Starting phenix.real_space_refine on Fri Feb 16 12:06:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6szu_10354/02_2024/6szu_10354_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6szu_10354/02_2024/6szu_10354.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6szu_10354/02_2024/6szu_10354.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6szu_10354/02_2024/6szu_10354.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6szu_10354/02_2024/6szu_10354_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6szu_10354/02_2024/6szu_10354_updated.pdb" } resolution = 2.41 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 56 5.49 5 Mg 6 5.21 5 S 92 5.16 5 C 9213 2.51 5 N 2605 2.21 5 O 3273 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 64": "OE1" <-> "OE2" Residue "A ARG 266": "NH1" <-> "NH2" Residue "A ARG 279": "NH1" <-> "NH2" Residue "A ARG 396": "NH1" <-> "NH2" Residue "A ARG 503": "NH1" <-> "NH2" Residue "A ARG 507": "NH1" <-> "NH2" Residue "A GLU 519": "OE1" <-> "OE2" Residue "A ARG 608": "NH1" <-> "NH2" Residue "A ARG 610": "NH1" <-> "NH2" Residue "B ARG 97": "NH1" <-> "NH2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B ARG 209": "NH1" <-> "NH2" Residue "B GLU 311": "OE1" <-> "OE2" Residue "B GLU 383": "OE1" <-> "OE2" Residue "B ARG 434": "NH1" <-> "NH2" Residue "B ARG 560": "NH1" <-> "NH2" Residue "B ARG 571": "NH1" <-> "NH2" Residue "B PHE 696": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 706": "NH1" <-> "NH2" Residue "B ARG 707": "NH1" <-> "NH2" Residue "B ARG 723": "NH1" <-> "NH2" Residue "C ARG 3": "NH1" <-> "NH2" Residue "C ARG 15": "NH1" <-> "NH2" Residue "C ARG 62": "NH1" <-> "NH2" Residue "C ARG 88": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15245 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 5761 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 705, 5750 Classifications: {'peptide': 705} Link IDs: {'PTRANS': 25, 'TRANS': 679} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 705, 5750 Classifications: {'peptide': 705} Link IDs: {'PTRANS': 25, 'TRANS': 679} Chain breaks: 2 bond proxies already assigned to first conformer: 5860 Chain: "B" Number of atoms: 5964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 5964 Classifications: {'peptide': 745} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 716} Chain breaks: 1 Chain: "C" Number of atoms: 2022 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 249, 2012 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 12, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 249, 2012 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 12, 'TRANS': 236} bond proxies already assigned to first conformer: 2040 Chain: "V" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 929 Classifications: {'RNA': 44} Modifications used: {'p5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 10, 'rna3p_pur': 12, 'rna3p_pyr': 15} Link IDs: {'rna2p': 17, 'rna3p': 26} Chain: "M" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 217 Classifications: {'RNA': 10} Modifications used: {'rna3p_pur': 7, 'rna3p_pyr': 3} Link IDs: {'rna3p': 9} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Unusual residues: {' MG': 2, 'M4H': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 11 Unusual residues: {' MG': 2, 'POP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 93 Classifications: {'water': 93} Link IDs: {None: 92} Chain: "B" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 136 Classifications: {'water': 136} Link IDs: {None: 135} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "V" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 64 Classifications: {'water': 64} Link IDs: {None: 63} Chain: "M" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AARG A 491 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 491 " occ=0.50 residue: pdb=" N AHIS C 27 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS C 27 " occ=0.50 Time building chain proxies: 11.93, per 1000 atoms: 0.78 Number of scatterers: 15245 At special positions: 0 Unit cell: (97.524, 119.467, 117.841, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 92 16.00 P 56 15.00 Mg 6 11.99 O 3273 8.00 N 2605 7.00 C 9213 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.45 Conformation dependent library (CDL) restraints added in 3.7 seconds 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3216 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 71 helices and 16 sheets defined 44.8% alpha, 11.5% beta 12 base pairs and 26 stacking pairs defined. Time for finding SS restraints: 7.13 Creating SS restraints... Processing helix chain 'A' and resid 3 through 8 Processing helix chain 'A' and resid 11 through 24 Processing helix chain 'A' and resid 32 through 47 Processing helix chain 'A' and resid 84 through 97 Processing helix chain 'A' and resid 127 through 137 Processing helix chain 'A' and resid 165 through 182 Processing helix chain 'A' and resid 209 through 217 removed outlier: 3.709A pdb=" N GLN A 217 " --> pdb=" O ARG A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 234 Processing helix chain 'A' and resid 241 through 248 Processing helix chain 'A' and resid 303 through 313 removed outlier: 3.785A pdb=" N THR A 313 " --> pdb=" O ALA A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 346 Processing helix chain 'A' and resid 359 through 364 Processing helix chain 'A' and resid 376 through 378 No H-bonds generated for 'chain 'A' and resid 376 through 378' Processing helix chain 'A' and resid 401 through 409 Processing helix chain 'A' and resid 429 through 445 removed outlier: 3.646A pdb=" N PHE A 440 " --> pdb=" O ARG A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 470 Processing helix chain 'A' and resid 525 through 527 No H-bonds generated for 'chain 'A' and resid 525 through 527' Processing helix chain 'A' and resid 529 through 532 Processing helix chain 'A' and resid 567 through 574 Processing helix chain 'A' and resid 576 through 598 removed outlier: 3.955A pdb=" N SER A 583 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLN A 585 " --> pdb=" O GLN A 582 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU A 588 " --> pdb=" O GLN A 585 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU A 594 " --> pdb=" O ILE A 591 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS A 598 " --> pdb=" O SER A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 608 Processing helix chain 'A' and resid 628 through 644 Processing helix chain 'A' and resid 648 through 668 removed outlier: 3.970A pdb=" N LYS A 659 " --> pdb=" O ALA A 655 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU A 660 " --> pdb=" O GLU A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 686 Processing helix chain 'A' and resid 693 through 713 Processing helix chain 'B' and resid 5 through 10 Processing helix chain 'B' and resid 15 through 21 removed outlier: 3.578A pdb=" N ILE B 18 " --> pdb=" O GLN B 15 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N SER B 19 " --> pdb=" O ASN B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 48 Processing helix chain 'B' and resid 85 through 98 Processing helix chain 'B' and resid 102 through 116 removed outlier: 3.785A pdb=" N GLN