A 372 ARG 0.007 0.000 ARG B 335 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 102 time to evaluate : 1.099 Fit side-chains REVERT: A 341 MET cc_start: 0.6314 (mtt) cc_final: 0.6099 (mtt) REVERT: A 370 MET cc_start: 0.8553 (mtt) cc_final: 0.7997 (mmt) REVERT: B 9 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7481 (tt) REVERT: B 247 ASN cc_start: 0.7287 (m-40) cc_final: 0.6869 (p0) REVERT: B 310 MET cc_start: 0.9265 (mmt) cc_final: 0.8352 (mmt) REVERT: B 368 GLU cc_start: 0.7345 (mt-10) cc_final: 0.6621 (mm-30) REVERT: B 473 GLU cc_start: 0.7870 (tt0) cc_final: 0.7656 (tt0) REVERT: B 505 GLU cc_start: 0.6834 (mm-30) cc_final: 0.6504 (mm-30) REVERT: B 559 LYS cc_start: 0.7674 (OUTLIER) cc_final: 0.6583 (mptp) outliers start: 34 outliers final: 30 residues processed: 127 average time/residue: 0.1948 time to fit residues: 35.5479 Evaluate side-chains 134 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 102 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 332 ASN Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 467 TRP Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 654 CYS Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 331 ASP Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 377 GLN Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 559 LYS Chi-restraints excluded: chain B residue 584 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 86 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 88 optimal weight: 0.7980 chunk 10 optimal weight: 0.2980 chunk 15 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.165807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.137306 restraints weight = 18365.348| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.10 r_work: 0.3404 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3100 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3099 r_free = 0.3099 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3099 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8673 Z= 0.211 Angle : 0.552 8.317 11770 Z= 0.273 Chirality : 0.042 0.150 1371 Planarity : 0.004 0.040 1477 Dihedral : 6.254 70.681 1215 Min Nonbonded Distance : 1.115 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.59 % Allowed : 21.89 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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 (0.26), residues: 1074 helix: 1.41 (0.23), residues: 502 sheet: 0.22 (0.34), residues: 227 loop : -0.84 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 467 HIS 0.004 0.001 HIS B 437 PHE 0.014 0.001 PHE B 75 TYR 0.017 0.001 TYR A 372 ARG 0.007 0.000 ARG B 335 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2175.22 seconds wall clock time: 40 minutes 4.84 seconds (2404.84 seconds total)