Starting phenix.real_space_refine on Mon Nov 18 16:44:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cf1_45526/11_2024/9cf1_45526_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cf1_45526/11_2024/9cf1_45526.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cf1_45526/11_2024/9cf1_45526.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cf1_45526/11_2024/9cf1_45526.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cf1_45526/11_2024/9cf1_45526_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cf1_45526/11_2024/9cf1_45526_neut.cif" } resolution = 3.52 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.038 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 82 5.49 5 S 35 5.16 5 C 5416 2.51 5 N 1570 2.21 5 O 1836 1.98 5 H 8199 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 17138 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 2426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 2426 Classifications: {'peptide': 162} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 10, 'TRANS': 151} Chain: "N" Number of atoms: 349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 349 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "P" Number of atoms: 12097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 12097 Classifications: {'peptide': 726} Link IDs: {'PTRANS': 26, 'TRANS': 699} Chain breaks: 1 Chain: "T" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 639 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "W" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 1627 Classifications: {'DNA': 10, 'RNA': 41} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 17, 'rna3p_pyr': 13} Link IDs: {'rna2p': 11, 'rna3p': 39} Time building chain proxies: 8.22, per 1000 atoms: 0.48 Number of scatterers: 17138 At special positions: 0 Unit cell: (80.025, 118.8, 122.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 35 16.00 P 82 15.00 O 1836 8.00 N 1570 7.00 C 5416 6.00 H 8199 1.00 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: 4.94 Conformation dependent library (CDL) restraints added in 1.3 seconds 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1684 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 7 sheets defined 53.8% alpha, 11.8% beta 28 base pairs and 43 stacking pairs defined. Time for finding SS restraints: 9.86 Creating SS restraints... Processing helix chain 'B' and resid 27 through 40 Processing helix chain 'B' and resid 117 through 121 Processing helix chain 'B' and resid 133 through 143 Processing helix chain 'P' and resid 114 through 118 Processing helix chain 'P' and resid 119 through 121 No H-bonds generated for 'chain 'P' and resid 119 through 121' Processing helix chain 'P' and resid 122 through 155 removed outlier: 3.633A pdb=" N LEU P 135 " --> pdb=" O HIS P 131 " (cutoff:3.500A) Processing helix chain 'P' and resid 159 through 163 Processing helix chain 'P' and resid 165 through 176 removed outlier: 3.726A pdb=" N LEU P 176 " --> pdb=" O VAL P 172 " (cutoff:3.500A) Processing helix chain 'P' and resid 183 through 187 Processing helix chain 'P' and resid 188 through 209 removed outlier: 3.837A pdb=" N HIS P 201 " --> pdb=" O LEU P 197 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ASP P 203 " --> pdb=" O GLY P 199 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ALA P 204 " --> pdb=" O LYS P 200 " (cutoff:3.500A) Processing helix chain 'P' and resid 219 through 254 removed outlier: 3.615A pdb=" N LYS P 229 " --> pdb=" O TYR P 225 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA P 240 " --> pdb=" O ASN P 236 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N GLY P 243 " --> pdb=" O LYS P 239 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ASN P 244 " --> pdb=" O ALA P 240 " (cutoff:3.500A) Processing helix chain 'P' and resid 255 through 270 Processing helix chain 'P' and resid 273 through 285 Processing helix chain 'P' and resid 285 through 298 Processing helix chain 'P' and resid 308 through 321 Processing helix chain 'P' and resid 328 through 331 Processing helix chain 'P' and resid 332 through 340 removed outlier: 3.707A pdb=" N VAL P 338 " --> pdb=" O PHE P 334 " (cutoff:3.500A) Processing helix chain 'P' and resid 341 