Starting phenix.real_space_refine on Sun Jul 21 05:42:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rkt_19282/07_2024/8rkt_19282_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rkt_19282/07_2024/8rkt_19282.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rkt_19282/07_2024/8rkt_19282.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rkt_19282/07_2024/8rkt_19282.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rkt_19282/07_2024/8rkt_19282_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rkt_19282/07_2024/8rkt_19282_neut.cif" } resolution = 2.35 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 ------------------------------------------------------------------------------- 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= 0.002 sd= 0.075 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 310 5.49 5 Mg 1 5.21 5 S 30 5.16 5 C 7329 2.51 5 N 2427 2.21 5 O 3695 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 13794 Number of models: 1 Model: "" Number of chains: 14 Chain: "1" Number of atoms: 5239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 5239 Classifications: {'RNA': 246} Modifications used: {'5*END': 1, 'rna2p_pur': 21, 'rna2p_pyr': 17, 'rna3p_pur': 107, 'rna3p_pyr': 101} Link IDs: {'rna2p': 38, 'rna3p': 207} Chain: "2" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 696 Classifications: {'DNA': 34} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 33} Chain: "3" Number of atoms: 647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 647 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain: "A" Number of atoms: 4872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4872 Classifications: {'peptide': 602} Link IDs: {'PTRANS': 18, 'TRANS': 583} Chain breaks: 2 Chain: "B" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 708 Classifications: {'peptide': 87} Link IDs: {'TRANS': 86} Chain: "C" Number of atoms: 1306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1306 Classifications: {'peptide': 164} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 150} Chain: "1" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "1" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "2" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "3" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} 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: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "C" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 13205 SG CYS C 133 40.436 123.263 33.806 1.00 30.64 S ATOM 13226 SG CYS C 136 38.341 120.320 32.674 1.00 34.07 S ATOM 13342 SG CYS C 151 41.754 120.712 31.254 1.00 40.26 S ATOM 13369 SG CYS C 154 39.055 123.236 30.327 1.00 46.87 S ATOM 12930 SG CYS C 100 51.117 131.217 40.191 1.00 34.05 S ATOM 12945 SG CYS C 103 54.710 131.386 39.195 1.00 29.68 S ATOM 13114 SG CYS C 122 53.673 132.699 42.623 1.00 35.65 S Time building chain proxies: 8.22, per 1000 atoms: 0.60 Number of scatterers: 13794 At special positions: 0 Unit cell: (116.48, 144.144, 117.936, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 30 16.00 P 310 15.00 Mg 1 11.99 O 3695 8.00 N 2427 7.00 C 7329 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: 6.94 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 200 " pdb="ZN ZN C 200 " - pdb=" SG CYS C 136 " pdb="ZN ZN C 200 " - pdb=" SG CYS C 133 " pdb="ZN ZN C 200 " - pdb=" SG CYS C 151 " pdb="ZN ZN C 200 " - pdb=" SG CYS C 154 " pdb=" ZN C 201 " pdb="ZN ZN C 201 " - pdb=" ND1 HIS C 125 " pdb="ZN ZN C 201 " - pdb=" SG CYS C 100 " pdb="ZN ZN C 201 " - pdb=" SG CYS C 103 " pdb="ZN ZN C 201 " - pdb=" SG CYS C 122 " Number of angles added : 9 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1616 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 3 sheets defined 62.8% alpha, 7.9% beta 109 base pairs and 188 stacking pairs defined. Time for finding SS restraints: 5.59 Creating SS restraints... Processing helix chain 'A' and resid 13 through 27 Processing helix chain 'A' and resid 27 through 40 Processing helix chain 'A' and resid 44 through 52 removed outlier: 3.532A pdb=" N GLN A 50 " --> pdb=" O GLU A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 67 Proline residue: A 65 - end of helix Processing helix chain 'A' and resid 76 through 115 Processing helix chain 'A' and resid 117 through 126 removed outlier: 3.730A pdb=" N GLU A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 144 Processing helix chain 'A' and resid 174 through 185 removed outlier: 3.641A pdb=" N GLN A 183 " --> pdb=" O PHE A 179 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLU A 184 " --> pdb=" O ASP A 180 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR A 185 " --> pdb=" O ALA A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 200 removed outlier: 3.531A pdb=" N ASN A 200 " --> pdb=" O TYR A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 232 Processing helix chain 'A' and resid 244 through 257 removed outlier: 3.500A pdb=" N LEU A 248 " --> pdb=" O ASN A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 274 Processing helix chain 'A' and resid 287 through 289 No H-bonds generated for 'chain 'A' and resid 287 through 289' Processing helix chain 'A' and resid 318 through 338 removed outlier: 4.167A pdb=" N HIS A 323 " --> pdb=" O ASN A 319 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N TRP A 324 " --> pdb=" O ARG A 320 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE A 325 " --> pdb=" O GLN A 321 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 329 " --> pdb=" O PHE A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 347 Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 380 through 382 No H-bonds generated for 'chain 'A' and resid 380 through 382' Processing helix chain 'A' and resid 383 through 406 removed outlier: 3.583A pdb=" N LYS A 406 " --> pdb=" O ILE A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 429 Processing helix chain 'A' and resid 476 through 482 Processing helix chain 'A' and resid 485 through 508 removed outlier: 4.086A pdb=" N ASN A 489 " --> pdb=" O TYR A 485 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS A 507 " --> pdb=" O HIS A 503 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN A 508 " --> pdb=" O LYS A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 538 Processing helix chain 'A' and resid 550 through 567 removed outlier: 3.600A pdb=" N GLN A 565 " --> pdb=" O ALA A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 577 Processing helix chain 'A' and resid 578 through 588 Processing helix chain 'A' and resid 589 through 604 Processing helix chain 'A' and resid 618 through 633 Processing helix chain 'B' and resid 5 through 17 Processing helix chain 'B' and resid 25 through 47 removed outlier: 3.566A pdb=" N ALA B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 73 removed outlier: 3.641A pdb=" N GLY B 56 " --> pdb=" O SER B 52 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS B 73 " --> pdb=" O ALA B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 87 Processing helix chain 'C' and resid 21 through 33 Processing helix chain 'C' and resid 36 through 45 Processing helix chain 'C' and resid 48 through 55 removed outlier: 3.568A pdb=" N ARG C 52 " --> pdb=" O ALA C 48 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG C 55 " --> pdb=" O ALA C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 74 removed outlier: 3.841A pdb=" N VAL C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 83 Processing helix chain 'C' and resid 111 through 116 Processing helix chain 'C' and resid 142 through 146 Processing helix chain 'C' and resid 159 through 165 removed outlier: 3.544A pdb=" N ALA C 162 " --> pdb=" O ALA C 159 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN C 165 " --> pdb=" O ALA C 162 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 283 through 285 removed outlier: 6.562A pdb=" N LEU A 349 " --> pdb=" O ASP A 378 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ASP A 378 " --> pdb=" O LEU A 349 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN A 351 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LEU A 371 " --> pdb=" O LEU A 10 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N LEU A 301 " --> pdb=" O VAL A 315 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 470 through 475 removed outlier: 6.558A pdb=" N VAL A 463 " --> pdb=" O LEU A 472 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N TYR A 474 " --> pdb=" O VAL A 461 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL A 461 " --> pdb=" O TYR A 474 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N SER A 445 " --> pdb=" O ALA A 540 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N SER A 542 " --> pdb=" O SER A 445 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ILE A 447 " --> pdb=" O SER A 542 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N VAL A 544 " --> pdb=" O ILE A 447 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL A 449 " --> pdb=" O VAL A 544 " (cutoff:3.500A) removed outlier: 8.939A pdb=" N VAL A 451 " --> pdb=" O PRO A 546 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 121 through 122 404 hydrogen bonds defined for protein. 