Starting phenix.real_space_refine on Mon Nov 18 04:45:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ces_45517/11_2024/9ces_45517_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ces_45517/11_2024/9ces_45517.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ces_45517/11_2024/9ces_45517.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ces_45517/11_2024/9ces_45517.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ces_45517/11_2024/9ces_45517_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ces_45517/11_2024/9ces_45517_neut.cif" } resolution = 3.28 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= 0.002 sd= 0.036 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 181 5.49 5 S 38 5.16 5 C 4897 2.51 5 N 1619 2.21 5 O 2103 1.98 5 H 7001 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 15839 Number of models: 1 Model: "" Number of chains: 4 Chain: "N" Number of atoms: 475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 475 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "P" Number of atoms: 10029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 10029 Classifications: {'peptide': 612} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 591} Chain breaks: 3 Chain: "T" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 761 Classifications: {'DNA': 24} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 23} Chain: "W" Number of atoms: 4574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 4574 Classifications: {'RNA': 142} Modifications used: {'3*END': 1, 'rna2p_pur': 14, 'rna2p_pyr': 9, 'rna3p_pur': 69, 'rna3p_pyr': 50} Link IDs: {'rna2p': 23, 'rna3p': 118} Time building chain proxies: 9.46, per 1000 atoms: 0.60 Number of scatterers: 15839 At special positions: 0 Unit cell: (81.549, 111.384, 166.413, 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 38 16.00 P 181 15.00 O 2103 8.00 N 1619 7.00 C 4897 6.00 H 7001 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: 4.26 Conformation dependent library (CDL) restraints added in 929.3 milliseconds 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1164 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 3 sheets defined 57.0% alpha, 8.8% beta 54 base pairs and 93 stacking pairs defined. Time for finding SS restraints: 8.54 Creating SS restraints... Processing helix chain 'P' and resid 16 through 53 Processing helix chain 'P' and resid 65 through 77 Processing helix chain 'P' and resid 88 through 110 Processing helix chain 'P' and resid 114 through 119 Processing helix chain 'P' and resid 124 through 162 removed outlier: 3.862A pdb=" N ALA P 129 " --> pdb=" O SER P 125 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N TYR P 130 " --> pdb=" O HIS P 126 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER P 131 " --> pdb=" O VAL P 127 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N HIS P 146 " --> pdb=" O ASN P 142 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N SER P 148 " --> pdb=" O GLU P 144 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LYS P 149 " --> pdb=" O ALA P 145 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR P 150 " --> pdb=" O HIS P 146 " (cutoff:3.500A) Processing helix chain 'P' and resid 165 through 182 Processing helix chain 'P' and resid 217 through 222 removed outlier: 3.943A pdb=" N ASP P 221 " --> pdb=" O PRO P 217 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU P 222 " --> pdb=" O ARG P 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 217 through 222' Processing helix chain 'P' and resid 225 through 228 Processing helix chain 'P' and resid 229 through 243 Processing helix chain 'P' and resid 273 through 281 Processing helix chain 'P' and resid 282 through 298 removed outlier: 4.355A pdb=" N ASP P 288 " --> pdb=" O ASP P 284 " (cutoff:3.500A) Processing helix chain 'P' and resid 312 through 318 Processing helix chain 'P' and resid 323 through 339 removed outlier: 3.621A pdb=" N ALA P 327 " --> pdb=" O SER P 323 " (cutoff:3.500A) Processing helix chain 'P' and resid 346 through 351 removed outlier: 3.671A pdb=" N LEU P 350 " --> pdb=" O GLN P 346 " (cutoff:3.500A) Processing helix chain 'P' and resid 385 through 387 No H-bonds generated for 'chain 'P' and resid 385 through 387' Processing helix chain 'P' and resid 416 through 