through 343 No H-bonds generated for 'chain 'P' and resid 341 through 343' Processing helix chain 'P' and resid 344 through 358 Processing helix chain 'P' and resid 381 through 388 Processing helix chain 'P' and resid 396 through 398 No H-bonds generated for 'chain 'P' and resid 396 through 398' Processing helix chain 'P' and resid 399 through 408 removed outlier: 3.995A pdb=" N VAL P 407 " --> pdb=" O ALA P 403 " (cutoff:3.500A) Processing helix chain 'P' and resid 412 through 416 Processing helix chain 'P' and resid 419 through 423 Processing helix chain 'P' and resid 466 through 470 Processing helix chain 'P' and resid 471 through 478 Processing helix chain 'P' and resid 512 through 516 Processing helix chain 'P' and resid 516 through 530 Processing helix chain 'P' and resid 531 through 543 Processing helix chain 'P' and resid 550 through 574 removed outlier: 3.553A pdb=" N VAL P 564 " --> pdb=" O ALA P 560 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ASP P 566 " --> pdb=" O ALA P 562 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ILE P 567 " --> pdb=" O SER P 563 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU P 568 " --> pdb=" O VAL P 564 " (cutoff:3.500A) Processing helix chain 'P' and resid 622 through 639 removed outlier: 4.208A pdb=" N LYS P 626 " --> pdb=" O ASP P 622 " (cutoff:3.500A) Processing helix chain 'P' and resid 640 through 645 Processing helix chain 'P' and resid 648 through 665 Processing helix chain 'P' and resid 668 through 680 removed outlier: 3.866A pdb=" N LYS P 672 " --> pdb=" O GLU P 668 " (cutoff:3.500A) Processing helix chain 'P' and resid 681 through 684 Processing helix chain 'P' and resid 686 through 713 removed outlier: 3.505A pdb=" N LYS P 711 " --> pdb=" O LYS P 707 " (cutoff:3.500A) Processing helix chain 'P' and resid 737 through 747 removed outlier: 3.734A pdb=" N ARG P 741 " --> pdb=" O ASN P 737 " (cutoff:3.500A) Processing helix chain 'P' and resid 782 through 787 removed outlier: 4.159A pdb=" N LYS P 786 " --> pdb=" O HIS P 782 " (cutoff:3.500A) Processing helix chain 'P' and resid 800 through 806 removed outlier: 4.207A pdb=" N GLN P 806 " --> pdb=" O CYS P 803 " (cutoff:3.500A) Processing helix chain 'P' and resid 818 through 837 Processing helix chain 'P' and resid 840 through 844 Processing sheet with id=AA1, first strand: chain 'B' and resid 53 through 55 removed outlier: 4.104A pdb=" N LEU B 95 " --> pdb=" O THR B 113 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU B 96 " --> pdb=" O PHE B 127 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL B 19 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ALA B 10 " --> pdb=" O PRO B 14 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY B 16 " --> pdb=" O VAL B 8 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS B 158 " --> pdb=" O ASP B 7 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLU B 9 " --> pdb=" O VAL B 156 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N VAL B 156 " --> pdb=" O GLU B 9 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'P' and resid 107 through 113 removed outlier: 3.858A pdb=" N LEU P 440 " --> pdb=" O THR P 429 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N THR P 429 " --> pdb=" O LEU P 440 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N GLN P 442 " --> pdb=" O GLN P 427 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N GLN P 427 " --> pdb=" O GLN P 442 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'P' and resid 177 through 178 Processing sheet with id=AA4, first strand: chain 'P' and resid 507 through 511 removed outlier: 6.222A pdb=" N LEU P 719 " --> pdb=" O TYR P 752 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N ILE P 754 " --> pdb=" O LEU P 719 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N LEU P 721 " --> pdb=" O ILE P 754 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'P' and resid 591 through 593 removed outlier: 6.207A pdb=" N TYR P 601 " --> pdb=" O PHE P 605 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N PHE P 605 " --> pdb=" O TYR P 601 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'P' and resid 770 through 771 Processing sheet with id=AA7, first strand: chain 'P' and resid 775 through 777 364 hydrogen bonds defined for protein. 