1164 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 277 hydrogen bonds 522 hydrogen bond angles 0 basepair planarities 109 basepair parallelities 188 stacking parallelities Total time for adding SS restraints: 6.51 Time building geometry restraints manager: 7.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1889 1.32 - 1.45: 5358 1.45 - 1.57: 6467 1.57 - 1.69: 619 1.69 - 1.81: 44 Bond restraints: 14377 Sorted by residual: bond pdb=" CE1 HIS C 94 " pdb=" NE2 HIS C 94 " ideal model delta sigma weight residual 1.321 1.356 -0.035 1.00e-02 1.00e+04 1.20e+01 bond pdb=" N ILE C 97 " pdb=" CA ILE C 97 " ideal model delta sigma weight residual 1.458 1.500 -0.042 1.20e-02 6.94e+03 1.20e+01 bond pdb=" N GLN C 93 " pdb=" CA GLN C 93 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.21e-02 6.83e+03 6.86e+00 bond pdb=" N GLU C 95 " pdb=" CA GLU C 95 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.41e-02 5.03e+03 4.80e+00 bond pdb=" N HIS C 94 " pdb=" CA HIS C 94 " ideal model delta sigma weight residual 1.458 1.484 -0.026 1.28e-02 6.10e+03 4.28e+00 ... (remaining 14372 not shown) Histogram of bond angle deviations from ideal: 97.83 - 105.09: 1370 105.09 - 112.34: 7750 112.34 - 119.60: 5272 119.60 - 126.86: 5683 126.86 - 134.11: 823 Bond angle restraints: 20898 Sorted by residual: angle pdb=" C3' DT 3 130 " pdb=" O3' DT 3 130 " pdb=" P DC 3 131 " ideal model delta sigma weight residual 120.20 108.76 11.44 1.50e+00 4.44e-01 5.82e+01 angle pdb=" O3' A 1 196 " pdb=" C3' A 1 196 " pdb=" C2' A 1 196 " ideal model delta sigma weight residual 109.50 118.10 -8.60 1.50e+00 4.44e-01 3.29e+01 angle pdb=" C3' DT 3 129 " pdb=" O3' DT 3 129 " pdb=" P DT 3 130 " ideal model delta sigma weight residual 120.20 113.20 7.00 1.50e+00 4.44e-01 2.18e+01 angle pdb=" C4' DA 2 5 " pdb=" C3' DA 2 5 " pdb=" O3' DA 2 5 " ideal model delta sigma weight residual 110.00 116.80 -6.80 1.50e+00 4.44e-01 2.06e+01 angle pdb=" C4' A 1 196 " pdb=" C3' A 1 196 " pdb=" O3' A 1 196 " ideal model delta sigma weight residual 109.40 116.05 -6.65 1.50e+00 4.44e-01 1.96e+01 ... (remaining 20893 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 8063 35.96 - 71.91: 729 71.91 - 107.87: 37 107.87 - 143.82: 6 143.82 - 179.78: 7 Dihedral angle restraints: 8842 sinusoidal: 6355 harmonic: 2487 Sorted by residual: dihedral pdb=" O4' U 1 170 " pdb=" C1' U 1 170 " pdb=" N1 U 1 170 " pdb=" C2 U 1 170 " ideal model delta sinusoidal sigma weight residual 200.00 33.10 166.90 1 1.50e+01 4.44e-03 8.42e+01 dihedral pdb=" O4' U 1 41 " pdb=" C1' U 1 41 " pdb=" N1 U 1 41 " pdb=" C2 U 1 41 " ideal model delta sinusoidal sigma weight residual 200.00 36.46 163.54 1 1.50e+01 4.44e-03 8.36e+01 dihedral pdb=" O4' U 1 39 " pdb=" C1' U 1 39 " pdb=" N1 U 1 39 " pdb=" C2 U 1 39 " ideal model delta sinusoidal sigma weight residual 200.00 38.24 161.76 1 1.50e+01 4.44e-03 8.32e+01 ... (remaining 8839 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.124: 2348 0.124 - 0.249: 155 0.249 - 0.373: 15 0.373 - 0.498: 5 0.498 - 0.622: 1 Chirality restraints: 2524 Sorted by residual: chirality pdb=" C3' A 1 196 " pdb=" C4' A 1 196 " pdb=" O3' A 1 196 " pdb=" C2' A 1 196 " both_signs ideal model delta sigma weight residual False -2.74 -2.12 -0.62 2.00e-01 2.50e+01 9.67e+00 chirality pdb=" C3' DA 2 5 " pdb=" C4' DA 2 5 " pdb=" O3' DA 2 5 " pdb=" C2' DA 2 5 " both_signs ideal model delta sigma weight residual False -2.66 -2.17 -0.49 2.00e-01 2.50e+01 6.03e+00 chirality pdb=" P DT 3 129 " pdb=" OP1 DT 3 129 " pdb=" OP2 DT 3 129 " pdb=" O5' DT 3 129 " both_signs ideal model delta sigma weight residual True 2.35 -2.80 -0.45 2.00e-01 2.50e+01 5.10e+00 ... (remaining 2521 not shown) Planarity restraints: 1532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C 1 99 " 0.084 2.00e-02 2.50e+03 4.90e-02 5.41e+01 pdb=" N1 C 1 99 " -0.074 2.00e-02 2.50e+03 pdb=" C2 C 1 99 " -0.024 2.00e-02 2.50e+03 pdb=" O2 C 1 99 " 0.004 2.00e-02 2.50e+03 pdb=" N3 C 1 99 " 0.002 2.00e-02 2.50e+03 pdb=" C4 C 1 99 " 0.004 2.00e-02 2.50e+03 pdb=" N4 C 1 99 " 0.013 2.00e-02 2.50e+03 pdb=" C5 C 1 99 " 0.059 2.00e-02 2.50e+03 pdb=" C6 C 1 99 " -0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U 1 127 " -0.079 2.00e-02 2.50e+03 4.75e-02 5.08e+01 pdb=" N1 U 1 127 " 0.074 2.00e-02 2.50e+03 pdb=" C2 U 1 127 " 0.002 2.00e-02 2.50e+03 pdb=" O2 U 1 127 " 0.005 2.00e-02 2.50e+03 pdb=" N3 U 1 127 " -0.003 2.00e-02 2.50e+03 pdb=" C4 U 1 127 " -0.007 2.00e-02 2.50e+03 pdb=" O4 U 1 127 " -0.008 2.00e-02 