B 116 " --> pdb=" O ASP B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 139 through 152 Processing helix chain 'B' and resid 157 through 160 Processing helix chain 'B' and resid 163 through 175 removed outlier: 3.926A pdb=" N PHE B 174 " --> pdb=" O VAL B 170 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N GLU B 175 " --> pdb=" O LEU B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 221 Processing helix chain 'B' and resid 246 through 265 removed outlier: 4.038A pdb=" N GLY B 250 " --> pdb=" O MET B 246 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N PHE B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE B 254 " --> pdb=" O GLY B 250 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ARG B 265 " --> pdb=" O ASN B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 291 Processing helix chain 'B' and resid 309 through 312 No H-bonds generated for 'chain 'B' and resid 309 through 312' Processing helix chain 'B' and resid 315 through 325 Processing helix chain 'B' and resid 331 through 345 removed outlier: 3.681A pdb=" N VAL B 339 " --> pdb=" O ASP B 335 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ALA B 340 " --> pdb=" O LEU B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix Processing helix chain 'B' and resid 378 through 380 No H-bonds generated for 'chain 'B' and resid 378 through 380' Processing helix chain 'B' and resid 383 through 395 removed outlier: 5.312A pdb=" N HIS B 394 " --> pdb=" O GLU B 390 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N LEU B 395 " --> pdb=" O LYS B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 427 removed outlier: 4.068A pdb=" N GLY B 427 " --> pdb=" O VAL B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 432 No H-bonds generated for 'chain 'B' and resid 429 through 432' Processing helix chain 'B' and resid 456 through 472 Processing helix chain 'B' and resid 505 through 511 Proline residue: B 510 - end of helix Processing helix chain 'B' and resid 519 through 536 Processing helix chain 'B' and resid 541 through 558 Processing helix chain 'B' and resid 573 through 582 Processing helix chain 'B' and resid 586 through 588 No H-bonds generated for 'chain 'B' and resid 586 through 588' Processing helix chain 'B' and resid 591 through 593 No H-bonds generated for 'chain 'B' and resid 591 through 593' Processing helix chain 'B' and resid 608 through 611 No H-bonds generated for 'chain 'B' and resid 608 through 611' Processing helix chain 'B' and resid 613 through 615 No H-bonds generated for 'chain 'B' and resid 613 through 615' Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 680 through 696 removed outlier: 5.400A pdb=" N ASP B 685 " --> pdb=" O GLY B 681 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N GLU B 686 " --> pdb=" O ILE B 682 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG B 687 " --> pdb=" O LEU B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 731 Processing helix chain 'B' and resid 737 through 755 Processing helix chain 'C' and resid 1 through 12 Processing helix chain 'C' and resid 14 through 22 Processing helix chain 'C' and resid 25 through 32 removed outlier: 3.818A pdb=" N ALA C 29 " --> pdb=" O VAL C 25 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N VAL C 30 " --> pdb=" O ASP C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 50 Processing helix chain 'C' and resid 61 through 66 Processing helix chain 'C' and resid 93 through 102 Processing helix chain 'C' and resid 111 through 114 No H-bonds generated for 'chain 'C' and resid 111 through 114' Processing helix chain 'C' and resid 116 through 126 Processing helix chain 'C' and resid 156 through 167 Processing helix chain 'C' and resid 169 through 171 No H-bonds generated for 'chain 'C' and resid 169 through 171' Processing helix chain 'C' and resid 180 through 192 Processing helix chain 'C' and resid 200 through 211 Processing helix chain 'C' and resid 226 through 229 No H-bonds generated for 'chain 'C' and resid 226 through 229' Processing helix chain 'C' and resid 232 through 235 No H-bonds generated for 'chain 'C' and resid 232 through 235' Processing sheet with id= A, first strand: chain 'A' and resid 52 through 54 Processing sheet with id= B, first strand: chain 'A' and resid 76 through 78 Processing sheet with id= C, first strand: chain 'A' and resid 290 through 293 Processing sheet with id= D, first strand: chain 'A' and resid 477 through 479 removed outlier: 6.460A pdb=" N LEU A 558 " --> pdb=" O GLU A 539 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N GLU A 539 " --> pdb=" O LEU A 558 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL A 560 " --> pdb=" O VAL A 537 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N VAL A 537 " --> pdb=" O VAL A 560 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU A 539 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ILE A 322 " --> pdb=" O GLU A 539 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 614 through 619 removed outlier: 6.578A pdb=" N GLU A 624 " --> pdb=" O ILE A 616 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLU A 618 " --> pdb=" O GLY A 622 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLY A 622 " --> pdb=" O GLU A 618 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 54 through 57 Processing sheet with id= G, first strand: chain 'B' and resid 127 through 130 Processing sheet with id= H, first strand: chain 'B' and resid 178 through 192 Processing sheet with id= I, first strand: chain 'B' and resid 224 through 228 Processing sheet with id= J, first strand: chain 'B' and resid 483 through 486 Processing sheet with id= K, first strand: chain 'B' and resid 348 through 350 Processing sheet with id= L, first strand: chain 'B' and resid 355 through 359 Processing sheet with id= M, first strand: chain 'B' and resid 489 through 492 Processing sheet with id= N, first strand: chain 'C' and resid 57 through 60 Processing sheet with id= O, first strand: chain 'C' and resid 133 through 135 Processing sheet with id= P, first strand: chain 'C' and resid 141 through 148 removed outlier: 6.419A pdb=" N ARG C 214 " --> pdb=" O ILE C 147 " (cutoff:3.500A) 584 hydrogen bonds defined for protein. 1612 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 31 hydrogen bonds 62 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 26 stacking parallelities Total time for adding SS restraints: 5.28 Time building geometry restraints manager: 6.