Starting phenix.real_space_refine on Fri Dec 8 13:37:37 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbh_34632/12_2023/8hbh_34632_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbh_34632/12_2023/8hbh_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_34632/12_2023/8hbh_34632.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbh_34632/12_2023/8hbh_34632.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbh_34632/12_2023/8hbh_34632_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbh_34632/12_2023/8hbh_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-1.21rc1-5172/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: 6.96, per 1000 atoms: 0.82 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: 3.37 Conformation dependent library (CDL) restraints added in 2.6 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: 1.86 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: 2.62 Time building geometry restraints manager: 3.65 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: 0.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.060 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 29.740 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.790 ------------------------------------------------------------------------------- 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 : 0.991 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 107 average time/residue: 0.2175 time to fit residues: 32.4485 Evaluate side-chains 104 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 100 time to evaluate : 0.876 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0865 time to fit residues: 1.9293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 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: 0.4116 ------------------------------------------------------------------------------- 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: 0.7490 moved from start: 0.0677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8673 Z= 0.181 Angle : 0.559 7.782 11770 Z= 0.279 Chirality : 0.041 0.149 1371 Planarity : 0.004 0.039 1477 Dihedral : 6.454 69.918 1213 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.58 % Allowed : 19.75 % Favored : 77.67 % 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: 0.31 (0.25), residues: 1074 helix: 1.06 (0.23), residues: 500 sheet: 0.21 (0.34), residues: 222 loop : -0.93 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 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 0.011 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 137 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 114 time to evaluate : 0.932 Fit side-chains outliers start: 23 outliers final: 14 residues processed: 131 average time/residue: 0.1892 time to fit residues: 35.6891 Evaluate side-chains 119 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 105 time to evaluate : 1.017 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0870 time to fit residues: 3.5613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 67 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 99 optimal weight: 0.4980 chunk 107 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.7514 moved from start: 0.0768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8673 Z= 0.234 Angle : 0.572 8.389 11770 Z= 0.286 Chirality : 0.042 0.146 1371 Planarity : 0.004 0.040 1477 Dihedral : 6.244 67.890 1213 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.80 % Allowed : 21.55 % Favored : 76.66 % 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: 1.11 (0.23), residues: 501 sheet: 0.17 (0.34), residues: 224 loop : -0.91 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 467 HIS 0.005 0.001 HIS B 437 PHE 0.014 0.001 PHE B 75 TYR 0.013 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 127 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 111 time to evaluate : 1.029 Fit side-chains outliers start: 16 outliers final: 7 residues processed: 121 average time/residue: 0.2021 time to fit residues: 34.8142 Evaluate side-chains 112 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 105 time to evaluate : 0.959 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0942 time to fit residues: 2.4261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 47 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 94 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 87 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.7510 moved from start: 0.0940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8673 Z= 0.227 Angle : 0.553 8.273 11770 Z= 0.278 Chirality : 0.042 0.145 1371 Planarity : 0.004 0.040 1477 Dihedral : 6.122 66.199 1213 Min Nonbonded Distance : 1.615 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.24 % Allowed : 21.55 % Favored : 76.21 % 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: 0.37 (0.25), residues: 1074 helix: 1.15 (0.23), residues: 502 sheet: 0.16 (0.34), residues: 224 loop : -0.93 (0.32), residues: 348 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 0.013 0.001 PHE B 75 TYR 0.014 0.001 TYR B 237 ARG 0.005 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 133 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 113 time to evaluate : 0.959 Fit side-chains outliers start: 20 outliers final: 12 residues processed: 128 average time/residue: 0.1889 time to fit residues: 34.9125 Evaluate side-chains 114 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 102 time to evaluate : 0.996 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0841 time to fit residues: 3.2284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 89 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 53 optimal weight: 0.0980 chunk 94 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 35 optimal weight: 8.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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: 0.7503 moved from start: 0.1039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8673 Z= 0.210 Angle : 0.547 8.215 11770 Z= 0.275 Chirality : 0.042 0.157 1371 Planarity : 0.004 0.040 1477 Dihedral : 6.076 67.160 1213 Min Nonbonded Distance : 1.389 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.01 % Allowed : 22.67 % Favored : 76.32 % 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: 0.45 (0.25), residues: 1074 helix: 1.23 (0.23), residues: 501 sheet: 0.19 (0.34), residues: 224 loop : -0.91 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 467 HIS 0.007 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 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 114 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 105 time to evaluate : 1.001 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 112 average time/residue: 0.1956 time to fit residues: 31.3699 Evaluate side-chains 108 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 103 time to evaluate : 0.986 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0827 time to fit residues: 2.1699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 61 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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: 0.7553 moved from start: 0.0934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 8673 Z= 0.356 Angle : 0.619 8.930 11770 Z= 0.310 Chirality : 0.045 0.160 1371 Planarity : 0.004 0.042 1477 Dihedral : 6.235 70.828 1213 Min Nonbonded Distance : 0.999 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.68 % Allowed : 22.45 % Favored : 75.87 % 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: 0.20 (0.25), residues: 1074 helix: 0.96 (0.23), residues: 503 sheet: 0.15 (0.34), residues: 223 loop : -0.98 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 467 HIS 0.007 0.001 HIS B 105 PHE 0.015 0.002 PHE B 75 TYR 0.028 0.002 TYR A 372 ARG 0.006 0.001 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 120 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 105 time to evaluate : 1.031 Fit side-chains outliers start: 15 outliers final: 9 residues processed: 116 average time/residue: 0.1935 time to fit residues: 32.4385 Evaluate side-chains 111 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 102 time to evaluate : 0.929 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1014 time to fit residues: 2.9365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 5.9990 chunk 60 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 88 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 48 optimal weight: 0.1980 chunk 41 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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: 0.7515 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8673 Z= 0.226 Angle : 0.559 8.359 11770 Z= 0.280 Chirality : 0.042 0.152 1371 Planarity : 0.004 0.040 1477 Dihedral : 6.116 69.504 1213 Min Nonbonded Distance : 1.123 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.79 % Allowed : 22.67 % Favored : 76.54 % 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: 0.40 (0.25), residues: 1074 helix: 1.18 (0.23), residues: 501 sheet: 0.17 (0.34), residues: 224 loop : -0.93 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP A 467 HIS 0.005 0.001 HIS B 437 PHE 0.015 0.001 PHE B 223 TYR 0.014 0.001 TYR B 136 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 115 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 108 time to evaluate : 1.018 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 113 average time/residue: 0.1982 time to fit residues: 31.9106 Evaluate side-chains 105 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 101 time to evaluate : 0.973 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0829 time to fit residues: 1.9625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 20 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 100 optimal weight: 0.0970 chunk 91 optimal weight: 0.5980 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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: 0.7499 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8673 Z= 0.201 Angle : 0.552 8.194 11770 Z= 0.277 Chirality : 0.042 0.149 1371 Planarity : 0.004 0.040 1477 Dihedral : 6.062 69.982 1213 Min Nonbonded Distance : 1.114 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.45 % Allowed : 23.57 % Favored : 75.98 % 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: 0.53 (0.25), residues: 1074 helix: 1.31 (0.23), residues: 503 sheet: 0.27 (0.34), residues: 222 loop : -0.93 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 467 HIS 0.005 0.001 HIS B 437 PHE 0.014 0.001 PHE B 75 TYR 0.013 0.001 TYR B 136 ARG 0.007 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 105 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 101 time to evaluate : 1.010 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 104 average time/residue: 0.2059 time to fit residues: 30.3818 Evaluate side-chains 104 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 101 time to evaluate : 0.880 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1804 time to fit residues: 2.1414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 58 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 88 optimal weight: 0.5980 chunk 92 optimal weight: 4.9990 chunk 64 optimal weight: 0.6980 chunk 103 optimal weight: 0.6980 chunk 63 optimal weight: 0.0270 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.1317 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= 0.197 Angle : 0.544 8.230 11770 Z= 0.272 Chirality : 0.042 0.149 1371 Planarity : 0.004 0.040 1477 Dihedral : 6.022 70.454 1213 Min Nonbonded Distance : 1.120 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.34 % Allowed : 23.57 % Favored : 76.09 % 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: 0.61 (0.25), residues: 1074 helix: 1.38 (0.23), residues: 504 sheet: 0.28 (0.34), residues: 222 loop : -0.90 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 467 HIS 0.004 0.001 HIS B 437 PHE 0.013 0.001 PHE B 75 TYR 0.014 0.001 TYR B 479 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 103 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 100 time to evaluate : 0.917 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 101 average time/residue: 0.2003 time to fit residues: 28.8885 Evaluate side-chains 100 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 98 time to evaluate : 0.997 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0855 time to fit residues: 1.8016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 0.7980 chunk 71 optimal weight: 0.0070 chunk 108 optimal weight: 5.9990 chunk 99 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 26 optimal weight: 0.0470 overall best weight: 0.5296 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.1396 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= 0.192 Angle : 0.553 8.140 11770 Z= 0.275 Chirality : 0.042 0.147 1371 Planarity : 0.004 0.040 1477 Dihedral : 6.021 70.822 1213 Min Nonbonded Distance : 1.125 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.11 % Allowed : 24.13 % Favored : 75.76 % 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: 0.67 (0.25), residues: 1074 helix: 1.44 (0.23), residues: 503 sheet: 0.22 (0.34), residues: 226 loop : -0.82 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 467 HIS 0.005 0.001 HIS B 437 PHE 0.013 0.001 PHE B 223 TYR 0.013 0.001 TYR B 136 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 106 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 105 time to evaluate : 0.961 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 106 average time/residue: 0.1979 time to fit residues: 29.8389 Evaluate side-chains 98 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.867 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 chunk 10 optimal weight: 8.9990 chunk 15 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 ASN ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.165403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.136002 restraints weight = 18361.816| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.36 r_work: 0.3366 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3071 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3070 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8673 Z= 0.260 Angle : 0.582 8.665 11770 Z= 0.290 Chirality : 0.043 0.154 1371 Planarity : 0.004 0.041 1477 Dihedral : 6.084 72.640 1213 Min Nonbonded Distance : 1.073 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.22 % Allowed : 24.35 % Favored : 75.42 % 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: 0.54 (0.25), residues: 1074 helix: 1.32 (0.23), residues: 504 sheet: 0.21 (0.34), residues: 223 loop : -0.89 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP A 467 HIS 0.005 0.001 HIS B 105 PHE 0.015 0.001 PHE B 75 TYR 0.014 0.001 TYR B 479 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: 2114.57 seconds wall clock time: 39 minutes 5.15 seconds (2345.15 seconds total)