2.50e+03 pdb=" C5 U 1 127 " -0.057 2.00e-02 2.50e+03 pdb=" C6 U 1 127 " 0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C 1 245 " 0.063 2.00e-02 2.50e+03 3.96e-02 3.52e+01 pdb=" N1 C 1 245 " -0.051 2.00e-02 2.50e+03 pdb=" C2 C 1 245 " 0.006 2.00e-02 2.50e+03 pdb=" O2 C 1 245 " -0.011 2.00e-02 2.50e+03 pdb=" N3 C 1 245 " -0.001 2.00e-02 2.50e+03 pdb=" C4 C 1 245 " 0.003 2.00e-02 2.50e+03 pdb=" N4 C 1 245 " 0.006 2.00e-02 2.50e+03 pdb=" C5 C 1 245 " 0.053 2.00e-02 2.50e+03 pdb=" C6 C 1 245 " -0.068 2.00e-02 2.50e+03 ... (remaining 1529 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 240 2.62 - 3.19: 11521 3.19 - 3.76: 26435 3.76 - 4.33: 36697 4.33 - 4.90: 50343 Nonbonded interactions: 125236 Sorted by model distance: nonbonded pdb="MG MG 1 300 " pdb=" O HOH 1 447 " model vdw 2.046 2.170 nonbonded pdb="MG MG 1 300 " pdb=" O HOH C 317 " model vdw 2.056 2.170 nonbonded pdb="MG MG 1 300 " pdb=" O HOH 1 492 " model vdw 2.058 2.170 nonbonded pdb="MG MG 1 300 " pdb=" O HOH 1 527 " model vdw 2.071 2.170 nonbonded pdb=" OP1 A 1 173 " pdb="MG MG 1 300 " model vdw 2.185 2.170 ... (remaining 125231 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.570 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: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 46.490 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 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 : 0.006 0.056 14377 Z= 0.332 Angle : 0.955 11.440 20898 Z= 0.597 Chirality : 0.071 0.622 2524 Planarity : 0.012 0.118 1532 Dihedral : 22.001 179.780 7226 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.24 (0.26), residues: 843 helix: -0.20 (0.20), residues: 493 sheet: 0.11 (0.63), residues: 62 loop : 0.22 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 94 HIS 0.015 0.002 HIS A 353 PHE 0.027 0.003 PHE A 13 TYR 0.022 0.005 TYR A 91 ARG 0.021 0.004 ARG A 490 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.998 Fit side-chains REVERT: A 24 MET cc_start: 0.9093 (mtp) cc_final: 0.8777 (mtp) REVERT: A 226 GLN cc_start: 0.8022 (tt0) cc_final: 0.7812 (tm-30) REVERT: A 252 LEU cc_start: 0.8776 (mt) cc_final: 0.8568 (mp) REVERT: A 260 GLU cc_start: 0.7600 (pt0) cc_final: 0.7381 (pt0) REVERT: A 267 ARG cc_start: 0.8076 (mtm110) cc_final: 0.7866 (mtp180) REVERT: A 397 GLU cc_start: 0.8185 (tt0) cc_final: 0.7877 (tt0) REVERT: A 416 GLN cc_start: 0.7708 (tp40) cc_final: 0.7398 (tp-100) REVERT: A 496 GLN cc_start: 0.8474 (mt0) cc_final: 0.8251 (mt0) REVERT: A 612 LYS cc_start: 0.7488 (tppt) cc_final: 0.7067 (ttpt) REVERT: A 621 ASP cc_start: 0.7717 (t0) cc_final: 0.7500 (t70) REVERT: B 9 LYS cc_start: 0.6910 (ttpt) cc_final: 0.6095 (ttpt) REVERT: C 93 GLN cc_start: 0.8254 (mt0) cc_final: 0.7264 (pm20) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 2.0362 time to fit residues: 271.8187 Evaluate side-chains 101 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 58 optimal weight: 9.9990 chunk 46 optimal weight: 7.9990 chunk 89 optimal weight: 9.9990 chunk 34 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 423 GLN A 431 ASN B 10 GLN B 80 GLN C 135 ASN C 137 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 14377 Z= 0.319 Angle : 0.690 6.702 20898 Z= 0.377 Chirality : 0.044 0.350 2524 Planarity : 0.005 0.047 1532 Dihedral : 24.031 179.898 5469 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 1.08 % Allowed : 7.40 % Favored : 91.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.29), residues: 843 helix: 1.24 (0.22), residues: 504 sheet: 0.80 (0.65), residues: 65 loop : 0.56 (0.40), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 382 HIS 0.011 0.002 HIS A 353 PHE 0.023 0.003 PHE A 214 TYR 0.021 0.003 TYR A 91 ARG 0.005 0.001 ARG C 98 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 97 time to evaluate : 0.987 Fit side-chains REVERT: A 226 GLN cc_start: 0.8051 (tt0) cc_final: 0.7812 (tm-30) REVERT: A 252 LEU cc_start: 0.8586 (mt) cc_final: 0.8355 (mp) REVERT: A 336 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.7655 (mtt180) REVERT: A 341 GLN cc_start: 0.7939 (OUTLIER) cc_final: 0.7523 (mp-120) REVERT: A 397 GLU cc_start: 0.8135 (tt0) cc_final: 0.7857 (tt0) REVERT: A 416 GLN cc_start: 0.7590 (tp40) cc_final: 0.7228 (tp-100) REVERT: A 566 LYS cc_start: 0.8099 (tttp) cc_final: 0.7742 (ttmp) REVERT: A 621 ASP cc_start: 0.7627 (t0) cc_final: 0.7376 (t70) REVERT: B 9 LYS cc_start: 0.6667 (ttpt) cc_final: 0.5912 (ttpt) REVERT: C 93 GLN cc_start: 0.8544 (mt0) cc_final: 0.7213 (pm20) outliers start: 8 outliers final: 2 residues processed: 98 average time/residue: 2.0712 time to fit residues: 215.2844 Evaluate side-chains 94 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 90 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain C residue 73 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 28 optimal weight: 8.9990 chunk 103 optimal weight: 5.9990 chunk 112 optimal weight: 7.9990 chunk 92 optimal weight: 0.6980 chunk 102 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 chunk 83 optimal weight: 2.