Starting phenix.real_space_refine on Sun Jun 15 04:48:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cf1_45526/06_2025/9cf1_45526_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cf1_45526/06_2025/9cf1_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/cci-nas-00/data/ceres_data/9cf1_45526/06_2025/9cf1_45526.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cf1_45526/06_2025/9cf1_45526.map" model { file = "/net/cci-nas-00/data/ceres_data/9cf1_45526/06_2025/9cf1_45526_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cf1_45526/06_2025/9cf1_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 8.94, per 1000 atoms: 0.52 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: 4.76 Conformation dependent library (CDL) restraints added in 1.1 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: 7.57 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: 6.85 Time building geometry restraints manager: 5.75 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: 1.610 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: 0.290 Extract box with map and model: 0.660 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 45.050 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.590 ------------------------------------------------------------------------------- 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= 0.727 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 Details of bonding type rmsd hydrogen bonds : bond 0.14812 ( 436) hydrogen bonds : angle 7.41978 ( 1167) covalent geometry : bond 0.01259 ( 9302) covalent geometry : angle 1.84432 (12894) *********************** 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 : 1.183 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: 0.6772 time to fit residues: 163.9323 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 : 1.150 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.120976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.095453 restraints weight = 68214.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.099407 restraints weight = 29192.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.101828 restraints weight = 18126.063| |-----------------------------------------------------------------------------| r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 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= 0.182 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 Details of bonding type rmsd hydrogen bonds : bond 0.05138 ( 436) hydrogen bonds : angle 5.11089 ( 1167) covalent geometry : bond 0.00391 ( 9302) covalent geometry : angle 0.76196 (12894) *********************** 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 : 2.290 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 256 LYS cc_start: 0.8166 (tttt) cc_final: 0.7958 (ttmm) REVERT: P 301 MET cc_start: 0.8066 (mmm) cc_final: 0.7707 (mmm) REVERT: P 397 MET cc_start: 0.7080 (ptt) cc_final: 0.6429 (ttp) REVERT: P 523 ARG cc_start: 0.7913 (ttp-170) cc_final: 0.7109 (mtm-85) REVERT: P 575 GLU cc_start: 0.7238 (mt-10) cc_final: 0.6588 (mt-10) outliers start: 8 outliers final: 6 residues processed: 122 average time/residue: 0.8030 time to fit residues: 127.9513 Evaluate side-chains 102 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 96 time to evaluate : 1.642 ------------------------------------------------------------------------------- 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 60 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 85 optimal weight: 9.9990 chunk 87 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.118820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.093052 restraints weight = 66272.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.096890 restraints weight = 28152.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.099277 restraints weight = 17462.894| |-----------------------------------------------------------------------------| r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.4451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9302 Z= 0.177 Angle : 0.663 7.229 12894 Z= 0.373 Chirality : 0.042 0.199 1434 Planarity : 0.004 0.046 1352 Dihedral : 23.643 174.634 2028 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.42 % Favored : 95.46 % Rotamer: Outliers : 1.77 % Allowed : 9.47 % Favored : 88.76 % 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: -0.12 (0.27), residues: 882 helix: 1.17 (0.25), residues: 405 sheet: -1.26 (0.44), residues: 91 loop : -1.11 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP P 724 HIS 0.004 0.001 HIS P 201 PHE 0.021 0.002 PHE P 158 TYR 0.014 0.002 TYR P 225 ARG 0.003 0.000 ARG P 652 Details of bonding type rmsd hydrogen bonds : bond 0.04777 ( 436) hydrogen bonds : angle 