1023 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 72 hydrogen bonds 144 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 43 stacking parallelities Total time for adding SS restraints: 8.04 Time building geometry restraints manager: 5.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.92 - 1.10: 8182 1.10 - 1.28: 1247 1.28 - 1.46: 3374 1.46 - 1.64: 4645 1.64 - 1.82: 53 Bond restraints: 17501 Sorted by residual: bond pdb=" C8 DA W 48 " pdb=" H8 DA W 48 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" C5 U W 31 " pdb=" H5 U W 31 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N CYS P 792 " pdb=" H CYS P 792 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N6 DA W 46 " pdb=" H61 DA W 46 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" CE3 TRP P 724 " pdb=" HE3 TRP P 724 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.67e+01 ... (remaining 17496 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.85: 27772 2.85 - 5.70: 3120 5.70 - 8.55: 716 8.55 - 11.40: 20 11.40 - 14.25: 14 Bond angle restraints: 31642 Sorted by residual: angle pdb=" O3' U W 31 " pdb=" C3' U W 31 " pdb=" C2' U W 31 " ideal model delta sigma weight residual 109.50 123.75 -14.25 1.50e+00 4.44e-01 9.02e+01 angle pdb=" O3' U W 30 " pdb=" C3' U W 30 " pdb=" C2' U W 30 " ideal model delta sigma weight residual 109.50 121.78 -12.28 1.50e+00 4.44e-01 6.71e+01 angle pdb=" CA PHE P 826 " pdb=" CB PHE P 826 " pdb=" CG PHE P 826 " ideal model delta sigma weight residual 113.80 121.87 -8.07 1.00e+00 1.00e+00 6.51e+01 angle pdb=" CA ASP P 769 " pdb=" CB ASP P 769 " pdb=" CG ASP P 769 " ideal model delta sigma weight residual 112.60 120.06 -7.46 1.00e+00 1.00e+00 5.56e+01 angle pdb=" CA PRO P 103 " pdb=" N PRO P 103 " pdb=" CD PRO P 103 " ideal model delta sigma weight residual 112.00 102.24 9.76 1.40e+00 5.10e-01 4.86e+01 ... (remaining 31637 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.44: 7584 35.44 - 70.88: 459 70.88 - 106.32: 30 106.32 - 141.75: 9 141.75 - 177.19: 7 Dihedral angle restraints: 8089 sinusoidal: 4963 harmonic: 3126 Sorted by residual: dihedral pdb=" C5' A W 32 " pdb=" C4' A W 32 " pdb=" C3' A W 32 " pdb=" O3' A W 32 " ideal model delta sinusoidal sigma weight residual 147.00 75.55 71.45 1 8.00e+00 1.56e-02 1.02e+02 dihedral pdb=" O4' A W 32 " pdb=" C4' A W 32 " pdb=" C3' A W 32 " pdb=" C2' A W 32 " ideal model delta sinusoidal sigma weight residual 24.00 -38.49 62.49 1 8.00e+00 1.56e-02 8.07e+01 dihedral pdb=" C5' A W 29 " pdb=" C4' A W 29 " pdb=" C3' A W 29 " pdb=" O3' A W 29 " ideal model delta sinusoidal sigma weight residual 147.00 88.16 58.84 1 8.00e+00 1.56e-02 7.24e+01 ... (remaining 8086 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 1012 0.094 - 0.188: 345 0.188 - 0.281: 63 0.281 - 0.375: 11 0.375 - 0.469: 3 Chirality restraints: 1434 Sorted by residual: chirality pdb=" CA TYR P 613 " pdb=" N TYR P 613 " pdb=" C TYR P 613 " pdb=" CB TYR P 613 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.49e+00 chirality pdb=" C3' U W 31 " pdb=" C4' U W 31 " pdb=" O3' U W 31 " pdb=" C2' U W 31 " both_signs ideal model delta sigma weight residual False -2.74 -2.33 -0.41 2.00e-01 2.50e+01 4.24e+00 chirality pdb=" C3' DT T 0 " pdb=" C4' DT T 0 " pdb=" O3' DT T 0 " pdb=" C2' DT T 0 " both_signs ideal model delta sigma weight residual False -2.66 -2.27 -0.39 2.00e-01 2.50e+01 3.82e+00 ... (remaining 1431 not shown) Planarity restraints: 2263 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C W 18 " -0.576 2.00e-02 2.50e+03 2.48e-01 1.69e+03 pdb=" N1 C W 18 " 0.014 2.00e-02 2.50e+03 pdb=" C2 C W 18 " 0.110 2.00e-02 2.50e+03 pdb=" O2 C W 18 " 0.375 2.00e-02 2.50e+03 pdb=" N3 C W 18 " -0.040 2.00e-02 2.50e+03 pdb=" C4 C W 18 " -0.080 2.00e-02 2.50e+03 pdb=" N4 C W 18 " -0.326 2.00e-02 2.50e+03 pdb=" C5 C W 18 " 0.077 2.00e-02 2.50e+03 pdb=" C6 C W 18 " 0.112 2.00e-02 2.50e+03 pdb=" H5 C W 18 " 0.150 2.00e-02 2.50e+03 pdb=" H6 C W 18 " 0.184 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G W 19 " 0.534 2.00e-02 2.50e+03 1.90e-01 1.27e+03 pdb=" N9 G W 19 " -0.046 2.00e-02 2.50e+03 pdb=" C8 G W 19 " -0.134 2.00e-02 2.50e+03 pdb=" N7 G W 19 " -0.151 2.00e-02 2.50e+03 pdb=" C5 G W 19 " -0.058 2.00e-02 2.50e+03 pdb=" C6 G W 19 " 0.098 2.00e-02 2.50e+03 pdb=" O6 G W 19 " 0.306 2.00e-02 2.50e+03 pdb=" N1 G W 19 " 0.007 2.00e-02 2.50e+03 pdb=" C2 G W 19 " -0.067 2.00e-02 2.50e+03 pdb=" N2 G W 19 " -0.109 2.00e-02 2.50e+03 pdb=" N3 G W 19 " -0.145 2.00e-02 2.50e+03 pdb=" C4 G W 19 " -0.119 2.00e-02 2.50e+03 pdb=" H8 G W 19 " -0.142 2.00e-02 2.50e+03 pdb=" H1 G W 19 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U W 30 " 0.482 2.00e-02 2.50e+03 1.90e-01 1.08e+03 pdb=" N1 U W 30 " -0.042 2.00e-02 2.50e+03 pdb=" C2 U W 30 " -0.134 2.00e-02 2.50e+03 pdb=" O2 U W 30 " -0.182 2.00e-02 2.50e+03 pdb=" N3 U W 30 " -0.102 2.00e-02 2.50e+03 pdb=" C4 U W 30 " 0.064 2.00e-02 2.50e+03 pdb=" O4 U W 30 " 0.302 2.00e-02 2.50e+03 pdb=" C5 U W 30 " -0.055 2.00e-02 2.50e+03 pdb=" C6 U W 30 " -0.118 2.00e-02 2.50e+03 pdb=" H5 U W 30 " -0.056 2.00e-02 2.50e+03 pdb=" H3 U W 30 " -0.013 2.00e-02 2.50e+03 pdb=" H6 U W 30 " -0.145 2.00e-02 2.50e+03 ... (remaining 2260 not shown) Histogram of nonbonded interaction distances: 1.36 - 2.01: 522 2.01 - 2.65: 19700 2.65 - 3.30: 51926 3.30 - 3.95: 67667 3.95 - 4.60: 100314 Nonbonded interactions: 240129 Sorted by model distance: nonbonded pdb=" OH TYR P 225 " pdb=" O2 DT T 0 " model vdw 1.358 2.800 nonbonded pdb="HO2' A W 16 " pdb=" OP1 U W 17 " model vdw 1.560 2.450 nonbonded pdb="HO2' U W 30 " pdb=" OP1 U W 31 " model vdw 1.566 2.450 nonbonded pdb="HO2' A W 7 " pdb=" OP1 C W 8 " model vdw 1.568 2.450 nonbonded pdb=" HG1 THR P 499 " pdb=" OE1 GLU P 506 " model vdw 1.569 2.450 ... (remaining 240124 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 group one per residue 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: 1.200 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: 0.260 Extract box with map and model: 0.640 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 48.300 Find NCS groups from input model: 0.130 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5947 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 : 0.013 0.052 9302 Z= 0.778 Angle : 1.844 14.246 12894 Z= 1.225 Chirality : 0.096 0.469 1434 Planarity : 0.024 0.245 1352 Dihedral : 20.920 177.192 3882 Min Nonbonded Distance : 1.358 Molprobity Statistics. All-atom Clashscore : 1.05 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.01 % Favored : 93.54 % Rotamer: Outliers : 0.76 % Allowed : 3.28 % Favored : 95.96 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % 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: -1.31 (0.26), residues: 882 helix: -0.72 (0.22), residues: 402 sheet: -0.90 (0.55), residues: 67 loop : -0.86 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.100 0.029 TRP P 724 HIS 0.012 0.003 HIS P 667 PHE 0.061 0.014 PHE B 111 TYR 0.148 0.020 TYR P 146 ARG 0.009 0.001 ARG B 53 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Evaluate side-chains 197 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 191 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 523 ARG cc_start: 0.7826 (ttp-170) cc_final: 0.7547 (ttt180) outliers start: 6 outliers final: 2 residues processed: 194 average time/residue: 0.7051 time to fit residues: 171.4865 Evaluate side-chains 110 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 108 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 810 GLU Chi-restraints excluded: chain P residue 814 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 595 GLN P 665 GLN P 825 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5895 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9302 Z= 0.238 Angle : 0.762 8.290 12894 Z= 0.421 Chirality : 0.045 0.236 1434 Planarity : 0.005 0.060 1352 Dihedral : 24.115 172.139 2031 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.85 % Favored : 96.03 % Rotamer: Outliers : 1.01 % Allowed : 8.96 % Favored : 90.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.30 (0.27), residues: 882 helix: 0.82 (0.24), residues: 404 sheet: -0.96 (0.46), residues: 91 loop : -1.06 (0.30), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP P 816 HIS 0.004 0.001 HIS P 201 PHE 0.025 0.002 PHE P 143 TYR 0.023 0.002 TYR P 349 ARG 0.004 0.001 ARG P 489 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Evaluate side-chains 126 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 118 time to evaluate : 1.