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 ASN B 80 GLN C 137 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14377 Z= 0.230 Angle : 0.599 7.449 20898 Z= 0.330 Chirality : 0.039 0.320 2524 Planarity : 0.004 0.033 1532 Dihedral : 23.921 179.679 5469 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 1.35 % Allowed : 9.56 % Favored : 89.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.29), residues: 843 helix: 1.68 (0.23), residues: 503 sheet: 0.84 (0.64), residues: 65 loop : 0.62 (0.40), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 382 HIS 0.006 0.001 HIS A 353 PHE 0.019 0.002 PHE A 214 TYR 0.020 0.002 TYR A 91 ARG 0.004 0.001 ARG A 490 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 95 time to evaluate : 1.034 Fit side-chains REVERT: A 226 GLN cc_start: 0.8023 (tt0) cc_final: 0.7461 (tp-100) REVERT: A 230 GLU cc_start: 0.8347 (mt-10) cc_final: 0.8141 (mt-10) REVERT: A 252 LEU cc_start: 0.8552 (mt) cc_final: 0.8318 (mp) REVERT: A 336 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.7603 (mtt180) REVERT: A 341 GLN cc_start: 0.7916 (OUTLIER) cc_final: 0.7466 (mp-120) REVERT: A 397 GLU cc_start: 0.8121 (tt0) cc_final: 0.7819 (tt0) REVERT: A 416 GLN cc_start: 0.7583 (tp40) cc_final: 0.7349 (tp-100) REVERT: A 566 LYS cc_start: 0.8039 (tttp) cc_final: 0.7676 (ttmp) REVERT: A 621 ASP cc_start: 0.7678 (t0) cc_final: 0.7474 (t70) REVERT: B 9 LYS cc_start: 0.6572 (ttpt) cc_final: 0.5834 (ttpt) REVERT: C 93 GLN cc_start: 0.8519 (mt0) cc_final: 0.7184 (pm20) outliers start: 10 outliers final: 4 residues processed: 99 average time/residue: 2.1829 time to fit residues: 228.8313 Evaluate side-chains 100 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 94 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain C residue 73 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 104 optimal weight: 0.6980 chunk 110 optimal weight: 6.9990 chunk 54 optimal weight: 8.9990 chunk 98 optimal weight: 20.0000 chunk 29 optimal weight: 7.9990 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 ASN B 80 GLN C 137 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14377 Z= 0.229 Angle : 0.596 7.924 20898 Z= 0.326 Chirality : 0.039 0.321 2524 Planarity : 0.004 0.034 1532 Dihedral : 23.945 179.788 5469 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.48 % Allowed : 10.09 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.29), residues: 843 helix: 1.77 (0.23), residues: 504 sheet: 0.80 (0.65), residues: 65 loop : 0.58 (0.39), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 382 HIS 0.003 0.001 HIS A 353 PHE 0.018 0.002 PHE A 214 TYR 0.018 0.002 TYR A 91 ARG 0.003 0.001 ARG A 350 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 99 time to evaluate : 0.964 Fit side-chains REVERT: A 226 GLN cc_start: 0.8032 (tt0) cc_final: 0.7466 (tp-100) REVERT: A 230 GLU cc_start: 0.8276 (mt-10) cc_final: 0.8076 (mt-10) REVERT: A 252 LEU cc_start: 0.8515 (mt) cc_final: 0.8305 (mp) REVERT: A 336 ARG cc_start: 0.7819 (OUTLIER) cc_final: 0.7592 (mtt180) REVERT: A 341 GLN cc_start: 0.7948 (OUTLIER) cc_final: 0.7489 (mp-120) REVERT: A 397 GLU cc_start: 0.8097 (tt0) cc_final: 0.7836 (tt0) REVERT: A 416 GLN cc_start: 0.7611 (tp40) cc_final: 0.7361 (tp-100) REVERT: A 566 LYS cc_start: 0.8102 (tttp) cc_final: 0.7715 (ttmp) REVERT: A 612 LYS cc_start: 0.7633 (tptt) cc_final: 0.7093 (ttpt) REVERT: B 9 LYS cc_start: 0.6583 (ttpt) cc_final: 0.5709 (ttpt) REVERT: C 93 GLN cc_start: 0.8521 (mt0) cc_final: 0.7192 (pm20) outliers start: 11 outliers final: 3 residues processed: 102 average time/residue: 2.2374 time to fit residues: 242.5348 Evaluate side-chains 97 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 92 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain C residue 73 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 0.7980 chunk 62 optimal weight: 10.0000 chunk 1 optimal weight: 30.0000 chunk 82 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 chunk 76 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 56 optimal weight: 0.1980 chunk 98 optimal weight: 20.0000 chunk 27 optimal weight: 10.0000 overall best weight: 4.