4.84498 ( 1167) covalent geometry : bond 0.00376 ( 9302) covalent geometry : angle 0.66322 (12894) *********************** 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 114 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 1.154 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 256 LYS cc_start: 0.8185 (tttt) cc_final: 0.7960 (ttmm) REVERT: P 301 MET cc_start: 0.8117 (mmm) cc_final: 0.7723 (mmm) REVERT: P 494 TYR cc_start: 0.7990 (t80) cc_final: 0.7592 (t80) REVERT: P 523 ARG cc_start: 0.8018 (ttp-170) cc_final: 0.7212 (mtm-85) REVERT: P 575 GLU cc_start: 0.7259 (mt-10) cc_final: 0.6628 (mt-10) outliers start: 14 outliers final: 8 residues processed: 109 average time/residue: 0.5834 time to fit residues: 82.8103 Evaluate side-chains 92 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 1.194 ------------------------------------------------------------------------------- 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 512 LYS Chi-restraints excluded: chain P residue 590 ASP Chi-restraints excluded: chain P residue 709 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 45 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 40 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 chunk 69 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 603 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.117389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.091234 restraints weight = 68311.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.095052 restraints weight = 30150.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.097393 restraints weight = 19026.509| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.5066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9302 Z= 0.206 Angle : 0.667 8.545 12894 Z= 0.371 Chirality : 0.042 0.185 1434 Planarity : 0.005 0.048 1352 Dihedral : 23.367 177.246 2028 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.99 % Favored : 94.90 % Rotamer: Outliers : 2.02 % Allowed : 10.23 % Favored : 87.75 % 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: -0.19 (0.28), residues: 882 helix: 1.13 (0.25), residues: 409 sheet: -1.55 (0.44), residues: 90 loop : -1.13 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP P 724 HIS 0.004 0.001 HIS P 201 PHE 0.021 0.002 PHE P 158 TYR 0.013 0.002 TYR P 205 ARG 0.003 0.000 ARG P 758 Details of bonding type rmsd hydrogen bonds : bond 0.04936 ( 436) hydrogen bonds : angle 4.80145 ( 1167) covalent geometry : bond 0.00442 ( 9302) covalent geometry : angle 0.66670 (12894) *********************** 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 108 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 1.250 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: P 256 LYS cc_start: 0.8101 (tttt) cc_final: 0.7790 (ttmm) REVERT: P 301 MET cc_start: 0.8224 (mmm) cc_final: 0.7739 (mmm) REVERT: P 494 TYR cc_start: 0.7903 (t80) cc_final: 0.7552 (t80) REVERT: P 513 ASN cc_start: 0.8160 (p0) cc_final: 0.7941 (p0) REVERT: P 575 GLU cc_start: 0.7377 (mt-10) cc_final: 0.6672 (mt-10) REVERT: P 756 GLU cc_start: 0.5679 (OUTLIER) cc_final: 0.5332 (pt0) outliers start: 16 outliers final: 11 residues processed: 101 average time/residue: 0.5458 time to fit residues: 74.2669 Evaluate side-chains 90 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 1.181 ------------------------------------------------------------------------------- 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 180 LYS 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 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 814 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 41 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 63 optimal weight: 0.0970 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 300 ASN ** P 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.118572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.092573 restraints weight = 68756.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.096446 restraints weight = 29967.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.098827 restraints weight = 18786.319| |-----------------------------------------------------------------------------| r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.5433 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= 0.151 Angle : 0.596 7.178 12894 Z= 0.331 Chirality : 0.039 0.176 1434 Planarity : 0.004 0.048 1352 Dihedral : 23.315 177.428 2028 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.63 % Favored : 96.26 % Rotamer: Outliers : 1.26 % Allowed : 11.49 % Favored : 87.25 % 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: 0.12 (0.28), residues: 882 helix: 1.50 (0.25), residues: 403 sheet: -1.47 (0.44), residues: 90 loop : -1.04 