Starting phenix.real_space_refine on Thu Jun 12 02:23:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rkt_19282/06_2025/8rkt_19282.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rkt_19282/06_2025/8rkt_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/cci-nas-00/data/ceres_data/8rkt_19282/06_2025/8rkt_19282.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rkt_19282/06_2025/8rkt_19282.map" model { file = "/net/cci-nas-00/data/ceres_data/8rkt_19282/06_2025/8rkt_19282.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rkt_19282/06_2025/8rkt_19282.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. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 7.83, per 1000 atoms: 0.57 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 - 3.00 Amino acid : True - 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: 2.99 Conformation dependent library (CDL) restraints added in 1.0 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: 6.47 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: 7.32 Time building geometry restraints manager: 3.64 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: 0.00 - 2.29: 20126 2.29 - 4.58: 716 4.58 - 6.86: 53 6.86 - 9.15: 2 9.15 - 11.44: 1 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 Time spend for trying shortcut: 0.00 ========== 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: 1.140 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: 0.540 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 41.540 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.630 ------------------------------------------------------------------------------- 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 14385 Z= 0.288 Angle : 0.956 11.440 20907 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 Details of bonding type rmsd hydrogen bonds : bond 0.13813 ( 681) hydrogen bonds : angle 5.42584 ( 1686) metal coordination : bond 0.02466 ( 8) metal coordination : angle 1.85305 ( 9) covalent geometry : bond 0.00564 (14377) covalent geometry : angle 0.95538 (20898) *********************** 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 to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 1.122 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: 2.0790 time to fit residues: 277.1900 Evaluate side-chains 101 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 1.024 ------------------------------------------------------------------------------- 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: 8.9990 chunk 86 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 chunk 46 optimal weight: 6.9990 chunk 89 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 C 165 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.175864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.133500 restraints weight = 12078.584| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 0.84 r_work: 0.3278 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14385 Z= 0.247 Angle : 0.691 6.825 20907 Z= 0.377 Chirality : 0.044 0.346 2524 Planarity : 0.005 0.045 1532 Dihedral : 23.946 178.743 5469 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % 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: 1.46 (0.29), residues: 843 helix: 1.29 (0.22), residues: 504 sheet: 0.80 (0.66), residues: 65 loop : 0.63 (0.40), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 382 HIS 0.010 0.002 HIS A 353 PHE 0.023 0.003 PHE A 214 TYR 0.022 0.002 TYR A 91 ARG 0.004 0.001 ARG A 218 Details of bonding type rmsd hydrogen bonds : bond 0.05576 ( 681) hydrogen bonds : angle 3.65213 ( 1686) metal coordination : bond 0.01537 ( 8) metal coordination : angle 2.71367 ( 9) covalent geometry : bond 0.00514 (14377) covalent geometry : angle 0.68911 (20898) *********************** 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 102 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 1.134 Fit side-chains REVERT: A 252 LEU cc_start: 0.8731 (mt) cc_final: 0.8490 (mp) REVERT: A 341 GLN cc_start: 0.7996 (OUTLIER) cc_final: 0.7613 (mp-120) REVERT: A 397 GLU cc_start: 0.8075 (tt0) cc_final: 0.7867 (tt0) REVERT: A 416 GLN cc_start: 0.7697 (tp40) cc_final: 0.7458 (tp-100) REVERT: A 566 LYS cc_start: 0.8255 (tttp) cc_final: 0.7971 (ttmp) REVERT: B 9 LYS cc_start: 0.7140 (ttpt) cc_final: 0.6608 (ttpt) REVERT: C 93 GLN cc_start: 0.8607 (mt0) cc_final: 0.7197 (pm20) outliers start: 8 outliers final: 4 residues processed: 95 average time/residue: 2.1001 time to fit residues: 212.0294 Evaluate side-chains 93 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 88 time to evaluate : 1.075 ------------------------------------------------------------------------------- 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 B residue 76 ARG 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 66 optimal weight: 1.9990 chunk 44 optimal weight: 9.9990 chunk 102 optimal weight: 8.9990 chunk 109 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 93 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 111 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 A 620 HIS B 80 GLN C 137 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.176950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.134640 restraints weight = 12132.836| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 0.79 r_work: 0.3297 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14385 Z= 0.195 Angle : 0.616 6.918 20907 Z= 0.338 Chirality : 0.040 0.324 2524 Planarity : 0.004 0.034 1532 Dihedral : 23.879 179.866 5469 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 1.75 % Allowed : 8.88 % Favored : 89.37 % 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: 1.65 (0.22), residues: 503 sheet: 0.75 (0.65), residues: 65 loop : 0.66 (0.41), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 382 HIS 0.007 0.001 HIS A 353 PHE 0.019 0.002 PHE A 214 TYR 0.019 0.002 TYR A 91 ARG 0.003 0.001 ARG A 492 Details of bonding type rmsd hydrogen bonds : bond 0.04971 ( 681) hydrogen bonds : angle 3.45650 ( 1686) metal coordination : bond 0.01027 ( 8) metal coordination : angle 2.52464 ( 9) covalent geometry : bond 0.00401 (14377) covalent geometry : angle 0.61393 (20898) *********************** 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 106 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 1.038 Fit side-chains REVERT: A 230 GLU cc_start: 0.8362 (mt-10) cc_final: 0.8144 (mt-10) REVERT: A 252 LEU cc_start: 0.8720 (mt) cc_final: 0.8476 (mp) REVERT: A 336 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.7688 (mtt180) REVERT: A 341 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.7667 (mp-120) REVERT: A 566 LYS cc_start: 0.8282 (tttp) cc_final: 0.8009 (ttmp) REVERT: A 612 LYS cc_start: 0.7734 (tptt) cc_final: 0.7420 (ttpt) REVERT: B 9 LYS cc_start: 0.7150 (ttpt) cc_final: 0.6657 (ttpt) REVERT: B 76 ARG cc_start: 0.7772 (OUTLIER) cc_final: 0.7355 (mtt90) REVERT: C 93 GLN cc_start: 0.8603 (mt0) cc_final: 0.7295 (pm20) outliers start: 13 outliers final: 3 residues processed: 97 average time/residue: 2.1784 time to fit residues: 223.5590 Evaluate side-chains 97 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 91 time to evaluate : 1.008 ------------------------------------------------------------------------------- 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 A residue 438 GLN Chi-restraints excluded: chain B residue 76 ARG 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 37 optimal weight: 4.9990 chunk 9 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 98 optimal weight: 20.0000 chunk 50 optimal weight: 10.0000 chunk 71 optimal weight: 7.9990 chunk 69 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 103 optimal weight: 8.9990 chunk 35 optimal weight: 9.9990 chunk 21 optimal weight: 40.0000 overall best weight: 8.3990 ------------------------------------------------------------------------------- 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 423 GLN A 431 ASN A 500 HIS A 620 HIS B 80 GLN C 135 ASN C 137 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.172742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.130987 restraints weight = 12075.183| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.03 r_work: 0.3236 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.053 14385 Z= 0.370 Angle : 0.798 9.195 20907 Z= 0.423 Chirality : 0.050 0.408 2524 Planarity : 0.006 0.049 1532 Dihedral : 24.078 179.809 5469 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.88 % Allowed : 10.36 % Favored : 87.75 % 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: 1.28 (0.28), residues: 843 helix: 1.22 (0.22), residues: 504 sheet: 0.38 (0.65), residues: 60 loop : 0.51 (0.39), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP A 21 HIS 0.006 0.002 HIS C 24 PHE 0.026 0.003 PHE A 214 TYR 0.023 0.003 TYR A 91 ARG 0.006 0.001 ARG A 492 Details of bonding type rmsd hydrogen bonds : bond 0.06257 ( 681) hydrogen bonds : angle 3.67662 ( 1686) metal coordination : bond 0.01855 ( 8) metal coordination : angle 3.21565 ( 9) covalent geometry : bond 0.00776 (14377) covalent geometry : angle 0.79588 (20898) *********************** 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 