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 GLN A 431 ASN B 80 GLN C 137 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14377 Z= 0.260 Angle : 0.617 7.662 20898 Z= 0.336 Chirality : 0.040 0.335 2524 Planarity : 0.004 0.035 1532 Dihedral : 23.983 179.881 5469 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.62 % Allowed : 11.44 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.29), residues: 843 helix: 1.73 (0.22), residues: 504 sheet: 0.79 (0.65), residues: 63 loop : 0.47 (0.39), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 21 HIS 0.004 0.001 HIS C 24 PHE 0.019 0.002 PHE A 214 TYR 0.020 0.002 TYR A 91 ARG 0.003 0.001 ARG C 98 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 91 time to evaluate : 1.095 Fit side-chains REVERT: A 226 GLN cc_start: 0.8055 (tt0) cc_final: 0.7470 (tp-100) REVERT: A 230 GLU cc_start: 0.8286 (mt-10) cc_final: 0.8082 (mt-10) REVERT: A 252 LEU cc_start: 0.8566 (mt) cc_final: 0.8335 (mp) REVERT: A 336 ARG cc_start: 0.7840 (OUTLIER) cc_final: 0.7594 (mtt180) REVERT: A 397 GLU cc_start: 0.8111 (tt0) cc_final: 0.7819 (tt0) REVERT: A 416 GLN cc_start: 0.7637 (tp40) cc_final: 0.7299 (tp-100) REVERT: A 477 ILE cc_start: 0.9027 (OUTLIER) cc_final: 0.8795 (tp) REVERT: A 566 LYS cc_start: 0.8118 (tttp) cc_final: 0.7717 (ttmp) REVERT: A 612 LYS cc_start: 0.7641 (OUTLIER) cc_final: 0.7086 (ttpt) REVERT: B 9 LYS cc_start: 0.6570 (ttpt) cc_final: 0.5615 (ttpt) REVERT: C 93 GLN cc_start: 0.8517 (mt0) cc_final: 0.7171 (pm20) outliers start: 12 outliers final: 3 residues processed: 96 average time/residue: 2.2581 time to fit residues: 229.2809 Evaluate side-chains 97 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 91 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 612 LYS Chi-restraints excluded: chain C residue 73 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 21 optimal weight: 40.0000 chunk 64 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 110 optimal weight: 0.0970 chunk 91 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 chunk 36 optimal weight: 7.9990 chunk 57 optimal weight: 6.9990 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 ASN A 500 HIS B 80 GLN C 137 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14377 Z= 0.243 Angle : 0.604 7.574 20898 Z= 0.330 Chirality : 0.039 0.328 2524 Planarity : 0.004 0.035 1532 Dihedral : 23.984 179.846 5469 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.48 % Allowed : 12.11 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.29), residues: 843 helix: 1.75 (0.22), residues: 504 sheet: 0.79 (0.65), residues: 63 loop : 0.47 (0.39), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 382 HIS 0.003 0.001 HIS C 24 PHE 0.019 0.002 PHE A 214 TYR 0.019 0.002 TYR A 91 ARG 0.004 0.001 ARG C 61 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 92 time to evaluate : 1.057 Fit side-chains REVERT: A 226 GLN cc_start: 0.8058 (tt0) cc_final: 0.7468 (tp-100) REVERT: A 230 GLU cc_start: 0.8279 (mt-10) cc_final: 0.8078 (mt-10) REVERT: A 252 LEU cc_start: 0.8522 (mt) cc_final: 0.8297 (mp) REVERT: A 275 ARG cc_start: 0.7617 (tmm160) cc_final: 0.6578 (tpp80) REVERT: A 336 ARG cc_start: 0.7830 (OUTLIER) cc_final: 0.7587 (mtt180) REVERT: A 341 GLN cc_start: 0.7915 (OUTLIER) cc_final: 0.7519 (mp10) REVERT: A 397 GLU cc_start: 0.8112 (tt0) cc_final: 0.7835 (tt0) REVERT: A 416 GLN cc_start: 0.7620 (tp40) cc_final: 0.7302 (tp-100) REVERT: A 477 ILE cc_start: 0.9024 (OUTLIER) cc_final: 0.8794 (tp) REVERT: A 566 LYS cc_start: 0.8105 (tttp) cc_final: 0.7756 (ttmp) REVERT: A 612 LYS cc_start: 0.7636 (tptt) cc_final: 0.7084 (ttpt) REVERT: B 9 LYS cc_start: 0.6577 (ttpt) cc_final: 0.5595 (ttpt) REVERT: C 93 GLN cc_start: 0.8516 (mt0) cc_final: 0.7165 (pm20) outliers start: 11 outliers final: 3 residues processed: 98 average time/residue: 2.2097 time to fit residues: 228.9572 Evaluate side-chains 98 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 92 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain C residue 73 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 80 optimal weight: 9.9990 chunk 92 optimal weight: 4.9990 chunk 61 optimal weight: 9.9990 chunk 109 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 ASN B 80 GLN C 137 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14377 Z= 0.169 Angle : 0.541 6.736 20898 Z= 0.298 Chirality : 0.035 0.294 2524 Planarity : 0.004 0.037 1532 Dihedral : 23.925 179.751 5469 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.35 % Allowed : 12.25 