421 Processing helix chain 'P' and resid 447 through 454 Processing helix chain 'P' and resid 455 through 470 Processing helix chain 'P' and resid 472 through 479 Processing helix chain 'P' and resid 480 through 483 Processing helix chain 'P' and resid 489 through 512 removed outlier: 3.729A pdb=" N TYR P 496 " --> pdb=" O MET P 492 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG P 502 " --> pdb=" O CYS P 498 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET P 503 " --> pdb=" O SER P 499 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N HIS P 505 " --> pdb=" O LYS P 501 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N MET P 506 " --> pdb=" O ARG P 502 " (cutoff:3.500A) Processing helix chain 'P' and resid 513 through 543 removed outlier: 4.155A pdb=" N ARG P 517 " --> pdb=" O HIS P 513 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TYR P 524 " --> pdb=" O LYS P 520 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS P 528 " --> pdb=" O TYR P 524 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER P 529 " --> pdb=" O ASN P 525 " (cutoff:3.500A) Processing helix chain 'P' and resid 556 through 564 Processing helix chain 'P' and resid 569 through 571 No H-bonds generated for 'chain 'P' and resid 569 through 571' Processing helix chain 'P' and resid 600 through 604 Processing helix chain 'P' and resid 657 through 670 Processing sheet with id=AA1, first strand: chain 'P' and resid 4 through 10 removed outlier: 6.995A pdb=" N SER P 376 " --> pdb=" O VAL P 371 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL P 371 " --> pdb=" O SER P 376 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N SER P 378 " --> pdb=" O ALA P 369 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N ALA P 369 " --> pdb=" O SER P 378 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N GLN P 380 " --> pdb=" O ASP P 367 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'P' and resid 442 through 446 removed outlier: 6.298A pdb=" N LYS P 422 " --> pdb=" O ILE P 574 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N GLY P 576 " --> pdb=" O LYS P 422 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU P 424 " --> pdb=" O GLY P 576 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N GLY P 578 " --> pdb=" O LEU P 424 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N CYS P 426 " --> pdb=" O GLY P 578 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'P' and resid 629 through 631 258 hydrogen bonds defined for protein. 762 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 138 hydrogen bonds 268 hydrogen bond angles 0 basepair planarities 54 basepair parallelities 93 stacking parallelities Total time for adding SS restraints: 6.69 Time building geometry restraints manager: 5.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.11: 6984 1.11 - 1.29: 958 1.29 - 1.47: 4240 1.47 - 1.64: 4163 1.64 - 1.82: 59 Bond restraints: 16404 Sorted by residual: bond pdb=" C2 A W 137 " pdb=" H2 A W 137 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" C5 U W 41 " pdb=" H5 U W 41 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" C8 A W 141 " pdb=" H8 A W 141 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" C5 U W 20 " pdb=" H5 U W 20 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" N ASN P 114 " pdb=" H ASN P 114 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.66e+01 ... (remaining 16399 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 25375 2.71 - 5.41: 3355 5.41 - 8.12: 707 8.12 - 10.82: 37 10.82 - 13.53: 19 Bond angle restraints: 29493 Sorted by residual: angle pdb=" C4' C W 81 " pdb=" O4' C W 81 " pdb=" C1' C W 81 " ideal model delta sigma weight residual 109.70 99.16 10.54 1.00e+00 1.00e+00 1.11e+02 angle pdb=" C4' G W 79 " pdb=" O4' G W 79 " pdb=" C1' G W 79 " ideal model delta sigma weight residual 109.70 100.22 9.48 1.00e+00 1.00e+00 8.99e+01 angle pdb=" O4' C W 81 " pdb=" C1' C W 81 " pdb=" C2' C W 81 " ideal model delta sigma weight residual 105.80 96.55 9.25 1.00e+00 1.00e+00 8.55e+01 angle pdb=" O3' A W 82 " pdb=" C3' A W 82 " pdb=" C2' A W 82 " ideal model delta sigma weight residual 109.50 123.03 -13.53 1.50e+00 4.44e-01 8.13e+01 angle pdb=" C4' U W 41 " pdb=" C3' U W 41 " pdb=" C2' U W 41 " ideal model delta sigma weight residual 102.60 