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 397 MET cc_start: 0.6853 (ptt) cc_final: 0.6274 (ttp) REVERT: P 523 ARG cc_start: 0.7810 (ttp-170) cc_final: 0.7069 (mtm-85) REVERT: P 575 GLU cc_start: 0.7458 (mt-10) cc_final: 0.6903 (mt-10) outliers start: 8 outliers final: 6 residues processed: 122 average time/residue: 0.6761 time to fit residues: 105.9700 Evaluate side-chains 101 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 95 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain P residue 108 ILE Chi-restraints excluded: chain P residue 410 LEU Chi-restraints excluded: chain P residue 675 ILE Chi-restraints excluded: chain P residue 709 ILE Chi-restraints excluded: chain P residue 814 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 94 optimal weight: 7.9990 chunk 77 optimal weight: 4.9990 chunk 86 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 52 HIS P 300 ASN P 603 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6094 moved from start: 0.4701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 9302 Z= 0.369 Angle : 0.754 9.853 12894 Z= 0.421 Chirality : 0.046 0.229 1434 Planarity : 0.005 0.049 1352 Dihedral : 23.679 170.899 2028 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.56 % Favored : 94.33 % Rotamer: Outliers : 2.15 % Allowed : 9.97 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.72 (0.27), residues: 882 helix: 0.62 (0.25), residues: 409 sheet: -1.29 (0.45), residues: 91 loop : -1.45 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP P 724 HIS 0.006 0.002 HIS P 131 PHE 0.027 0.003 PHE P 158 TYR 0.020 0.002 TYR P 141 ARG 0.004 0.001 ARG P 758 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Evaluate side-chains 110 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 494 TYR cc_start: 0.7572 (t80) cc_final: 0.7274 (t80) REVERT: P 575 GLU cc_start: 0.7590 (mt-10) cc_final: 0.6989 (mt-10) outliers start: 17 outliers final: 9 residues processed: 103 average time/residue: 0.5007 time to fit residues: 70.4875 Evaluate side-chains 82 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain P residue 108 ILE Chi-restraints excluded: chain P residue 448 ARG Chi-restraints excluded: chain P residue 467 ILE Chi-restraints excluded: chain P residue 590 ASP Chi-restraints excluded: chain P residue 709 ILE Chi-restraints excluded: chain P residue 776 ILE Chi-restraints excluded: chain P residue 790 VAL Chi-restraints excluded: chain P residue 814 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 92 optimal weight: 8.9990 chunk 83 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 300 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6039 moved from start: 0.5120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9302 Z= 0.253 Angle : 0.655 8.242 12894 Z= 0.364 Chirality : 0.042 0.183 1434 Planarity : 0.005 0.050 1352 Dihedral : 23.481 177.262 2028 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.10 % Favored : 94.78 % Rotamer: Outliers : 1.52 % Allowed : 11.49 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.32 (0.28), residues: 882 helix: 1.03 (0.25), residues: 407 sheet: -1.53 (0.44), residues: 90 loop : -1.21 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP P 724 HIS 0.003 0.001 HIS P 201 PHE 0.020 0.002 PHE P 318 TYR 0.014 0.001 TYR P 205 ARG 0.002 0.000 ARG P 780 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Evaluate side-chains 94 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 494 TYR cc_start: 0.7287 (t80) cc_final: 0.7036 (t80) REVERT: P 575 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7022 (mt-10) REVERT: P 756 GLU cc_start: 0.5349 (OUTLIER) cc_final: 0.4789 (pt0) outliers start: 12 outliers final: 7 residues processed: 89 average time/residue: 0.5337 time to fit residues: 64.4684 Evaluate side-chains 87 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain P residue 108 ILE Chi-restraints excluded: chain P residue 448 ARG Chi-restraints excluded: chain P residue 709 ILE Chi-restraints excluded: chain P residue 756 GLU Chi-restraints excluded: chain P residue 776 ILE Chi-restraints