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 2.17 (0.29), residues: 843 helix: 2.06 (0.23), residues: 504 sheet: 0.90 (0.66), residues: 63 loop : 0.52 (0.39), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 21 HIS 0.003 0.001 HIS A 304 PHE 0.014 0.001 PHE A 13 TYR 0.017 0.002 TYR A 91 ARG 0.003 0.000 ARG C 61 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 96 time to evaluate : 1.155 Fit side-chains REVERT: A 113 GLU cc_start: 0.6594 (tm-30) cc_final: 0.6339 (tm-30) REVERT: A 226 GLN cc_start: 0.8068 (tt0) cc_final: 0.7488 (tp-100) REVERT: A 246 LYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7718 (ttmm) REVERT: A 252 LEU cc_start: 0.8495 (mt) cc_final: 0.8294 (mp) REVERT: A 275 ARG cc_start: 0.7620 (tmm160) cc_final: 0.6565 (tpp80) REVERT: A 336 ARG cc_start: 0.7812 (OUTLIER) cc_final: 0.7611 (mtt180) REVERT: A 397 GLU cc_start: 0.8061 (tt0) cc_final: 0.7764 (tt0) REVERT: A 416 GLN cc_start: 0.7568 (tp40) cc_final: 0.7362 (tp-100) REVERT: A 477 ILE cc_start: 0.8972 (OUTLIER) cc_final: 0.8719 (tp) REVERT: A 566 LYS cc_start: 0.7976 (tttp) cc_final: 0.7637 (ttmp) REVERT: A 612 LYS cc_start: 0.7611 (tptt) cc_final: 0.7095 (ttpt) REVERT: B 9 LYS cc_start: 0.6479 (ttpt) cc_final: 0.5531 (ttpt) REVERT: B 76 ARG cc_start: 0.7820 (OUTLIER) cc_final: 0.7487 (mtt90) REVERT: C 161 MET cc_start: 0.8508 (mtm) cc_final: 0.8184 (mtt) outliers start: 10 outliers final: 2 residues processed: 100 average time/residue: 2.1905 time to fit residues: 231.6453 Evaluate side-chains 99 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 93 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain C residue 73 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 0.7980 chunk 65 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 21 optimal weight: 40.0000 chunk 69 optimal weight: 3.9990 chunk 74 optimal weight: 7.9990 chunk 54 optimal weight: 8.9990 chunk 10 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 chunk 105 optimal weight: 7.9990 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 423 GLN B 80 GLN C 137 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 14377 Z= 0.306 Angle : 0.651 7.617 20898 Z= 0.351 Chirality : 0.042 0.349 2524 Planarity : 0.004 0.034 1532 Dihedral : 24.047 179.574 5469 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.48 % Allowed : 11.57 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.29), residues: 843 helix: 1.73 (0.22), residues: 504 sheet: 0.80 (0.64), residues: 63 loop : 0.44 (0.39), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 21 HIS 0.003 0.001 HIS C 24 PHE 0.019 0.002 PHE A 214 TYR 0.021 0.002 TYR A 91 ARG 0.004 0.001 ARG C 61 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 93 time to evaluate : 1.019 Fit side-chains REVERT: A 226 GLN cc_start: 0.8105 (tt0) cc_final: 0.7497 (tp-100) REVERT: A 252 LEU cc_start: 0.8564 (mt) cc_final: 0.8327 (mp) REVERT: A 275 ARG cc_start: 0.7632 (tmm160) cc_final: 0.6597 (tpp80) REVERT: A 336 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.7602 (mtt180) REVERT: A 397 GLU cc_start: 0.8128 (tt0) cc_final: 0.7850 (tt0) REVERT: A 416 GLN cc_start: 0.7615 (tp40) cc_final: 0.7304 (tp-100) REVERT: A 477 ILE cc_start: 0.9044 (OUTLIER) cc_final: 0.8818 (tp) REVERT: A 501 GLU cc_start: 0.8849 (mm-30) cc_final: 0.8642 (mm-30) REVERT: B 9 LYS cc_start: 0.6664 (ttpt) cc_final: 0.5609 (ttpt) outliers start: 11 outliers final: 3 residues processed: 95 average time/residue: 2.1591 time to fit residues: 216.9085 Evaluate side-chains 95 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 90 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain C residue 163 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 3.9990 chunk 102 optimal weight: 8.9990 chunk 105 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 44 optimal weight: 0.2980 chunk 80 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 67 optimal weight: 9.9990 chunk 108 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 ASN B 80 GLN C 137 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14377 Z= 0.182 Angle : 0.554 7.004 20898 Z= 0.304 Chirality : 0.036 0.301 2524 Planarity : 0.004 0.036 1532 Dihedral : 23.959 179.410 5469 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.81 % Allowed : 12.65 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 (0.29), residues: 843 helix: 1.99 (0.22), residues: 505 sheet: 0.90 (0.66), residues: 63 loop : 0.51 (0.39), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 21 HIS 0.002 0.001 HIS A 304 PHE 0.015 0.002 PHE A 13 TYR 0.017 0.002 TYR