105 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.980 Fit side-chains REVERT: A 230 GLU cc_start: 0.8305 (mt-10) cc_final: 0.8071 (mt-10) REVERT: A 336 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.7762 (mtt180) REVERT: A 341 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7733 (mp-120) REVERT: A 477 ILE cc_start: 0.9079 (OUTLIER) cc_final: 0.8838 (tp) REVERT: B 9 LYS cc_start: 0.7328 (ttpt) cc_final: 0.6538 (ttpt) REVERT: B 76 ARG cc_start: 0.7771 (OUTLIER) cc_final: 0.7344 (mtt90) REVERT: C 93 GLN cc_start: 0.8669 (mt0) cc_final: 0.7300 (pm20) outliers start: 14 outliers final: 2 residues processed: 95 average time/residue: 2.0862 time to fit residues: 209.8407 Evaluate side-chains 95 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.988 ------------------------------------------------------------------------------- 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 A residue 470 LYS Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain B residue 76 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 4 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 3 optimal weight: 20.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 ASN A 620 HIS B 80 GLN C 137 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.174789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.132829 restraints weight = 12128.461| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 0.83 r_work: 0.3270 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14385 Z= 0.245 Angle : 0.667 7.933 20907 Z= 0.361 Chirality : 0.043 0.354 2524 Planarity : 0.005 0.036 1532 Dihedral : 23.977 179.858 5469 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.88 % Allowed : 11.71 % 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: 1.46 (0.29), residues: 843 helix: 1.40 (0.22), residues: 505 sheet: 0.71 (0.65), residues: 63 loop : 0.42 (0.39), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 382 HIS 0.004 0.001 HIS A 620 PHE 0.020 0.002 PHE A 214 TYR 0.021 0.002 TYR A 91 ARG 0.004 0.001 ARG A 218 Details of bonding type rmsd hydrogen bonds : bond 0.05337 ( 681) hydrogen bonds : angle 3.52116 ( 1686) metal coordination : bond 0.01173 ( 8) metal coordination : angle 3.05756 ( 9) covalent geometry : bond 0.00509 (14377) covalent geometry : angle 0.66448 (20898) *********************** 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 106 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 1.401 Fit side-chains REVERT: A 230 GLU cc_start: 0.8293 (mt-10) cc_final: 0.8064 (mt-10) REVERT: A 275 ARG cc_start: 0.7635 (tmm160) cc_final: 0.6932 (tpt170) REVERT: A 336 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.7690 (mtt180) REVERT: A 341 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7708 (mp-120) REVERT: A 477 ILE cc_start: 0.9028 (OUTLIER) cc_final: 0.8752 (tp) REVERT: A 566 LYS cc_start: 0.8321 (tttp) cc_final: 0.8012 (ttmp) REVERT: B 9 LYS cc_start: 0.7245 (ttpt) cc_final: 0.6439 (ttpt) REVERT: B 76 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.7337 (mtt90) REVERT: C 93 GLN cc_start: 0.8652 (mt0) cc_final: 0.7297 (pm20) outliers start: 14 outliers final: 2 residues processed: 95 average time/residue: 2.9443 time to fit residues: 297.9255 Evaluate side-chains 99 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 93 time to evaluate : 1.206 ------------------------------------------------------------------------------- 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 A residue 470 LYS Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain B residue 76 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 61 optimal weight: 9.9990 chunk 50 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 110 optimal weight: 8.9990 chunk 49 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 6 optimal weight: 20.0000 chunk 97 optimal weight: 7.9990 chunk 79 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 ASN A 620 HIS B 80 GLN C 135 ASN C 137 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.174545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.132505 restraints weight = 12181.471| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 0.80 r_work: 0.3239 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14385 Z= 0.230 Angle : 0.647 6.681 20907 Z= 0.350 Chirality : 0.041 0.345 2524 Planarity : 0.004 0.036 1532 Dihedral : 23.967 179.026 5469 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.88 % Allowed : 11.84 % Favored : 86.27 % 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: 1.56 (0.29), residues: 843 helix: 1.50 (0.22), residues: 505 sheet: 0.73 (0.66), residues: 63 loop : 0.42 (0.39), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 382 HIS 0.005 0.001 HIS A 620 PHE 0.019 0.002 PHE A 214 TYR 0.020 0.002 TYR A 91 ARG 0.003 0.001 ARG A 218 Details of bonding type rmsd hydrogen bonds : bond 0.05161 ( 681) hydrogen bonds : angle 3.46943 ( 1686) metal coordination : bond 0.01036 ( 8) metal coordination : angle 2.92104 ( 9) covalent geometry : bond 0.00478 (14377) covalent geometry : angle 0.64404 (20898) *********************** 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 101 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 3.355 Fit side-chains REVERT: A 230 GLU cc_start: 0.8277 (mt-10) cc_final: 0.8052 (mt-10) REVERT: A 275 ARG cc_start: 0.7677 (tmm160) cc_final: 0.6974 (tpp80) REVERT: A 336 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.7664 (mtt180) REVERT: A 341 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.7687 (mp-120) REVERT: A 420 GLN cc_start: 0.7579 (OUTLIER) cc_final: 0.7268 (tm-30) REVERT: A 477 ILE cc_start: 0.9019 (OUTLIER) cc_final: 0.8743 (tp) REVERT: A 566 LYS cc_start: 0.8331 (tttp) cc_final: 0.8015 (ttmp) REVERT: B 9 LYS cc_start: 0.7256 (ttpt) cc_final: 0.6426 (ttpt) REVERT: C 93 GLN cc_start: 0.8650 (mt0) cc_final: 0.7317 (pm20) outliers start: 14 outliers final: 2 residues processed: 92 average time/residue: 3.3860 time to fit residues: 335.0048 Evaluate side-chains 91 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 1.070 ------------------------------------------------------------------------------- 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 A residue 420 GLN Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 477 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 84 optimal weight: 10.0000 chunk 60 optimal weight: 3.9990 chunk 28 optimal weight: 8.9990 chunk 50 optimal weight: 5.9990 chunk 21 optimal weight: 40.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 ASN A 620 HIS B 80 GLN C 137 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.175030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.132523 restraints weight = 12085.223| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 0.80 r_work: 0.3247 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14385 Z= 0.209 Angle : 0.628 6.666 20907 Z= 0.340 Chirality : 0.040 0.333 2524 Planarity : 0.004 0.036 1532 Dihedral : 23.955 178.963 5469 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.75 % Allowed : 12.38 % 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: 1.68 (0.29), residues: 843 helix: 1.61 (0.22), residues: 505 sheet: 0.73 (0.66), residues: 63 loop : 0.44 (0.39), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 382 HIS 0.005 0.001 HIS A 620 PHE 0.017 0.002 PHE A 214 TYR 0.019 0.002 TYR A 91 ARG 0.003 0.001 ARG B 39 Details of bonding type rmsd hydrogen bonds : bond 0.04988 ( 681) hydrogen bonds : angle 3.41742 ( 1686) metal coordination : bond 0.00897 ( 8) metal coordination : angle 2.72742 ( 9) covalent geometry : bond 0.00433 (14377) covalent geometry : angle 0.62522 (20898) *********************** 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 102 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 1.036 Fit side-chains REVERT: A 230 GLU cc_start: 0.8258 (mt-10) cc_final: 0.8049 (mt-10) REVERT: A 275 ARG cc_start: 0.7661 (tmm160) cc_final: 0.6954 (tpp80) REVERT: A 336 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.7671 (mtt180) REVERT: A 341 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.7678 (mp-120) REVERT: A 420 GLN cc_start: 0.7564 (OUTLIER) cc_final: 0.7238 (tm-30) REVERT: A 566 LYS cc_start: 0.8323 (tttp) cc_final: 0.7995 (ttmp) REVERT: B 9 LYS cc_start: 0.7264 (ttpt) cc_final: 0.6365 (ttpt) REVERT: C 83 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7756 (mt0) REVERT: C 93 GLN cc_start: 0.8638 (mt0) cc_final: 0.7270 (pm20) outliers start: 13 outliers final: 3 residues processed: 94 average time/residue: 2.1676 time to fit residues: 215.4955 Evaluate side-chains 95 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR 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 A residue 420 GLN Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain C residue 83 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 2 optimal weight: 40.0000 chunk 68 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 chunk 26 optimal weight: 20.0000 chunk 80 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 64 optimal weight: 9.9990 chunk 77 optimal weight: 0.0270 chunk 48 optimal weight: 0.9990 chunk 16 optimal weight: 10.0000 