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3139 1.33 - 1.45: 3674 1.45 - 1.57: 8260 1.57 - 1.69: 108 1.69 - 1.81: 160 Bond restraints: 15341 Sorted by residual: bond pdb=" C19 M4H A 801 " pdb=" C20 M4H A 801 " ideal model delta sigma weight residual 1.414 1.464 -0.050 2.00e-02 2.50e+03 6.18e+00 bond pdb=" C1 M4H A 801 " pdb=" C6 M4H A 801 " ideal model delta sigma weight residual 1.437 1.481 -0.044 2.00e-02 2.50e+03 4.75e+00 bond pdb=" C13 M4H A 801 " pdb=" N18 M4H A 801 " ideal model delta sigma weight residual 1.459 1.498 -0.039 2.00e-02 2.50e+03 3.84e+00 bond pdb=" CB ARG B 135 " pdb=" CG ARG B 135 " ideal model delta sigma weight residual 1.520 1.465 0.055 3.00e-02 1.11e+03 3.40e+00 bond pdb=" CG1 ILE B 606 " pdb=" CD1 ILE B 606 " ideal model delta sigma weight residual 1.513 1.442 0.071 3.90e-02 6.57e+02 3.32e+00 ... (remaining 15336 not shown) Histogram of bond angle deviations from ideal: 97.12 - 105.58: 524 105.58 - 114.04: 8865 114.04 - 122.50: 9427 122.50 - 130.96: 2053 130.96 - 139.41: 80 Bond angle restraints: 20949 Sorted by residual: angle pdb=" N ILE A 79 " pdb=" CA ILE A 79 " pdb=" C ILE A 79 " ideal model delta sigma weight residual 112.96 107.05 5.91 1.00e+00 1.00e+00 3.50e+01 angle pdb=" N18 M4H A 801 " pdb=" C19 M4H A 801 " pdb=" N26 M4H A 801 " ideal model delta sigma weight residual 125.81 139.41 -13.60 3.00e+00 1.11e-01 2.06e+01 angle pdb=" O4' A V 7 " pdb=" C1' A V 7 " pdb=" N9 A V 7 " ideal model delta sigma weight residual 108.20 113.95 -5.75 1.50e+00 4.44e-01 1.47e+01 angle pdb=" C ASN B 628 " pdb=" N ASN B 629 " pdb=" CA ASN B 629 " ideal model delta sigma weight residual 121.80 131.07 -9.27 2.44e+00 1.68e-01 1.44e+01 angle pdb=" C MET B 407 " pdb=" N MET B 408 " pdb=" CA MET B 408 " ideal model delta sigma weight residual 121.54 128.45 -6.91 1.91e+00 2.74e-01 1.31e+01 ... (remaining 20944 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.80: 8400 18.80 - 37.59: 703 37.59 - 56.39: 214 56.39 - 75.18: 107 75.18 - 93.98: 16 Dihedral angle restraints: 9440 sinusoidal: 4470 harmonic: 4970 Sorted by residual: dihedral pdb=" CA VAL A 512 " pdb=" C VAL A 512 " pdb=" N VAL A 513 " pdb=" CA VAL A 513 " ideal model delta harmonic sigma weight residual 180.00 155.85 24.15 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA ILE A 481 " pdb=" C ILE A 481 " pdb=" N THR A 482 " pdb=" CA THR A 482 " ideal model delta harmonic sigma weight residual 180.00 156.20 23.80 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA ASN B 134 " pdb=" C ASN B 134 " pdb=" N ARG B 135 " pdb=" CA ARG B 135 " ideal model delta harmonic sigma weight residual -180.00 -157.02 -22.98 0 5.00e+00 4.00e-02 2.11e+01 ... (remaining 9437 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1712 0.057 - 0.113: 531 0.113 - 0.170: 76 0.170 - 0.226: 5 0.226 - 0.283: 1 Chirality restraints: 2325 Sorted by residual: chirality pdb=" C1' A V 7 " pdb=" O4' A V 7 " pdb=" C2' A V 7 " pdb=" N9 A V 7 " both_signs ideal model delta sigma weight residual False 2.44 2.15 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" C1' A V 4 " pdb=" O4' A V 4 " pdb=" C2' A V 4 " pdb=" N9 A V 4 " both_signs ideal model delta sigma weight residual False 2.46 2.24 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CB ILE B 392 " pdb=" CA ILE B 392 " pdb=" CG1 ILE B 392 " pdb=" CG2 ILE B 392 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 2322 not shown) Planarity restraints: 2493 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A V 7 " -0.046 2.00e-02 2.50e+03 1.99e-02 1.09e+01 pdb=" N9 A V 7 " 0.040 2.00e-02 2.50e+03 pdb=" C8 A V 7 " 0.005 2.00e-02 2.50e+03 pdb=" N7 A V 7 " 0.003 2.00e-02 2.50e+03 pdb=" C5 A V 7 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A V 7 " -0.004 2.00e-02 2.50e+03 pdb=" N6 A V 7 " -0.013 2.00e-02 2.50e+03 pdb=" N1 A V 7 " -0.012 2.00e-02 2.50e+03 pdb=" C2 A V 7 " 0.010 2.00e-02 2.50e+03 pdb=" N3 A V 7 " 0.010 2.00e-02 2.50e+03 pdb=" C4 A V 7 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 10 " 0.047 5.00e-02 4.00e+02 7.16e-02 8.21e+00 pdb=" N PRO A 11 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 11 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 11 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 557 " -0.036 2.00e-02 2.50e+03 1.92e-02 7.41e+00 pdb=" CG TYR B 557 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR B 557 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR B 557 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR B 557 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 557 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 557 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 557 " -0.014 2.00e-02 2.50e+03 ... (remaining 2490 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 279 2.59 - 3.17: 11939 3.17 - 3.75: 26716 3.75 - 4.32: 39267 4.32 - 4.90: 59228 Nonbonded interactions: 137429 Sorted by model distance: nonbonded pdb=" OD2 ASP A 108 " pdb="MG MG A 803 " model vdw 2.013 2.170 nonbonded pdb=" O11 M4H A 801 " pdb="MG MG A 803 " model vdw 2.026 2.170 nonbonded pdb=" OD1 ASP A 108 " pdb="MG MG A 802 " model vdw 2.027 2.170 nonbonded pdb=" O8 M4H A 801 " pdb="MG MG A 802 " model vdw 2.039 2.170 nonbonded pdb=" O10 M4H A 801 " pdb="MG MG A 803 " model vdw 2.090 2.170 ... (remaining 137424 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.560 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: 7.420 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 52.900 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 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 0.084 15341 Z= 0.484 Angle : 0.825 13.604 20949 Z= 0.459 Chirality : 0.052 0.283 2325 Planarity : 0.006 0.072 2493 Dihedral : 16.984 93.978 6224 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.21 % Favored : 95.67 % Rotamer: Outliers : 5.28 % Allowed : 7.53 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: -2.10 (0.17), residues: 1693 helix: -1.43 (0.14), residues: 815 sheet: -0.78 (0.35), residues: 173 loop : -1.30 (0.20), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP B 438 HIS 0.006 0.002 HIS B 605 PHE 0.024 0.003 PHE A 515 TYR 0.036 0.003 TYR B 557 ARG 0.008 0.001 ARG B 316 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 240 time to evaluate : 1.699 Fit side-chains REVERT: A 21 MET cc_start: 0.7606 (mtp) cc_final: 0.7108 (mtm) REVERT: A 26 GLU cc_start: 0.5885 (OUTLIER) cc_final: 0.5596 (pm20) REVERT: A 78 ILE cc_start: 0.8813 (mt) cc_final: 0.8587 (mt) REVERT: A 141 GLU cc_start: 0.6859 (OUTLIER) cc_final: 0.6379 (mm-30) REVERT: A 187 LEU cc_start: 0.6442 (OUTLIER) cc_final: 0.5849 (pp) REVERT: A 201 LEU cc_start: 0.4900 (OUTLIER) cc_final: 0.4542 (tt) REVERT: A 272 GLU cc_start: 0.7678 (tp30) cc_final: 0.7449 (mm-30) REVERT: A 346 LYS cc_start: 0.7987 (tttt) cc_final: 0.7684 (tppp) REVERT: A 578 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.7942 (ptm160) REVERT: A 618 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7570 (tt0) REVERT: B 120 ASP cc_start: 0.8181 (OUTLIER) cc_final: 0.7622 (p0) REVERT: B 367 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.8097 (tp40) REVERT: B 638 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6310 (mm-30) REVERT: B 672 ARG cc_start: 0.7345 (mtm180) cc_final: 0.7113 (ptp-170) REVERT: B 680 ARG cc_start: 0.7391 (mtt90) cc_final: 0.6903 (mtt90) REVERT: B 731 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7305 (mm-30) REVERT: C 192 GLU cc_start: 0.7295 (mt-10) cc_final: 0.7072 (mt-10) REVERT: C 214 ARG cc_start: 0.7808 (mmt180) cc_final: 0.7339 (mmt-90) REVERT: C 217 PHE cc_start: 0.8924 (OUTLIER) cc_final: 0.8703 (t80) outliers start: 80 outliers final: 32 residues processed: 303 average time/residue: 1.7510 time to fit residues: 570.0358 Evaluate side-chains 250 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 208 time to evaluate : 1.