excluded: chain P residue 790 VAL Chi-restraints excluded: chain P residue 814 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 8.9990 chunk 1 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 47 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 615 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6141 moved from start: 0.5630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 9302 Z= 0.358 Angle : 0.707 9.798 12894 Z= 0.392 Chirality : 0.044 0.184 1434 Planarity : 0.005 0.051 1352 Dihedral : 23.392 177.160 2028 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.03 % Favored : 92.86 % Rotamer: Outliers : 2.27 % Allowed : 11.24 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.74 (0.27), residues: 882 helix: 0.77 (0.25), residues: 401 sheet: -1.62 (0.46), residues: 91 loop : -1.54 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP P 724 HIS 0.005 0.001 HIS B 124 PHE 0.022 0.002 PHE P 158 TYR 0.017 0.002 TYR P 141 ARG 0.004 0.001 ARG P 758 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Evaluate side-chains 91 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 756 GLU cc_start: 0.5686 (OUTLIER) cc_final: 0.5188 (pt0) REVERT: P 810 GLU cc_start: 0.4436 (OUTLIER) cc_final: 0.3334 (tt0) outliers start: 18 outliers final: 10 residues processed: 83 average time/residue: 0.4881 time to fit residues: 57.0919 Evaluate side-chains 81 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain P residue 108 ILE Chi-restraints excluded: chain P residue 388 ILE Chi-restraints excluded: chain P residue 448 ARG Chi-restraints excluded: chain P residue 590 ASP Chi-restraints excluded: chain P residue 709 ILE Chi-restraints excluded: chain P residue 720 VAL Chi-restraints excluded: chain P residue 756 GLU Chi-restraints excluded: chain P residue 776 ILE Chi-restraints excluded: chain P residue 790 VAL Chi-restraints excluded: chain P residue 810 GLU Chi-restraints excluded: chain P residue 814 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 7 optimal weight: 9.9990 chunk 30 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5999 moved from start: 0.5843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9302 Z= 0.175 Angle : 0.595 7.572 12894 Z= 0.327 Chirality : 0.039 0.189 1434 Planarity : 0.004 0.051 1352 Dihedral : 23.210 177.601 2028 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.97 % Favored : 95.92 % Rotamer: Outliers : 1.52 % Allowed : 12.50 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.14 (0.28), residues: 882 helix: 1.32 (0.25), residues: 408 sheet: -1.56 (0.46), residues: 90 loop : -1.27 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP P 724 HIS 0.004 0.001 HIS B 90 PHE 0.020 0.001 PHE P 318 TYR 0.013 0.001 TYR P 205 ARG 0.002 0.000 ARG P 489 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Evaluate side-chains 92 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 1.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 494 TYR cc_start: 0.7277 (t80) cc_final: 0.7030 (t80) REVERT: P 756 GLU cc_start: 0.5191 (OUTLIER) cc_final: 0.4785 (pt0) outliers start: 12 outliers final: 8 residues processed: 89 average time/residue: 0.5433 time to fit residues: 68.1437 Evaluate side-chains 85 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain P residue 410 LEU Chi-restraints excluded: chain P residue 448 ARG Chi-restraints excluded: chain P residue 492 LEU Chi-restraints excluded: chain P residue 709 ILE Chi-restraints excluded: chain P residue 756 GLU Chi-restraints excluded: chain P residue 790 VAL Chi-restraints excluded: chain P residue 804 LEU Chi-restraints excluded: chain P residue 814 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 10.0000 chunk 52 optimal weight: 7.9990 chunk 67 optimal weight: 10.0000 chunk 78 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 92 optimal weight: 9.9990 chunk 57 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 42 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 300 ASN P 615 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6139 moved from start: 0.6076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 9302 Z= 0.361 Angle : 0.680 9.518 12894 Z= 0.374 Chirality : 0.043 0.181 1434 Planarity : 0.005 0.051 1352 Dihedral : 23.312 177.478 2028 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.80 % Favored : 93.08 % Rotamer: Outliers : 2.15 % Allowed : 11.87 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.65 (0.27), residues: 882 helix: 0.96 (0.25), residues: 402 sheet: -1.69 (0.48), residues: 91 loop : -1.61 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 724 HIS 0.004 0.001 HIS B 124 PHE 0.019 0.002 PHE P 158 TYR 0.014 0.002 TYR P 141 ARG 0.005 0.001 ARG P 758 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Evaluate side-chains 89 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 1.