94.59 8.01 1.00e+00 1.00e+00 6.41e+01 ... (remaining 29488 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.55: 6851 33.55 - 67.10: 711 67.10 - 100.65: 92 100.65 - 134.19: 9 134.19 - 167.74: 3 Dihedral angle restraints: 7666 sinusoidal: 5519 harmonic: 2147 Sorted by residual: dihedral pdb=" O4' A W 53 " pdb=" C2' A W 53 " pdb=" C1' A W 53 " pdb=" C3' A W 53 " ideal model delta sinusoidal sigma weight residual 25.00 -28.09 53.09 1 8.00e+00 1.56e-02 5.99e+01 dihedral pdb=" C5' G W 79 " pdb=" C4' G W 79 " pdb=" C3' G W 79 " pdb=" O3' G W 79 " ideal model delta sinusoidal sigma weight residual 147.00 94.16 52.84 1 8.00e+00 1.56e-02 5.94e+01 dihedral pdb=" C3' G W 45 " pdb=" C4' G W 45 " pdb=" O4' G W 45 " pdb=" C1' G W 45 " ideal model delta sinusoidal sigma weight residual 20.00 -32.55 52.55 1 8.00e+00 1.56e-02 5.88e+01 ... (remaining 7663 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 1216 0.105 - 0.210: 328 0.210 - 0.315: 37 0.315 - 0.420: 14 0.420 - 0.525: 2 Chirality restraints: 1597 Sorted by residual: chirality pdb=" C4' C W 81 " pdb=" C5' C W 81 " pdb=" O4' C W 81 " pdb=" C3' C W 81 " both_signs ideal model delta sigma weight residual False -2.50 -1.98 -0.53 2.00e-01 2.50e+01 6.90e+00 chirality pdb=" C4' A W 43 " pdb=" C5' A W 43 " pdb=" O4' A W 43 " pdb=" C3' A W 43 " both_signs ideal model delta sigma weight residual False -2.50 -2.06 -0.44 2.00e-01 2.50e+01 4.87e+00 chirality pdb=" C4' U W 41 " pdb=" C5' U W 41 " pdb=" O4' U W 41 " pdb=" C3' U W 41 " both_signs ideal model delta sigma weight residual False -2.50 -2.09 -0.40 2.00e-01 2.50e+01 4.07e+00 ... (remaining 1594 not shown) Planarity restraints: 1785 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G W 110 " -0.461 2.00e-02 2.50e+03 1.75e-01 1.07e+03 pdb=" N9 G W 110 " 0.001 2.00e-02 2.50e+03 pdb=" C8 G W 110 " 0.149 2.00e-02 2.50e+03 pdb=" N7 G W 110 " 0.133 2.00e-02 2.50e+03 pdb=" C5 G W 110 " 0.013 2.00e-02 2.50e+03 pdb=" C6 G W 110 " -0.112 2.00e-02 2.50e+03 pdb=" O6 G W 110 " -0.224 2.00e-02 2.50e+03 pdb=" N1 G W 110 " -0.057 2.00e-02 2.50e+03 pdb=" C2 G W 110 " 0.047 2.00e-02 2.50e+03 pdb=" N2 G W 110 " 0.246 2.00e-02 2.50e+03 pdb=" N3 G W 110 " 0.056 2.00e-02 2.50e+03 pdb=" C4 G W 110 " 0.041 2.00e-02 2.50e+03 pdb=" H8 G W 110 " 0.204 2.00e-02 2.50e+03 pdb=" H1 G W 110 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G W 71 " -0.457 2.00e-02 2.50e+03 1.74e-01 1.06e+03 pdb=" N9 G W 71 " 0.018 2.00e-02 2.50e+03 pdb=" C8 G W 71 " 0.156 2.00e-02 2.50e+03 pdb=" N7 G W 71 " 0.049 2.00e-02 2.50e+03 pdb=" C5 G W 71 " -0.021 2.00e-02 2.50e+03 pdb=" C6 G W 71 " -0.109 2.00e-02 2.50e+03 pdb=" O6 G W 71 " -0.237 2.00e-02 2.50e+03 pdb=" N1 G W 71 " -0.024 2.00e-02 2.50e+03 pdb=" C2 G W 71 " 0.045 2.00e-02 2.50e+03 pdb=" N2 G W 71 " 0.198 2.00e-02 2.50e+03 pdb=" N3 G W 71 " 0.043 2.00e-02 2.50e+03 pdb=" C4 G W 71 " 0.032 2.00e-02 2.50e+03 pdb=" H8 G W 71 " 0.268 2.00e-02 2.50e+03 pdb=" H1 G W 71 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C W 81 " 0.377 2.00e-02 2.50e+03 1.85e-01 9.43e+02 pdb=" N1 C W 81 " 0.058 2.00e-02 2.50e+03 pdb=" C2 C W 81 " -0.054 2.00e-02 2.50e+03 pdb=" O2 C W 81 " -0.357 2.00e-02 2.50e+03 pdb=" N3 C W 81 " 0.043 2.00e-02 2.50e+03 pdb=" C4 C W 81 " 0.104 2.00e-02 2.50e+03 pdb=" N4 C W 81 " 0.206 2.00e-02 2.50e+03 pdb=" C5 C W 81 " -0.052 2.00e-02 2.50e+03 pdb=" C6 C W 81 " -0.039 2.00e-02 2.50e+03 pdb=" H5 C W 81 " -0.164 2.00e-02 2.50e+03 pdb=" H6 C W 81 " -0.122 2.00e-02 2.50e+03 ... (remaining 1782 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.11: 770 2.11 - 2.73: 20927 2.73 - 3.35: 44014 3.35 - 3.98: 58796 3.98 - 4.60: 84987 Nonbonded interactions: 209494 Sorted by model distance: nonbonded pdb="HO2' C W 78 " pdb=" H4' G W 79 " model vdw 1.487 2.270 nonbonded pdb="HO2' G W 42 " pdb=" H4' A W 43 " model vdw 1.507 2.270 nonbonded pdb="HO2' C W 81 " pdb=" OP1 A W 82 " model vdw 1.561 2.450 nonbonded pdb="HO2' A W 123 " pdb=" OP2 A W 124 " model vdw 1.563 2.450 nonbonded pdb="HO2' A W 82 " pdb=" OP2 U W 83 " model vdw 1.565 2.450 ... (remaining 209489 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.170 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: 0.240 Extract box with map and model: 0.700 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 44.900 Find NCS groups from input model: 0.110 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: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4396 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 0.057 9403 Z= 0.814 Angle : 1.955 13.527 13534 Z= 1.297 Chirality : 0.096 0.525 1597 Planarity : 0.034 0.180 1055 Dihedral : 23.225 167.742 4512 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 1.