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 319 LYS Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 578 ARG Chi-restraints excluded: chain A residue 613 ASP Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 367 GLN Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 429 ARG Chi-restraints excluded: chain B residue 434 ARG Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 638 GLU Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 729 ASP Chi-restraints excluded: chain B residue 736 SER Chi-restraints excluded: chain B residue 741 SER Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 62 ARG Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 216 ARG Chi-restraints excluded: chain C residue 217 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 146 optimal weight: 0.9980 chunk 131 optimal weight: 3.9990 chunk 72 optimal weight: 8.9990 chunk 44 optimal weight: 0.9980 chunk 88 optimal weight: 0.1980 chunk 70 optimal weight: 4.9990 chunk 135 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 157 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 ASN ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 ASN A 254 ASN A 425 ASN B 134 ASN B 137 GLN B 202 GLN B 633 HIS C 27 HIS A C 75 ASN C 233 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 15341 Z= 0.130 Angle : 0.476 6.496 20949 Z= 0.258 Chirality : 0.038 0.208 2325 Planarity : 0.004 0.057 2493 Dihedral : 14.996 84.647 2820 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.17 % Allowed : 13.08 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: -0.56 (0.19), residues: 1693 helix: 0.18 (0.17), residues: 823 sheet: -0.35 (0.37), residues: 172 loop : -0.93 (0.21), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 363 HIS 0.003 0.001 HIS A 505 PHE 0.014 0.001 PHE A 35 TYR 0.027 0.001 TYR B 557 ARG 0.005 0.000 ARG B 135 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 219 time to evaluate : 1.543 Fit side-chains REVERT: A 14 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7532 (mp) REVERT: A 21 MET cc_start: 0.7605 (mtp) cc_final: 0.7180 (mtm) REVERT: A 26 GLU cc_start: 0.5641 (OUTLIER) cc_final: 0.5281 (pm20) REVERT: A 187 LEU cc_start: 0.6338 (OUTLIER) cc_final: 0.5926 (pp) REVERT: A 191 PHE cc_start: 0.4743 (OUTLIER) cc_final: 0.4273 (t80) REVERT: A 201 LEU cc_start: 0.4957 (OUTLIER) cc_final: 0.4658 (tt) REVERT: A 272 GLU cc_start: 0.7687 (tp30) cc_final: 0.7416 (mm-30) REVERT: A 346 LYS cc_start: 0.7975 (tttt) cc_final: 0.7660 (tppp) REVERT: A 372 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.7260 (tm-30) REVERT: A 578 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.7855 (ptm160) REVERT: A 656 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7341 (mm-30) REVERT: B 120 ASP cc_start: 0.8042 (OUTLIER) cc_final: 0.7635 (p0) REVERT: B 152 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.7787 (mttt) REVERT: B 362 MET cc_start: 0.7636 (mmm) cc_final: 0.7225 (mmp) REVERT: B 367 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.7963 (tp40) REVERT: B 414 MET cc_start: 0.8657 (mmt) cc_final: 0.8243 (mpp) REVERT: B 638 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.6322 (mm-30) REVERT: B 672 ARG cc_start: 0.7377 (mtm180) cc_final: 0.7135 (ptp-170) REVERT: B 679 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.8072 (pt0) REVERT: B 680 ARG cc_start: 0.7282 (mtt90) cc_final: 0.6944 (mtt180) REVERT: B 731 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7342 (mm-30) REVERT: C 62 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7495 (ptm-80) REVERT: C 192 GLU cc_start: 0.7207 (mt-10) cc_final: 0.6995 (mt-10) REVERT: C 214 ARG cc_start: 0.7699 (mmt180) cc_final: 0.7322 (mmt-90) REVERT: C 217 PHE cc_start: 0.8849 (OUTLIER) cc_final: 0.8616 (t80) outliers start: 48 outliers final: 17 residues processed: 256 average time/residue: 1.6592 time to fit residues: 458.9477 Evaluate side-chains 233 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 202 time to evaluate : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 578 ARG Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 367 GLN Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 434 ARG Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 638 GLU Chi-restraints excluded: chain B residue 679 GLN Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 729 ASP Chi-restraints excluded: chain C residue 62 ARG Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 217 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 87 optimal weight: 9.9990 chunk 48 optimal weight: 7.9990 chunk 130 optimal weight: 4.9990 chunk 106 optimal weight: 9.9990 chunk 43 optimal weight: 6.9990 chunk 157 optimal weight: 3.9990 chunk 170 optimal weight: 10.0000 chunk 140 optimal weight: 6.9990 chunk 156 optimal weight: 1.9990 chunk 53 optimal weight: 8.9990 chunk 126 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 ASN ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN A 582 GLN B 413 ASN B 633 HIS C 137 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 15341 Z= 0.376 Angle : 0.631 6.744 20949 Z= 0.336 Chirality : 0.046 0.240 2325 Planarity : 0.005 0.051 2493 Dihedral : 15.045 90.211 2788 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 4.16 % Allowed : 13.28 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: -0.04 (0.20), residues: 1693 helix: 0.64 (0.18), residues: 812 sheet: -0.35 (0.36), residues: 179 loop : -0.61 (0.22), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP C 98 HIS 0.005 0.001 HIS C 127 PHE 0.023 0.002 PHE A 702 TYR 0.037 0.003 TYR B 557 ARG 0.006 0.001 ARG B 233 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 204 time to evaluate : 1.641 Fit side-chains REVERT: A 1 MET cc_start: 0.2768 (OUTLIER) cc_final: 0.2528 (ttt) REVERT: A 14 LEU cc_start: 0.7836 (OUTLIER) cc_final: 0.7548 (mp) REVERT: A 21 MET cc_start: 0.7710 (mtp) cc_final: 0.7431 (mtm) REVERT: A 26 GLU cc_start: 0.5879 (OUTLIER) cc_final: 0.5505 (pm20) REVERT: A 171 ILE cc_start: 0.7259 (OUTLIER) cc_final: 0.6777 (mp) REVERT: A 187 LEU cc_start: 0.6370 (OUTLIER) cc_final: 0.5870 (pp) REVERT: A 191 PHE cc_start: 0.4686 (OUTLIER) cc_final: 0.4210 (t80) REVERT: A 201 LEU cc_start: 0.5054 (OUTLIER) cc_final: 0.4662 (tt) REVERT: A 272 GLU cc_start: 0.7749 (tp30) cc_final: 0.7449 (mm-30) REVERT: A 346 LYS cc_start: 0.7996 (tttt) cc_final: 0.7690 (tppp) REVERT: A 578 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.7835 (ptm160) REVERT: A 608 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.6154 (mpt180) REVERT: B 118 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.7712 (mmt180) REVERT: B 120 ASP cc_start: 0.8300 (OUTLIER) cc_final: 0.7757 (p0) REVERT: B 152 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.7930 (mttt) REVERT: B 171 LEU cc_start: 0.9410 (OUTLIER) cc_final: 0.9106 (mp) REVERT: B 367 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.8091 (tp40) REVERT: B 414 MET cc_start: 0.8867 (mmt) cc_final: 0.8486 (mpp) REVERT: B 638 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.6356 (mm-30) REVERT: B 672 ARG cc_start: 0.7470 (mtm180) cc_final: 0.7219 (ptp-170) REVERT: B 679 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.8072 (pt0) REVERT: B 680 ARG cc_start: 0.7317 (mtt90) cc_final: 0.6963 (mtt180) REVERT: B 691 LYS cc_start: 0.8176 (mttp) cc_final: 0.7873 (mttm) REVERT: B 731 GLU cc_start: 0.7660 (mm-30) cc_final: 0.7356 (mm-30) REVERT: C 1 MET cc_start: 0.6751 (mtm) cc_final: 0.6539 (mtm) REVERT: C 146 ASP cc_start: 0.7942 (OUTLIER) cc_final: 0.7708 (m-30) REVERT: C 214 ARG cc_start: 0.7799 (mmt180) cc_final: 0.7386 (mmt-90) outliers start: 63 outliers final: 29 residues processed: 251 average time/residue: 1.6492 time to fit residues: 447.3279 Evaluate side-chains 247 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 201 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 22 LYS Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 578 ARG Chi-restraints excluded: chain A residue 608 ARG Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 118 ARG Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 367 GLN Chi-restraints excluded: chain B residue 429 ARG Chi-restraints excluded: chain B residue 434 ARG Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 635 MET Chi-restraints excluded: chain B residue 638 GLU Chi-restraints excluded: chain B residue 679 GLN Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 729 ASP Chi-restraints excluded: chain B residue 741 SER Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 62 ARG Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 226 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 155 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 157 optimal weight: 0.2980 chunk 167 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 149 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 ASN ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN B 176 ASN B 567 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15341 Z= 0.148 Angle : 0.480 5.975 20949 Z= 0.259 Chirality : 0.039 0.204 2325 Planarity : 0.004 0.045 2493 Dihedral : 14.624 85.898 2786 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.04 % Allowed : 14.99 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 0.29 (0.20), residues: 1693 helix: 1.00 (0.18), residues: 825 sheet: -0.15 (0.37), residues: 173 loop : -0.61 (0.22), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 49 HIS 0.003 0.001 HIS A 505 PHE 0.012 0.001 PHE B 333 TYR 0.025 0.001 TYR B 557 ARG 0.003 0.000 ARG B 135 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 210 time to evaluate : 1.669 Fit side-chains REVERT: A 1 MET cc_start: 0.2735 (OUTLIER) cc_final: 0.2475 (ttt) REVERT: A 14 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7546 (mt) REVERT: A 21 MET cc_start: 0.7670 (mtp) cc_final: 0.7377 (mtm) REVERT: A 26 GLU cc_start: 0.5644 (OUTLIER) cc_final: 0.5293 (pm20) REVERT: A 171 ILE cc_start: 0.7265 (OUTLIER) cc_final: 0.6761 (mp) REVERT: A 187 LEU cc_start: 0.6362 (OUTLIER) cc_final: 0.5916 (pp) REVERT: A 191 PHE cc_start: 0.4670 (OUTLIER) cc_final: 0.4210 (t80) REVERT: A 272 GLU cc_start: 0.7717 (tp30) cc_final: 0.7467 (mm-30) REVERT: A 346 LYS cc_start: 0.7998 (tttt) cc_final: 0.7693 (tppp) REVERT: A 372 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.7292 (tm-30) REVERT: A 578 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.7839 (ptm160) REVERT: B 118 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7627 (mmt180) REVERT: B 120 ASP cc_start: 0.8155 (OUTLIER) cc_final: 0.7793 (p0) REVERT: B 152 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.7866 (mttt) REVERT: B 362 MET cc_start: 0.7647 (mmm) cc_final: 0.7330 (mmp) REVERT: B 414 MET cc_start: 0.8755 (mmt) cc_final: 0.8393 (mpp) REVERT: B 638 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.6405 (mm-30) REVERT: B 672 ARG cc_start: 0.7432 (mtm180) cc_final: 0.7168 (ptp-170) REVERT: B 679 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.8036 (pt0) REVERT: B 680 ARG cc_start: 0.7238 (mtt90) cc_final: 0.6953 (mtt180) REVERT: B 731 GLU cc_start: 0.7623 (mm-30) cc_final: 0.7316 (mm-30) REVERT: C 26 ASP cc_start: 0.8816 (m-30) cc_final: 0.8477 (m-30) REVERT: C 62 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7268 (ptm-80) REVERT: C 66 MET cc_start: 0.8343 (mtp) cc_final: 0.8125 (mtp) REVERT: C 146 ASP cc_start: 0.7795 (OUTLIER) cc_final: 0.7557 (m-30) REVERT: C 157 ARG cc_start: 0.6317 (mpp-170) cc_final: 0.5964 (mmt-90) REVERT: C 214 ARG cc_start: 0.7738 (mmt180) cc_final: 0.7320 (mmt-90) outliers start: 46 outliers final: 17 residues processed: 244 average time/residue: 1.7001 time to fit residues: 447.4579 Evaluate side-chains 240 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 208 time to evaluate : 1.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 578 ARG Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 118 ARG Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 638 GLU Chi-restraints excluded: chain B residue 679 GLN Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain C residue 62 ARG Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 217 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 139 optimal weight: 8.9990 chunk 94 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 142 optimal weight: 9.9990 chunk 115 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 85 optimal weight: 0.9990 chunk 150 optimal weight: 8.9990 chunk 42 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 ASN ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN C 137 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 15341 Z= 0.285 Angle : 0.563 5.823 20949 Z= 0.301 Chirality : 0.043 0.218 2325 Planarity : 0.004 0.040 2493 Dihedral : 14.516 85.736 2773 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 4.03 % Allowed : 14.99 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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 (0.20), residues: 1693 helix: 1.04 (0.18), residues: 812 sheet: -0.29 (0.36), residues: 178 loop : -0.45 (0.22), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 98 HIS 0.005 0.001 HIS A 505 PHE 0.019 0.002 PHE A 211 TYR 0.031 0.002 TYR B 557 ARG 0.004 0.001 ARG B 233 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 209 time to evaluate : 1.751 Fit side-chains REVERT: A 1 MET cc_start: 0.2697 (OUTLIER) cc_final: 0.2443 (ttt) REVERT: A 14 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7535 (mt) REVERT: A 21 MET cc_start: 0.7720 (mtp) cc_final: 0.7466 (mtm) REVERT: A 26 GLU cc_start: 0.5749 (OUTLIER) cc_final: 0.5423 (pm20) REVERT: A 38 ILE cc_start: 0.7656 (mt) cc_final: 0.7375 (mt) REVERT: A 171 ILE cc_start: 0.7261 (OUTLIER) cc_final: 0.6763 (mp) REVERT: A 187 LEU cc_start: 0.6359 (OUTLIER) cc_final: 0.5875 (pp) REVERT: A 191 PHE cc_start: 0.4683 (OUTLIER) cc_final: 0.4173 (t80) REVERT: A 272 GLU cc_start: 0.7728 (tp30) cc_final: 0.7422 (mm-30) REVERT: A 346 LYS cc_start: 0.7982 (tttt) cc_final: 0.7681 (tppp) REVERT: A 374 MET cc_start: 0.7862 (mtp) cc_final: 0.7614 (tpp) REVERT: A 378 ASP cc_start: 0.7845 (m-30) cc_final: 0.7294 (m-30) REVERT: A 578 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.7900 (ptm160) REVERT: A 616 ILE cc_start: 0.8602 (OUTLIER) cc_final: 0.8395 (pp) REVERT: A 618 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7405 (tt0) REVERT: B 118 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7893 (mmt180) REVERT: B 120 ASP cc_start: 0.8250 (OUTLIER) cc_final: 0.7717 (p0) REVERT: B 152 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.7921 (mttt) REVERT: B 211 LYS cc_start: 0.8127 (mttt) cc_final: 0.7730 (mtmm) REVERT: B 362 MET cc_start: 0.7643 (mmm) cc_final: 0.7323 (mmp) REVERT: B 367 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.7977 (tp40) REVERT: B 414 MET cc_start: 0.8854 (mmt) cc_final: 0.8484 (mpp) REVERT: B 638 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6522 (mm-30) REVERT: B 672 ARG cc_start: 0.7470 (mtm180) cc_final: 0.7201 (ptp-170) REVERT: B 679 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.8078 (pt0) REVERT: B 680 ARG cc_start: 0.7271 (mtt90) cc_final: 0.6967 (mtt180) REVERT: B 731 GLU cc_start: 0.7605 (mm-30) cc_final: 0.7286 (mm-30) REVERT: C 62 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7401 (ptm-80) REVERT: C 146 ASP cc_start: 0.7886 (OUTLIER) cc_final: 0.7656 (m-30) REVERT: C 214 ARG cc_start: 0.7808 (mmt180) cc_final: 0.7375 (mmt-90) outliers start: 61 outliers final: 30 residues processed: 253 average time/residue: 1.6816 time to fit residues: 460.1093 Evaluate side-chains 253 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 206 time to evaluate : 1.