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 618 HIS cc_start: 0.4584 (OUTLIER) cc_final: 0.4309 (t-170) REVERT: P 756 GLU cc_start: 0.5423 (OUTLIER) cc_final: 0.5097 (pt0) REVERT: P 810 GLU cc_start: 0.4347 (OUTLIER) cc_final: 0.3329 (tt0) outliers start: 17 outliers final: 10 residues processed: 86 average time/residue: 0.4211 time to fit residues: 53.6164 Evaluate side-chains 84 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain P residue 108 ILE Chi-restraints excluded: chain P residue 448 ARG Chi-restraints excluded: chain P residue 590 ASP Chi-restraints excluded: chain P residue 618 HIS Chi-restraints excluded: chain P residue 709 ILE Chi-restraints excluded: chain P residue 719 LEU Chi-restraints excluded: chain P residue 756 GLU Chi-restraints excluded: chain P residue 776 ILE Chi-restraints excluded: chain P residue 790 VAL Chi-restraints excluded: chain P residue 804 LEU Chi-restraints excluded: chain P residue 810 GLU Chi-restraints excluded: chain P residue 814 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 0.3980 chunk 18 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 chunk 72 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 88 optimal weight: 8.9990 chunk 80 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6006 moved from start: 0.6207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9302 Z= 0.172 Angle : 0.582 7.899 12894 Z= 0.318 Chirality : 0.038 0.193 1434 Planarity : 0.004 0.052 1352 Dihedral : 23.241 175.993 2028 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.20 % Favored : 95.69 % Rotamer: Outliers : 1.64 % Allowed : 12.37 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.08 (0.28), residues: 882 helix: 1.44 (0.25), residues: 409 sheet: -1.62 (0.48), residues: 90 loop : -1.32 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP P 724 HIS 0.003 0.001 HIS P 241 PHE 0.017 0.001 PHE P 318 TYR 0.011 0.001 TYR P 205 ARG 0.002 0.000 ARG P 646 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Evaluate side-chains 92 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 1.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 689 LYS cc_start: 0.7546 (mttt) cc_final: 0.6966 (mttp) REVERT: P 756 GLU cc_start: 0.5225 (OUTLIER) cc_final: 0.4918 (pt0) outliers start: 13 outliers final: 10 residues processed: 88 average time/residue: 0.4527 time to fit residues: 56.7312 Evaluate side-chains 84 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain P residue 140 THR Chi-restraints excluded: chain P residue 397 MET Chi-restraints excluded: chain P residue 410 LEU Chi-restraints excluded: chain P residue 448 ARG Chi-restraints excluded: chain P residue 590 ASP Chi-restraints excluded: chain P residue 709 ILE Chi-restraints excluded: chain P residue 719 LEU Chi-restraints excluded: chain P residue 756 GLU Chi-restraints excluded: chain P residue 790 VAL Chi-restraints excluded: chain P residue 804 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 6.9990 chunk 88 optimal weight: 7.9990 chunk 51 optimal weight: 8.9990 chunk 37 optimal weight: 0.0870 chunk 67 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 91 optimal weight: 8.9990 overall best weight: 2.