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP P 724 HIS 0.004 0.001 HIS P 387 PHE 0.017 0.001 PHE P 158 TYR 0.011 0.001 TYR P 205 ARG 0.002 0.000 ARG P 652 Details of bonding type rmsd hydrogen bonds : bond 0.04337 ( 436) hydrogen bonds : angle 4.61799 ( 1167) covalent geometry : bond 0.00324 ( 9302) covalent geometry : angle 0.59641 (12894) *********************** 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 89 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 1.224 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 256 LYS cc_start: 0.8049 (tttt) cc_final: 0.7746 (ttmm) REVERT: P 301 MET cc_start: 0.8257 (mmm) cc_final: 0.7748 (mmm) REVERT: P 494 TYR cc_start: 0.7903 (t80) cc_final: 0.7506 (t80) REVERT: P 521 HIS cc_start: 0.6391 (t70) cc_final: 0.6147 (t70) REVERT: P 575 GLU cc_start: 0.7314 (mt-10) cc_final: 0.6604 (mt-10) outliers start: 10 outliers final: 7 residues processed: 86 average time/residue: 0.5551 time to fit residues: 63.8151 Evaluate side-chains 82 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain P residue 448 ARG Chi-restraints excluded: chain P residue 709 ILE Chi-restraints excluded: chain P residue 719 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 615 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.114595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.088736 restraints weight = 68017.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.092320 restraints weight = 30236.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.094584 restraints weight = 19168.770| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.5792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 9302 Z= 0.280 Angle : 0.695 9.811 12894 Z= 0.386 Chirality : 0.044 0.206 1434 Planarity : 0.005 0.049 1352 Dihedral : 23.428 179.762 2028 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.35 % Favored : 93.54 % Rotamer: Outliers : 2.02 % Allowed : 11.49 % 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: -0.61 (0.27), residues: 882 helix: 0.96 (0.25), residues: 402 sheet: -1.70 (0.46), residues: 91 loop : -1.53 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 724 HIS 0.005 0.001 HIS B 124 PHE 0.021 0.002 PHE P 158 TYR 0.016 0.002 TYR P 141 ARG 0.005 0.001 ARG P 758 Details of bonding type rmsd hydrogen bonds : bond 0.05645 ( 436) hydrogen bonds : angle 4.93853 ( 1167) covalent geometry : bond 0.00606 ( 9302) covalent geometry : angle 0.69522 (12894) *********************** 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 85 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 1.606 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: P 494 TYR cc_start: 0.8087 (t80) cc_final: 0.7659 (t80) REVERT: P 575 GLU cc_start: 0.7573 (mt-10) cc_final: 0.6878 (mt-10) REVERT: P 756 GLU cc_start: 0.5902 (OUTLIER) cc_final: 0.5691 (pt0) REVERT: P 810 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.6653 (tt0) outliers start: 16 outliers final: 12 residues processed: 81 average time/residue: 0.6231 time to fit residues: 70.9889 Evaluate side-chains 79 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 1.163 ------------------------------------------------------------------------------- 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 467 ILE Chi-restraints excluded: chain P residue 492 LEU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 90 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 5 optimal weight: 0.3980 chunk 37 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 61 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- 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 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 615 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.116939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.091314 restraints weight = 66512.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.095004 restraints weight = 29189.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.097333 restraints weight = 18337.081| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.5977 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= 0.162 Angle : 0.601 8.327 12894 Z= 0.331 Chirality : 0.039 0.181 1434 Planarity : 0.004 0.050 1352 Dihedral : 23.385 178.385 2028 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.88 % Favored : 95.01 % 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: -0.31 (0.28), residues: 882 helix: 1.21 (0.25), residues: 410 sheet: -1.74 (0.46), residues: 89 loop : -1.38 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP P 724 HIS 0.004 0.001 HIS B 90 PHE 0.020 0.001 PHE P 318 TYR 0.012 0.001 TYR P 205 ARG 0.002 0.000 ARG P 646 Details of bonding type rmsd hydrogen bonds : bond 0.04478 ( 436) hydrogen