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 22 LYS Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 578 ARG Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 118 ARG Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 367 GLN Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 429 ARG Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 638 GLU Chi-restraints excluded: chain B residue 679 GLN Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 729 ASP Chi-restraints excluded: chain B residue 741 SER Chi-restraints excluded: chain C residue 62 ARG Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 226 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 56 optimal weight: 0.9990 chunk 150 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 167 optimal weight: 1.9990 chunk 138 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 13 optimal weight: 20.0000 chunk 55 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 ASN ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15341 Z= 0.186 Angle : 0.497 5.879 20949 Z= 0.268 Chirality : 0.040 0.205 2325 Planarity : 0.004 0.040 2493 Dihedral : 14.352 84.368 2773 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.76 % Allowed : 15.26 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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 (0.20), residues: 1693 helix: 1.12 (0.18), residues: 825 sheet: -0.23 (0.36), residues: 178 loop : -0.48 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 49 HIS 0.004 0.001 HIS A 505 PHE 0.014 0.001 PHE A 211 TYR 0.027 0.002 TYR B 557 ARG 0.003 0.000 ARG C 216 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 206 time to evaluate : 1.642 Fit side-chains REVERT: A 14 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7523 (mt) REVERT: A 21 MET cc_start: 0.7698 (mtp) cc_final: 0.7420 (mtm) REVERT: A 26 GLU cc_start: 0.5709 (OUTLIER) cc_final: 0.5363 (pm20) REVERT: A 38 ILE cc_start: 0.7650 (mt) cc_final: 0.7409 (mt) REVERT: A 171 ILE cc_start: 0.7288 (OUTLIER) cc_final: 0.6790 (mp) REVERT: A 187 LEU cc_start: 0.6357 (OUTLIER) cc_final: 0.5910 (pp) REVERT: A 191 PHE cc_start: 0.4655 (OUTLIER) cc_final: 0.4152 (t80) REVERT: A 272 GLU cc_start: 0.7722 (tp30) cc_final: 0.7471 (mm-30) REVERT: A 346 LYS cc_start: 0.8025 (tttt) cc_final: 0.7584 (pttp) REVERT: A 378 ASP cc_start: 0.7829 (m-30) cc_final: 0.7397 (m-30) REVERT: A 578 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.7858 (ptm160) REVERT: A 608 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.6193 (mpt180) REVERT: A 618 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7398 (tt0) REVERT: B 118 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7792 (mmt180) REVERT: B 120 ASP cc_start: 0.8166 (OUTLIER) cc_final: 0.7786 (p0) REVERT: B 152 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.7831 (mttt) REVERT: B 362 MET cc_start: 0.7632 (mmm) cc_final: 0.7275 (mmp) REVERT: B 367 GLN cc_start: 0.8730 (OUTLIER) cc_final: 0.7857 (tp40) REVERT: B 414 MET cc_start: 0.8790 (mmt) cc_final: 0.8471 (mpp) REVERT: B 638 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.6531 (mm-30) REVERT: B 672 ARG cc_start: 0.7539 (mtm180) cc_final: 0.7222 (ptp-170) REVERT: B 679 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.8032 (pt0) REVERT: B 680 ARG cc_start: 0.7249 (mtt90) cc_final: 0.6977 (mtt180) REVERT: C 26 ASP cc_start: 0.8834 (m-30) cc_final: 0.8588 (m-30) REVERT: C 62 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7387 (ptm-80) REVERT: C 146 ASP cc_start: 0.7802 (OUTLIER) cc_final: 0.7583 (m-30) REVERT: C 214 ARG cc_start: 0.7771 (mmt180) cc_final: 0.7335 (mmt-90) outliers start: 57 outliers final: 28 residues processed: 251 average time/residue: 1.7310 time to fit residues: 468.6540 Evaluate side-chains 250 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 206 time to evaluate : 1.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASN Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 22 LYS Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 578 ARG Chi-restraints excluded: chain A residue 608 ARG Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 118 ARG Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 367 GLN Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 638 GLU Chi-restraints excluded: chain B residue 679 GLN Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 729 ASP Chi-restraints excluded: chain B residue 741 SER Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain C residue 62 ARG Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 226 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 161 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 chunk 122 optimal weight: 10.0000 chunk 94 optimal weight: 0.9990 chunk 140 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 166 optimal weight: 8.9990 chunk 104 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 76 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 ASN ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN C 137 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 15341 Z= 0.335 Angle : 0.599 6.240 20949 Z= 0.320 Chirality : 0.045 0.255 2325 Planarity : 0.005 0.043 2493 Dihedral : 14.539 86.349 2772 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.63 % Allowed : 15.72 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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 (0.20), residues: 1693 helix: 1.02 (0.18), residues: 813 sheet: -0.33 (0.36), residues: 178 loop : -0.41 (0.22), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP C 98 HIS 0.005 0.001 HIS C 127 PHE 0.021 0.002 PHE A 211 TYR 0.033 0.002 TYR B 557 ARG 0.006 0.001 ARG A 492 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 205 time to evaluate : 1.667 Fit side-chains REVERT: A 14 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7507 (mt) REVERT: A 21 MET cc_start: 0.7744 (mtp) cc_final: 0.7482 (mtm) REVERT: A 26 GLU cc_start: 0.5757 (OUTLIER) cc_final: 0.5407 (pm20) REVERT: A 38 ILE cc_start: 0.7727 (mt) cc_final: 0.7460 (mt) REVERT: A 171 ILE cc_start: 0.7268 (OUTLIER) cc_final: 0.6771 (mp) REVERT: A 187 LEU cc_start: 0.6339 (OUTLIER) cc_final: 