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 615 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6106 moved from start: 0.6383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9302 Z= 0.294 Angle : 0.631 9.119 12894 Z= 0.347 Chirality : 0.041 0.191 1434 Planarity : 0.005 0.051 1352 Dihedral : 23.168 175.473 2024 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.58 % Favored : 93.31 % Rotamer: Outliers : 1.77 % Allowed : 12.50 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.42 (0.28), residues: 882 helix: 1.18 (0.25), residues: 409 sheet: -1.77 (0.49), residues: 89 loop : -1.54 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP P 724 HIS 0.004 0.001 HIS B 90 PHE 0.017 0.002 PHE P 158 TYR 0.012 0.001 TYR P 205 ARG 0.003 0.001 ARG P 758 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Evaluate side-chains 87 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 756 GLU cc_start: 0.5344 (OUTLIER) cc_final: 0.5113 (pt0) outliers start: 14 outliers final: 10 residues processed: 83 average time/residue: 0.3901 time to fit residues: 48.6181 Evaluate side-chains 82 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain P residue 108 ILE Chi-restraints excluded: chain P residue 140 THR Chi-restraints excluded: chain P residue 397 MET Chi-restraints excluded: chain P residue 448 ARG Chi-restraints excluded: chain P residue 590 ASP Chi-restraints excluded: chain P residue 709 ILE Chi-restraints excluded: chain P residue 719 LEU Chi-restraints excluded: chain P residue 756 GLU Chi-restraints excluded: chain P residue 790 VAL Chi-restraints excluded: chain P residue 804 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 0.6980 chunk 43 optimal weight: 0.0970 chunk 63 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 58 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 60 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5991 moved from start: 0.6509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9302 Z= 0.163 Angle : 0.566 7.801 12894 Z= 0.309 Chirality : 0.038 0.205 1434 Planarity : 0.004 0.051 1352 Dihedral : 23.031 175.901 2024 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.31 % Favored : 95.58 % Rotamer: Outliers : 1.14 % Allowed : 12.88 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.11 (0.28), residues: 882 helix: 1.68 (0.25), residues: 409 sheet: -1.45 (0.50), residues: 88 loop : -1.35 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP P 724 HIS 0.003 0.001 HIS B 90 PHE 0.012 0.001 PHE P 158 TYR 0.011 0.001 TYR P 600 ARG 0.002 0.000 ARG P 652 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Evaluate side-chains 90 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 494 TYR cc_start: 0.7363 (t80) cc_final: 0.7098 (t80) REVERT: P 535 ARG cc_start: 0.8082 (ptm-80) cc_final: 0.7327 (ptt90) REVERT: P 689 LYS cc_start: 0.7491 (mttt) cc_final: 0.7062 (mttt) REVERT: P 756 GLU cc_start: 0.5143 (OUTLIER) cc_final: 0.4882 (pt0) outliers start: 9 outliers final: 6 residues processed: 86 average time/residue: 0.4655 time to fit residues: 56.6687 Evaluate side-chains 83 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain P residue 397 MET Chi-restraints excluded: chain P residue 709 ILE Chi-restraints excluded: chain P residue 719 LEU Chi-restraints excluded: chain P residue 756 GLU Chi-restraints excluded: chain P residue 790 VAL Chi-restraints excluded: chain P residue 804 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 78 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.116351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.090780 restraints weight = 66356.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.094526 restraints weight = 29145.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.096865 restraints weight = 18249.288| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.6612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9302 Z= 0.189 Angle : 0.578 7.545 12894 Z= 0.317 Chirality : 0.038 0.211 1434 Planarity : 0.004 0.051 1352 Dihedral : 22.933 175.880 2024 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.76 % Favored : 95.12 % Rotamer: Outliers : 1.14 % Allowed : 13.13 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.14 (0.28), residues: 882 helix: 1.72 (0.25), residues: 409 sheet: -1.43 (0.50), residues: 88 loop : -1.36 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP P 724 HIS 0.003 0.001 HIS B 90 PHE 0.012 0.001 PHE P 158 TYR 0.011 0.001 TYR P 205 ARG 0.003 0.000 ARG P 652 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3959.41 seconds wall clock time: 71 minutes 37.99 seconds (4297.99 seconds total)