chunk 105 optimal weight: 0.9980 overall best weight: 1.0044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 ASN A 620 HIS B 80 GLN C 137 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.182415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.141114 restraints weight = 12437.838| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 0.83 r_work: 0.3377 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14385 Z= 0.117 Angle : 0.526 6.092 20907 Z= 0.287 Chirality : 0.033 0.271 2524 Planarity : 0.004 0.039 1532 Dihedral : 23.847 179.075 5469 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 0.67 % Allowed : 13.59 % Favored : 85.73 % 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: 2.12 (0.23), residues: 506 sheet: 0.79 (0.67), residues: 63 loop : 0.55 (0.39), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 111 HIS 0.004 0.001 HIS A 620 PHE 0.012 0.001 PHE A 13 TYR 0.013 0.001 TYR A 91 ARG 0.005 0.000 ARG A 100 Details of bonding type rmsd hydrogen bonds : bond 0.03886 ( 681) hydrogen bonds : angle 3.16282 ( 1686) metal coordination : bond 0.00483 ( 8) metal coordination : angle 2.12253 ( 9) covalent geometry : bond 0.00234 (14377) covalent geometry : angle 0.52443 (20898) *********************** 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 101 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 96 time to evaluate : 1.066 Fit side-chains REVERT: A 144 MET cc_start: 0.4250 (pp-130) cc_final: 0.3965 (mtm) REVERT: A 226 GLN cc_start: 0.7974 (tm-30) cc_final: 0.7682 (tp-100) REVERT: A 275 ARG cc_start: 0.7519 (tmm160) cc_final: 0.6841 (tpp80) REVERT: A 341 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.7686 (mp-120) REVERT: A 566 LYS cc_start: 0.8131 (tttp) cc_final: 0.7839 (ttmp) REVERT: B 9 LYS cc_start: 0.6953 (ttpt) cc_final: 0.6116 (ttpt) REVERT: B 15 ASN cc_start: 0.7990 (t0) cc_final: 0.7570 (t0) REVERT: C 93 GLN cc_start: 0.8573 (mt0) cc_final: 0.7211 (pm20) outliers start: 5 outliers final: 0 residues processed: 96 average time/residue: 2.1064 time to fit residues: 214.4211 Evaluate side-chains 93 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 92 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 1 optimal weight: 30.0000 chunk 33 optimal weight: 4.9990 chunk 105 optimal weight: 0.8980 chunk 112 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 99 optimal weight: 9.9990 chunk 6 optimal weight: 30.0000 chunk 48 optimal weight: 7.9990 chunk 32 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 ASN B 80 GLN C 137 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.179409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.137619 restraints weight = 12144.114| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 0.79 r_work: 0.3311 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14385 Z= 0.142 Angle : 0.547 6.016 20907 Z= 0.298 Chirality : 0.035 0.291 2524 Planarity : 0.004 0.039 1532 Dihedral : 23.827 179.817 5469 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 0.27 % Allowed : 13.86 % 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: 2.32 (0.29), residues: 843 helix: 2.23 (0.22), residues: 504 sheet: 0.67 (0.66), residues: 63 loop : 0.55 (0.39), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 111 HIS 0.003 0.001 HIS A 304 PHE 0.014 0.001 PHE A 13 TYR 0.015 0.001 TYR A 91 ARG 0.004 0.000 ARG A 100 Details of bonding type rmsd hydrogen bonds : bond 0.04213 ( 681) hydrogen bonds : angle 3.19782 ( 1686) metal coordination : bond 0.00499 ( 8) metal coordination : angle 2.15072 ( 9) covalent geometry : bond 0.00288 (14377) covalent geometry : angle 0.54505 (20898) *********************** 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 to be fit. rotamer outliers: 2 poor density : 95 time to evaluate : 0.950 Fit side-chains REVERT: A 144 MET cc_start: 0.4315 (pp-130) cc_final: 0.4081 (mtm) REVERT: A 226 GLN cc_start: 0.8024 (tt0) cc_final: 0.7740 (tp-100) REVERT: A 275 ARG cc_start: 0.7577 (tmm160) cc_final: 0.6866 (tpp80) REVERT: A 341 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.7710 (mp-120) REVERT: A 456 GLU cc_start: 0.8017 (mp0) cc_final: 0.7612 (tp30) REVERT: A 477 ILE cc_start: 0.8962 (OUTLIER) cc_final: 0.8739 (tp) REVERT: A 566 LYS cc_start: 0.8218 (tttp) cc_final: 0.7928 (ttmp) REVERT: A 612 LYS cc_start: 0.7726 (tptt) cc_final: 0.7291 (ttpt) REVERT: B 9 LYS cc_start: 0.7097 (ttpt) cc_final: 0.6254 (ttpt) REVERT: C 93 GLN cc_start: 0.8589 (mt0) cc_final: 0.7220 (pm20) outliers start: 2 outliers final: 0 residues processed: 96 average time/residue: 2.1437 time to fit residues: 