bonds : angle 4.67666 ( 1167) covalent geometry : bond 0.00348 ( 9302) covalent geometry : angle 0.60131 (12894) *********************** 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 94 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 1.876 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 494 TYR cc_start: 0.7989 (t80) cc_final: 0.7561 (t80) REVERT: P 575 GLU cc_start: 0.7486 (mt-10) cc_final: 0.6783 (mt-10) REVERT: P 756 GLU cc_start: 0.5657 (OUTLIER) cc_final: 0.5366 (pt0) outliers start: 13 outliers final: 10 residues processed: 91 average time/residue: 0.6116 time to fit residues: 78.8055 Evaluate side-chains 86 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain P residue 448 ARG Chi-restraints excluded: chain P residue 492 LEU 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 776 ILE Chi-restraints excluded: chain P residue 790 VAL 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 29 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 34 optimal weight: 7.9990 chunk 89 optimal weight: 6.9990 chunk 51 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.116451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.090855 restraints weight = 67037.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.094509 restraints weight = 29756.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.096827 restraints weight = 18738.194| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.6162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9302 Z= 0.184 Angle : 0.606 8.617 12894 Z= 0.334 Chirality : 0.040 0.180 1434 Planarity : 0.004 0.050 1352 Dihedral : 23.330 177.698 2028 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.01 % Favored : 93.88 % Rotamer: Outliers : 2.40 % Allowed : 11.99 % Favored : 85.61 % 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: -0.34 (0.28), residues: 882 helix: 1.24 (0.25), residues: 411 sheet: -1.72 (0.47), residues: 89 loop : -1.49 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP P 724 HIS 0.003 0.001 HIS P 387 PHE 0.018 0.002 PHE P 318 TYR 0.012 0.001 TYR P 205 ARG 0.003 0.000 ARG B 153 Details of bonding type rmsd hydrogen bonds : bond 0.04730 ( 436) hydrogen bonds : angle 4.66404 ( 1167) covalent geometry : bond 0.00397 ( 9302) covalent geometry : angle 0.60598 (12894) *********************** 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 94 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 1.365 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: 0.8002 (t80) cc_final: 0.7591 (t80) REVERT: P 575 GLU cc_start: 0.7456 (mt-10) cc_final: 0.6756 (mt-10) REVERT: P 618 HIS cc_start: 0.6046 (OUTLIER) cc_final: 0.5660 (t-170) REVERT: P 756 GLU cc_start: 0.5655 (OUTLIER) cc_final: 0.5445 (pt0) outliers start: 19 outliers final: 13 residues processed: 89 average time/residue: 0.4703 time to fit residues: 58.4742 Evaluate side-chains 88 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 77 TYR Chi-restraints excluded: chain B residue 108 SER 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 492 LEU 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 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 814 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 94 optimal weight: 7.9990 chunk 45 optimal weight: 0.1980 chunk 7 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.116369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.090839 restraints weight = 66856.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.094485 restraints weight = 29554.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.096718 restraints weight = 18599.794| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.6331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9302 Z= 0.181 Angle : 0.599 8.544 12894 Z= 0.330 Chirality : 0.039 0.184 1434 Planarity : 0.004 0.051 1352 Dihedral : 23.270 176.534 2028 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.56 % Favored : 94.33 % Rotamer: Outliers : 2.15 % Allowed : 12.50 % Favored : 85.35 % 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 (0.28), residues: 882 helix: 1.33 (0.25), residues: 409 sheet: -1.76 (0.49), residues: 89 loop : -1.52 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP P 724 HIS 0.003 0.001 HIS P 241 PHE 0.019 0.002 PHE P 318 TYR 0.011 0.001 TYR P 205 ARG 0.004 0.000 ARG P 489 Details of bonding type rmsd hydrogen bonds : bond 0.04628 ( 436) hydrogen bonds : angle 4.64244 ( 1167) covalent geometry : bond 0.00391 ( 9302) covalent geometry : angle 0.59927 (12894) *********************** 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 93 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 1.236 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 575 GLU cc_start: 0.7480 (mt-10) cc_final: 