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.91 % Allowed : 2.00 % Favored : 97.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.87 (0.32), residues: 604 helix: -0.39 (0.27), residues: 316 sheet: -1.56 (0.62), residues: 40 loop : -0.41 (0.39), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.116 0.021 TRP P 654 HIS 0.012 0.003 HIS P 641 PHE 0.054 0.012 PHE P 519 TYR 0.074 0.019 TYR P 445 ARG 0.015 0.001 ARG P 668 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 130 time to evaluate : 1.053 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: P 256 ASN cc_start: 0.5854 (t0) cc_final: 0.5475 (t0) REVERT: P 272 ASP cc_start: 0.7284 (p0) cc_final: 0.7032 (p0) REVERT: P 492 MET cc_start: 0.6846 (mmm) cc_final: 0.6321 (tpt) outliers start: 5 outliers final: 2 residues processed: 134 average time/residue: 0.7656 time to fit residues: 124.1323 Evaluate side-chains 75 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 73 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 567 VAL Chi-restraints excluded: chain P residue 654 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 20 optimal weight: 8.9990 chunk 39 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4359 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9403 Z= 0.241 Angle : 0.830 10.920 13534 Z= 0.454 Chirality : 0.047 0.290 1597 Planarity : 0.005 0.044 1055 Dihedral : 25.153 167.072 3246 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.64 % Allowed : 9.09 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.60 (0.34), residues: 604 helix: 1.18 (0.29), residues: 318 sheet: -1.77 (0.59), residues: 53 loop : 0.02 (0.42), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP P 655 HIS 0.005 0.001 HIS P 68 PHE 0.017 0.002 PHE P 67 TYR 0.011 0.001 TYR P 45 ARG 0.004 0.001 ARG P 291 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 140 LYS cc_start: 0.8087 (mtpt) cc_final: 0.7665 (pttt) REVERT: P 272 ASP cc_start: 0.7499 (p0) cc_final: 0.7217 (p0) REVERT: P 464 LEU cc_start: 0.6898 (OUTLIER) cc_final: 0.6622 (tt) REVERT: P 484 GLN cc_start: 0.4666 (tp-100) cc_final: 0.4248 (pt0) REVERT: P 492 MET cc_start: 0.6958 (mmm) cc_final: 0.6508 (tpt) outliers start: 9 outliers final: 5 residues processed: 88 average time/residue: 0.4885 time to fit residues: 57.5872 Evaluate side-chains 65 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 43 SER Chi-restraints excluded: chain P residue 96 ASP Chi-restraints excluded: chain P residue 464 LEU Chi-restraints excluded: chain P residue 489 HIS Chi-restraints excluded: chain P residue 654 TRP Chi-restraints excluded: chain P residue 667 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 58 optimal weight: 9.9990 chunk 48 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 24 optimal weight: 0.6980 chunk 56 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4469 moved from start: 0.5084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9403 Z= 0.284 Angle : 0.742 7.024 13534 Z= 0.412 Chirality : 0.043 0.216 1597 Planarity : 0.006 0.063 1055 Dihedral : 24.990 172.132 3245 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.91 % Allowed : 9.82 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.38 (0.34), residues: 604 helix: 1.01 (0.28), residues: 318 sheet: -1.79 (0.66), residues: 51 loop : -0.17 (0.41), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP P 364 HIS 0.005 0.001 HIS P 146 PHE 0.019 0.002 PHE P 260 TYR 0.018 0.002 TYR P 475 ARG 0.009 0.001 ARG P 42 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 5 ARG cc_start: 0.7028 (OUTLIER) cc_final: 0.5908 (mtt90) REVERT: P 263 SER cc_start: 0.8412 (m) cc_final: 0.8089 (p) REVERT: P 272 ASP cc_start: 0.7460 (p0) cc_final: 0.7255 (p0) REVERT: P 484 GLN cc_start: 0.5737 (tp-100) cc_final: 0.5367 (pm20) outliers start: 16 outliers final: 9 residues processed: 77 average time/residue: 0.6869 time to fit