217.8852 Evaluate side-chains 94 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 92 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain A residue 477 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 87 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 81 optimal weight: 0.9990 chunk 9 optimal weight: 10.0000 chunk 94 optimal weight: 0.0870 chunk 80 optimal weight: 0.9990 chunk 20 optimal weight: 20.0000 chunk 29 optimal weight: 8.9990 chunk 55 optimal weight: 0.5980 chunk 53 optimal weight: 0.5980 chunk 109 optimal weight: 0.1980 overall best weight: 0.4960 ------------------------------------------------------------------------------- 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 = 0.4071 r_free = 0.4071 target = 0.185973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.145612 restraints weight = 12544.667| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 0.76 r_work: 0.3433 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 14385 Z= 0.110 Angle : 0.513 5.856 20907 Z= 0.278 Chirality : 0.032 0.248 2524 Planarity : 0.003 0.039 1532 Dihedral : 23.771 178.676 5469 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 0.67 % Allowed : 13.59 % Favored : 85.73 % 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: 2.56 (0.29), residues: 843 helix: 2.45 (0.23), residues: 507 sheet: 0.37 (0.65), residues: 68 loop : 0.70 (0.40), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 111 HIS 0.004 0.001 HIS A 304 PHE 0.009 0.001 PHE A 13 TYR 0.009 0.001 TYR A 474 ARG 0.005 0.000 ARG A 100 Details of bonding type rmsd hydrogen bonds : bond 0.03757 ( 681) hydrogen bonds : angle 3.10695 ( 1686) metal coordination : bond 0.00272 ( 8) metal coordination : angle 1.77238 ( 9) covalent geometry : bond 0.00219 (14377) covalent geometry : angle 0.51206 (20898) ********************** 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 103 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 98 time to evaluate : 0.930 Fit side-chains REVERT: A 226 GLN cc_start: 0.7903 (tt0) cc_final: 0.7700 (tp-100) REVERT: A 275 ARG cc_start: 0.7384 (tmm160) cc_final: 0.6637 (tpt170) REVERT: A 477 ILE cc_start: 0.8915 (OUTLIER) cc_final: 0.8689 (tp) REVERT: A 566 LYS cc_start: 0.8078 (tttp) cc_final: 0.7764 (ttmp) REVERT: A 572 GLU cc_start: 0.7678 (tp30) cc_final: 0.7417 (tm-30) REVERT: A 612 LYS cc_start: 0.7653 (tptt) cc_final: 0.7300 (ttpt) REVERT: B 15 ASN cc_start: 0.7869 (t0) cc_final: 0.7554 (t0) REVERT: C 93 GLN cc_start: 0.8507 (mt0) cc_final: 0.7131 (pm20) outliers start: 5 outliers final: 1 residues processed: 100 average time/residue: 1.9940 time to fit residues: 211.7863 Evaluate side-chains 98 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 96 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain C residue 73 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 111 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 72 optimal weight: 0.0020 chunk 66 optimal weight: 4.9990 chunk 89 optimal weight: 7.9990 chunk 113 optimal weight: 9.9990 chunk 2 optimal weight: 40.0000 chunk 13 optimal weight: 10.0000 chunk 70 optimal weight: 0.0770 chunk 52 optimal weight: 10.0000 overall best weight: 2.8152 ------------------------------------------------------------------------------- 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 = 0.3995 r_free = 0.3995 target = 0.178140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.136263 restraints weight = 12272.759| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 0.81 r_work: 0.3289 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14385 Z= 0.168 Angle : 0.570 7.068 20907 Z= 0.309 Chirality : 0.036 0.307 2524 Planarity : 0.004 0.037 1532 Dihedral : 23.787 179.678 5469 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 0.67 % Allowed : 13.46 % 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: 2.39 (0.29), residues: 843 helix: 2.31 (0.22), residues: 505 sheet: 0.46 (0.65), residues: 63 loop : 0.58 (0.39), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 111 HIS 0.003 0.001 HIS A 304 PHE 0.016 0.002 PHE A 13 TYR 0.018 0.002 TYR A 91 ARG 0.007 0.000 ARG B 39 Details of bonding type rmsd hydrogen bonds : bond 0.04477 ( 681) hydrogen bonds : angle 3.24828 ( 1686) metal coordination : bond 0.00688 ( 8) metal coordination : angle 2.25299 ( 9) covalent geometry : bond 0.00345 (14377) covalent geometry : angle 0.56862 (20898) =============================================================================== Job complete usr+sys time: 15167.83 seconds wall clock time: 265 minutes 53.91 seconds (15953.91 seconds total)