0.6771 (mt-10) REVERT: P 618 HIS cc_start: 0.6195 (OUTLIER) cc_final: 0.5829 (t-170) outliers start: 17 outliers final: 12 residues processed: 88 average time/residue: 0.4528 time to fit residues: 56.0333 Evaluate side-chains 86 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 77 TYR Chi-restraints excluded: chain B residue 108 SER 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 492 LEU 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 776 ILE 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 76 optimal weight: 0.9980 chunk 49 optimal weight: 0.0040 chunk 15 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 40 optimal weight: 0.7980 chunk 51 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.9596 ------------------------------------------------------------------------------- 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 385 ASN ** 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 = 0.4112 r_free = 0.4112 target = 0.118342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.092879 restraints weight = 66340.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.096613 restraints weight = 28884.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.098933 restraints weight = 18028.839| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.6479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9302 Z= 0.126 Angle : 0.562 7.589 12894 Z= 0.308 Chirality : 0.038 0.205 1434 Planarity : 0.004 0.051 1352 Dihedral : 23.115 175.851 2024 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.54 % Favored : 95.35 % Rotamer: Outliers : 1.01 % Allowed : 13.51 % Favored : 85.48 % 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: 0.09 (0.28), residues: 882 helix: 1.68 (0.25), residues: 410 sheet: -1.65 (0.49), residues: 89 loop : -1.33 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP P 724 HIS 0.003 0.001 HIS P 241 PHE 0.019 0.001 PHE P 318 TYR 0.010 0.001 TYR P 205 ARG 0.005 0.000 ARG P 652 Details of bonding type rmsd hydrogen bonds : bond 0.04086 ( 436) hydrogen bonds : angle 4.48047 ( 1167) covalent geometry : bond 0.00273 ( 9302) covalent geometry : angle 0.56186 (12894) ********************** 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 88 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 1.211 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: P 256 LYS cc_start: 0.8121 (tttt) cc_final: 0.7771 (ttmm) REVERT: P 535 ARG cc_start: 0.8140 (ptm-80) cc_final: 0.7508 (ptt90) REVERT: P 575 GLU cc_start: 0.7386 (mt-10) cc_final: 0.6707 (mt-10) REVERT: P 618 HIS cc_start: 0.6142 (OUTLIER) cc_final: 0.5750 (t-170) REVERT: P 689 LYS cc_start: 0.7521 (mttt) cc_final: 0.7154 (mttt) outliers start: 8 outliers final: 7 residues processed: 87 average time/residue: 0.4297 time to fit residues: 53.4785 Evaluate side-chains 85 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 1.297 ------------------------------------------------------------------------------- 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 410 LEU Chi-restraints excluded: chain P residue 492 LEU 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 790 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 64 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 94 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 chunk 82 optimal weight: 0.9980 chunk 92 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.4044 r_free = 0.4044 target = 0.115271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.089469 restraints weight = 66943.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.093162 restraints weight = 29649.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.095550 restraints weight = 18642.279| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.6569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9302 Z= 0.183 Angle : 0.594 8.104 12894 Z= 0.326 Chirality : 0.039 0.200 1434 Planarity : 0.004 0.050 1352 Dihedral : 23.031 175.425 2024 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.90 % Favored : 93.99 % Rotamer: Outliers : 1.39 % Allowed : 13.76 % Favored : 84.85 % 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: -0.13 (0.28), residues: 882 helix: 1.51 (0.25), residues: 410 sheet: -1.67 (0.51), residues: 89 loop : -1.49 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 724 HIS 0.003 0.001 HIS B 90 PHE 0.018 0.002 PHE P 318 TYR 0.011 0.001 TYR P 205 ARG 0.006 0.001 ARG P 652 Details of bonding type rmsd hydrogen bonds : bond 0.04651 ( 436) hydrogen bonds : angle 4.56653 ( 1167) covalent geometry : bond 0.00397 ( 9302) covalent geometry : angle 0.59355 (12894) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6182.26 seconds wall clock time: 109 minutes 3.61 seconds (6543.61 seconds total)