0.5849 (pp) REVERT: A 191 PHE cc_start: 0.4652 (OUTLIER) cc_final: 0.4110 (t80) REVERT: A 272 GLU cc_start: 0.7710 (tp30) cc_final: 0.7407 (mm-30) REVERT: A 346 LYS cc_start: 0.8009 (tttt) cc_final: 0.7706 (tppp) REVERT: A 578 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.7885 (ptm160) REVERT: A 608 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.6242 (mpt180) REVERT: A 618 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7401 (tt0) REVERT: A 656 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7671 (mm-30) REVERT: B 118 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.8033 (mmt180) REVERT: B 120 ASP cc_start: 0.8291 (OUTLIER) cc_final: 0.7743 (p0) REVERT: B 152 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.7915 (mttt) REVERT: B 367 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.8164 (tp40) REVERT: B 414 MET cc_start: 0.8860 (mmt) cc_final: 0.8484 (mpp) REVERT: B 638 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6540 (mm-30) REVERT: B 672 ARG cc_start: 0.7528 (mtm180) cc_final: 0.7211 (ptp-170) REVERT: B 679 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.8083 (pt0) REVERT: B 680 ARG cc_start: 0.7267 (mtt90) cc_final: 0.6977 (mtt180) REVERT: C 62 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7537 (ptm-80) REVERT: C 146 ASP cc_start: 0.7926 (OUTLIER) cc_final: 0.7696 (m-30) REVERT: C 214 ARG cc_start: 0.7819 (mmt180) cc_final: 0.7379 (mmt-90) outliers start: 55 outliers final: 30 residues processed: 248 average time/residue: 1.6912 time to fit residues: 452.3902 Evaluate side-chains 249 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 203 time to evaluate : 1.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 22 LYS Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 578 ARG Chi-restraints excluded: chain A residue 608 ARG Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 118 ARG Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 367 GLN Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 429 ARG Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 635 MET Chi-restraints excluded: chain B residue 638 GLU Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 679 GLN Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 729 ASP Chi-restraints excluded: chain B residue 741 SER Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain C residue 62 ARG Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 226 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 103 optimal weight: 0.9980 chunk 66 optimal weight: 6.9990 chunk 99 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 82 optimal weight: 0.9980 chunk 15 optimal weight: 9.9990 chunk 131 optimal weight: 7.9990 chunk 151 optimal weight: 5.9990 overall best weight: 3.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 ASN ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 15341 Z= 0.318 Angle : 0.587 5.904 20949 Z= 0.314 Chirality : 0.044 0.233 2325 Planarity : 0.005 0.041 2493 Dihedral : 14.555 87.098 2772 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.76 % Allowed : 15.85 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 0.36 (0.20), residues: 1693 helix: 0.99 (0.18), residues: 813 sheet: -0.34 (0.36), residues: 180 loop : -0.39 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 98 HIS 0.005 0.001 HIS C 127 PHE 0.019 0.002 PHE A 211 TYR 0.032 0.002 TYR B 557 ARG 0.005 0.001 ARG B 560 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 204 time to evaluate : 1.818 Fit side-chains REVERT: A 1 MET cc_start: 0.2233 (ttp) cc_final: 0.1471 (tpt) REVERT: A 14 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7540 (mt) REVERT: A 21 MET cc_start: 0.7732 (mtp) cc_final: 0.7479 (mtm) REVERT: A 26 GLU cc_start: 0.5842 (OUTLIER) cc_final: 0.5461 (pm20) REVERT: A 38 ILE cc_start: 0.7732 (mt) cc_final: 0.7461 (mt) REVERT: A 171 ILE cc_start: 0.7269 (OUTLIER) cc_final: 0.6774 (mp) REVERT: A 187 LEU cc_start: 0.6329 (OUTLIER) cc_final: 0.5863 (pp) REVERT: A 191 PHE cc_start: 0.4617 (OUTLIER) cc_final: 0.4088 (t80) REVERT: A 272 GLU cc_start: 0.7749 (tp30) cc_final: 0.7451 (mm-30) REVERT: A 346 LYS cc_start: 0.8015 (tttt) cc_final: 0.7565 (pttp) REVERT: A 578 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.7848 (ptm160) REVERT: A 608 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.6255 (mpt180) REVERT: A 618 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7449 (tt0) REVERT: A 656 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7757 (mm-30) REVERT: B 118 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7957 (mmt180) REVERT: B 120 ASP cc_start: 0.8304 (OUTLIER) cc_final: 0.7757 (p0) REVERT: B 152 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.7910 (mttt) REVERT: B 362 MET cc_start: 0.7686 (mmm) cc_final: 0.7346 (mmt) REVERT: B 367 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.7992 (tp40) REVERT: B 414 MET cc_start: 0.8830 (mmt) cc_final: 0.8530 (mpp) REVERT: B 563 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.8283 (mtm180) REVERT: B 638 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.6534 (mm-30) REVERT: B 672 ARG cc_start: 0.7525 (mtm180) cc_final: 0.7218 (ptp-170) REVERT: B 679 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.8053 (pt0) REVERT: B 680 ARG cc_start: 0.7262 (mtt90) cc_final: 0.6958 (mtt180) REVERT: C 146 ASP cc_start: 0.7907 (OUTLIER) cc_final: 0.7675 (m-30) REVERT: C 214 ARG cc_start: 0.7818 (mmt180) cc_final: 0.7374 (mmt-90) outliers start: 57 outliers final: 31 residues processed: 247 average time/residue: 1.7115 time to fit residues: 457.4109 Evaluate side-chains 251 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 204 time to evaluate : 1.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 22 LYS Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 578 ARG Chi-restraints excluded: chain A residue 608 ARG Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 118 ARG Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 367 GLN Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 429 ARG Chi-restraints excluded: chain B residue 563 ARG Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 635 MET Chi-restraints excluded: chain B residue 638 GLU Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 679 GLN Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 729 ASP Chi-restraints excluded: chain B residue 741 SER Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain C residue 62 ARG Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 226 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 159 optimal weight: 4.9990 chunk 145 optimal weight: 0.0470 chunk 155 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 chunk 67 optimal weight: 0.8980 chunk 122 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 chunk 140 optimal weight: 4.9990 chunk 146 optimal weight: 5.9990 chunk 154 optimal weight: 0.8980 chunk 102 optimal weight: 0.6980 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15341 Z= 0.122 Angle : 0.454 6.227 20949 Z= 0.246 Chirality : 0.038 0.206 2325 Planarity : 0.003 0.039 2493 Dihedral : 14.190 82.652 2772 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.31 % Allowed : 17.24 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 