A 91 ARG 0.003 0.000 ARG C 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 91 time to evaluate : 0.982 Fit side-chains REVERT: A 113 GLU cc_start: 0.6613 (tm-30) cc_final: 0.6366 (tm-30) REVERT: A 226 GLN cc_start: 0.8096 (tt0) cc_final: 0.7510 (tp-100) REVERT: A 246 LYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7726 (ttmm) REVERT: A 252 LEU cc_start: 0.8512 (mt) cc_final: 0.8295 (mp) REVERT: A 275 ARG cc_start: 0.7617 (tmm160) cc_final: 0.6560 (tpp80) REVERT: A 336 ARG cc_start: 0.7819 (OUTLIER) cc_final: 0.7601 (mtt180) REVERT: A 397 GLU cc_start: 0.8099 (tt0) cc_final: 0.7788 (tt0) REVERT: A 416 GLN cc_start: 0.7594 (tp40) cc_final: 0.7374 (tp-100) REVERT: A 477 ILE cc_start: 0.8985 (OUTLIER) cc_final: 0.8745 (tp) REVERT: A 566 LYS cc_start: 0.8044 (tttp) cc_final: 0.7690 (ttmp) REVERT: A 612 LYS cc_start: 0.7584 (tptp) cc_final: 0.7050 (ttpt) REVERT: B 9 LYS cc_start: 0.6594 (ttpt) cc_final: 0.5558 (ttpt) REVERT: C 161 MET cc_start: 0.8479 (mtm) cc_final: 0.8194 (mtt) outliers start: 6 outliers final: 2 residues processed: 94 average time/residue: 2.1819 time to fit residues: 216.7868 Evaluate side-chains 95 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 90 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain C residue 163 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 113 optimal weight: 0.2980 chunk 104 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 chunk 27 optimal weight: 10.0000 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 80 GLN C 137 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14377 Z= 0.148 Angle : 0.531 5.883 20898 Z= 0.292 Chirality : 0.034 0.280 2524 Planarity : 0.003 0.036 1532 Dihedral : 23.958 179.881 5469 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.81 % Allowed : 13.06 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 2.24 (0.29), residues: 843 helix: 2.16 (0.22), residues: 504 sheet: 0.87 (0.66), residues: 63 loop : 0.46 (0.39), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 111 HIS 0.003 0.001 HIS A 304 PHE 0.014 0.001 PHE A 13 TYR 0.014 0.001 TYR A 91 ARG 0.005 0.000 ARG C 61 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 94 time to evaluate : 1.041 Fit side-chains REVERT: A 113 GLU cc_start: 0.6594 (tm-30) cc_final: 0.6332 (tm-30) REVERT: A 226 GLN cc_start: 0.8069 (tt0) cc_final: 0.7498 (tp-100) REVERT: A 246 LYS cc_start: 0.8052 (OUTLIER) cc_final: 0.7710 (ttmm) REVERT: A 275 ARG cc_start: 0.7597 (tmm160) cc_final: 0.6549 (tpp80) REVERT: A 336 ARG cc_start: 0.7819 (OUTLIER) cc_final: 0.7610 (mtt180) REVERT: A 397 GLU cc_start: 0.8065 (tt0) cc_final: 0.7753 (tt0) REVERT: A 416 GLN cc_start: 0.7558 (tp40) cc_final: 0.7350 (tp-100) REVERT: A 477 ILE cc_start: 0.8969 (OUTLIER) cc_final: 0.8709 (tp) REVERT: A 566 LYS cc_start: 0.8005 (tttp) cc_final: 0.7664 (ttmp) REVERT: A 612 LYS cc_start: 0.7584 (tptp) cc_final: 0.7054 (ttpt) REVERT: B 9 LYS cc_start: 0.6558 (ttpt) cc_final: 0.5538 (ttpt) REVERT: B 76 ARG cc_start: 0.7797 (OUTLIER) cc_final: 0.7487 (mtt90) outliers start: 6 outliers final: 2 residues processed: 96 average time/residue: 2.1850 time to fit residues: 221.7540 Evaluate side-chains 99 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 93 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain C residue 163 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 90 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 11 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 overall best weight: 5.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 80 GLN C 137 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.173785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.131625 restraints weight = 12147.367| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 0.86 r_work: 0.3246 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14377 Z= 0.327 Angle : 0.666 8.666 20898 Z= 0.357 Chirality : 0.043 0.356 2524 Planarity : 0.005 0.033 1532 Dihedral : 24.063 179.739 5469 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.08 % Allowed : 13.06 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.29), residues: 843 helix: 1.76 (0.22), residues: 507 sheet: 0.77 (0.65), residues: 63 loop : 0.45 (0.39), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 21 HIS 0.004 0.001 HIS C 24 PHE 0.019 0.002 PHE A 214 TYR 0.021 0.003 TYR A 91 ARG 0.004 0.001 ARG C 61 =============================================================================== Job complete usr+sys time: 4583.83 seconds wall clock time: 81 minutes 45.27 seconds (4905.27 seconds total)