0.64 (0.20), residues: 1693 helix: 1.27 (0.19), residues: 827 sheet: -0.02 (0.38), residues: 173 loop : -0.40 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 49 HIS 0.004 0.001 HIS A 505 PHE 0.014 0.001 PHE B 333 TYR 0.020 0.001 TYR B 557 ARG 0.004 0.000 ARG A 492 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 215 time to evaluate : 1.755 Fit side-chains REVERT: A 21 MET cc_start: 0.7683 (mtp) cc_final: 0.7403 (mtm) REVERT: A 38 ILE cc_start: 0.7598 (mt) cc_final: 0.7354 (mt) REVERT: A 187 LEU cc_start: 0.6372 (OUTLIER) cc_final: 0.5939 (pp) REVERT: A 191 PHE cc_start: 0.4668 (OUTLIER) cc_final: 0.4136 (t80) REVERT: A 272 GLU cc_start: 0.7685 (tp30) cc_final: 0.7424 (mm-30) REVERT: A 346 LYS cc_start: 0.8008 (tttt) cc_final: 0.7551 (pttp) REVERT: A 455 MET cc_start: 0.8947 (mmm) cc_final: 0.8692 (mmm) REVERT: A 604 GLU cc_start: 0.7788 (tt0) cc_final: 0.7386 (tt0) REVERT: A 608 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.6374 (mpt180) REVERT: B 52 ARG cc_start: 0.8248 (mtp85) cc_final: 0.8003 (mtp85) REVERT: B 118 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7708 (mmt180) REVERT: B 120 ASP cc_start: 0.8101 (OUTLIER) cc_final: 0.7769 (p0) REVERT: B 152 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.7856 (mttt) REVERT: B 362 MET cc_start: 0.7700 (mmm) cc_final: 0.7372 (mmp) REVERT: B 414 MET cc_start: 0.8716 (mmt) cc_final: 0.8296 (mpp) REVERT: B 638 GLU cc_start: 0.7196 (OUTLIER) cc_final: 0.6518 (mm-30) REVERT: B 672 ARG cc_start: 0.7445 (mtm180) cc_final: 0.7071 (ptp-170) REVERT: B 679 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.8023 (pt0) REVERT: B 680 ARG cc_start: 0.7227 (mtt90) cc_final: 0.6977 (mtt180) REVERT: C 81 THR cc_start: 0.7690 (m) cc_final: 0.7106 (p) REVERT: C 157 ARG cc_start: 0.6283 (mpp-170) cc_final: 0.5919 (mmt-90) REVERT: C 214 ARG cc_start: 0.7707 (mmt180) cc_final: 0.7233 (mmt-90) outliers start: 35 outliers final: 18 residues processed: 242 average time/residue: 1.6672 time to fit residues: 436.5814 Evaluate side-chains 235 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 209 time to evaluate : 1.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 608 ARG Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 118 ARG Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 638 GLU Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 679 GLN Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 729 ASP Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 226 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 164 optimal weight: 2.9990 chunk 100 optimal weight: 9.9990 chunk 77 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 172 optimal weight: 9.9990 chunk 158 optimal weight: 3.9990 chunk 137 optimal weight: 7.9990 chunk 14 optimal weight: 8.9990 chunk 106 optimal weight: 7.9990 chunk 84 optimal weight: 10.0000 chunk 109 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN C 137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 15341 Z= 0.271 Angle : 0.558 6.481 20949 Z= 0.298 Chirality : 0.042 0.214 2325 Planarity : 0.004 0.037 2493 Dihedral : 14.187 84.427 2759 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.98 % Allowed : 17.77 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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 (0.20), residues: 1693 helix: 1.17 (0.19), residues: 820 sheet: -0.18 (0.37), residues: 178 loop : -0.39 (0.22), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 98 HIS 0.004 0.001 HIS A 505 PHE 0.018 0.002 PHE A 211 TYR 0.031 0.002 TYR B 557 ARG 0.006 0.001 ARG A 492 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 214 time to evaluate : 1.713 Fit side-chains REVERT: A 21 MET cc_start: 0.7663 (mtp) cc_final: 0.7417 (mtm) REVERT: A 38 ILE cc_start: 0.7664 (mt) cc_final: 0.7351 (mt) REVERT: A 171 ILE cc_start: 0.7243 (OUTLIER) cc_final: 0.6761 (mp) REVERT: A 187 LEU cc_start: 0.6355 (OUTLIER) cc_final: 0.5892 (pp) REVERT: A 191 PHE cc_start: 0.4644 (OUTLIER) cc_final: 0.4113 (t80) REVERT: A 272 GLU cc_start: 0.7688 (tp30) cc_final: 0.7385 (mm-30) REVERT: A 346 LYS cc_start: 0.8001 (tttt) cc_final: 0.7564 (pttp) REVERT: A 374 MET cc_start: 0.7865 (mtp) cc_final: 0.7649 (tpp) REVERT: A 608 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.6279 (mpt180) REVERT: B 118 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.8022 (mmt180) REVERT: B 120 ASP cc_start: 0.8160 (OUTLIER) cc_final: 0.7767 (p0) REVERT: B 152 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.7888 (mttt) REVERT: B 362 MET cc_start: 0.7700 (mmm) cc_final: 0.7371 (mmp) REVERT: B 414 MET cc_start: 0.8849 (mmt) cc_final: 0.8422 (mpp) REVERT: B 638 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6549 (mm-30) REVERT: B 672 ARG cc_start: 0.7526 (mtm180) cc_final: 0.7220 (ptp-170) REVERT: B 679 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.8032 (pt0) REVERT: B 680 ARG cc_start: 0.7258 (mtt90) cc_final: 0.6979 (mtt180) REVERT: B 734 ARG cc_start: 0.7274 (mtt90) cc_final: 0.6687 (mtp180) REVERT: C 214 ARG cc_start: 0.7801 (mmt180) cc_final: 0.7353 (mmt-90) outliers start: 30 outliers final: 19 residues processed: 237 average time/residue: 1.6547 time to fit residues: 424.2954 Evaluate side-chains 238 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 210 time to evaluate : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 608 ARG Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 118 ARG Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 638 GLU Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 679 GLN Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 729 ASP Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 217 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 146 optimal weight: 8.9990 chunk 42 optimal weight: 4.9990 chunk 126 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 137 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 141 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN C 137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.146807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.114555 restraints weight = 16175.654| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.18 r_work: 0.3007 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2851 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2851 r_free = 0.2851 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2851 r_free = 0.2851 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2851 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15341 Z= 0.166 Angle : 0.490 6.457 20949 Z= 0.263 Chirality : 0.039 0.200 2325 Planarity : 0.004 0.038 2493 Dihedral : 14.066 83.725 2759 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.05 % Allowed : 17.44 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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 (0.20), residues: 1693 helix: 1.24 (0.19), residues: 826 sheet: -0.11 (0.37), residues: 178 loop : -0.36 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 49 HIS 0.004 0.001 HIS A 505 PHE 0.013 0.001 PHE A 211 TYR 0.024 0.001 TYR B 557 ARG 0.005 0.000 ARG A 492 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7108.02 seconds wall clock time: 126 minutes 17.57 seconds (7577.57 seconds total)