residues: 66.8751 Evaluate side-chains 66 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 5 ARG Chi-restraints excluded: chain P residue 43 SER Chi-restraints excluded: chain P residue 96 ASP Chi-restraints excluded: chain P residue 290 LYS Chi-restraints excluded: chain P residue 432 ASP Chi-restraints excluded: chain P residue 499 SER Chi-restraints excluded: chain P residue 538 VAL Chi-restraints excluded: chain P residue 654 TRP Chi-restraints excluded: chain P residue 655 TRP Chi-restraints excluded: chain P residue 667 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 71 optimal weight: 10.0000 chunk 75 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 77 GLN P 568 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4483 moved from start: 0.5798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 9403 Z= 0.285 Angle : 0.682 6.830 13534 Z= 0.373 Chirality : 0.040 0.196 1597 Planarity : 0.006 0.055 1055 Dihedral : 24.974 177.979 3245 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.18 % Allowed : 11.82 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 (0.34), residues: 604 helix: 1.03 (0.29), residues: 317 sheet: -1.76 (0.66), residues: 53 loop : -0.26 (0.42), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 227 HIS 0.008 0.001 HIS P 68 PHE 0.020 0.002 PHE P 260 TYR 0.018 0.002 TYR P 475 ARG 0.009 0.001 ARG P 81 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 5 ARG cc_start: 0.7013 (OUTLIER) cc_final: 0.6531 (mtt90) REVERT: P 367 ASP cc_start: 0.7803 (t0) cc_final: 0.7526 (t0) REVERT: P 380 GLN cc_start: 0.6953 (tt0) cc_final: 0.6488 (tt0) REVERT: P 492 MET cc_start: 0.7223 (mmm) cc_final: 0.7000 (mmp) outliers start: 12 outliers final: 10 residues processed: 76 average time/residue: 0.5272 time to fit residues: 52.7576 Evaluate side-chains 72 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 5 ARG Chi-restraints excluded: chain P residue 43 SER Chi-restraints excluded: chain P residue 96 ASP Chi-restraints excluded: chain P residue 290 LYS Chi-restraints excluded: chain P residue 432 ASP Chi-restraints excluded: chain P residue 464 LEU Chi-restraints excluded: chain P residue 499 SER Chi-restraints excluded: chain P residue 522 LEU Chi-restraints excluded: chain P residue 538 VAL Chi-restraints excluded: chain P residue 654 TRP Chi-restraints excluded: chain P residue 655 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 64 optimal weight: 8.9990 chunk 52 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 19 optimal weight: 8.9990 chunk 25 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4466 moved from start: 0.6198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9403 Z= 0.235 Angle : 0.635 6.359 13534 Z= 0.348 Chirality : 0.038 0.178 1597 Planarity : 0.005 0.045 1055 Dihedral : 24.848 177.560 3245 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.55 % Allowed : 12.18 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 (0.35), residues: 604 helix: 1.31 (0.29), residues: 317 sheet: -1.72 (0.62), residues: 58 loop : -0.17 (0.44), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 335 HIS 0.008 0.001 HIS P 68 PHE 0.014 0.002 PHE P 260 TYR 0.012 0.002 TYR P 105 ARG 0.004 0.001 ARG P 325 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 5 ARG cc_start: 0.7016 (OUTLIER) cc_final: 0.6085 (mtt90) outliers start: 14 outliers final: 11 residues processed: 72 average time/residue: 0.5691 time to fit residues: 53.8072 Evaluate side-chains 69 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 5 ARG Chi-restraints excluded: chain P residue 43 SER Chi-restraints excluded: chain P residue 96 ASP Chi-restraints excluded: chain P residue 263 SER Chi-restraints excluded: chain P residue 290 LYS Chi-restraints excluded: chain P residue 432 ASP Chi-restraints excluded: chain P residue 464 LEU Chi-restraints excluded: chain P residue 499 SER Chi-restraints excluded: chain P residue 538 VAL Chi-restraints excluded: chain P residue 654 TRP Chi-restraints excluded: chain P residue 655 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 7.9990 chunk 18 optimal weight: 8.9990 chunk 75 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 34 optimal weight: 0.0870 chunk 6 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 72 optimal weight: 20.0000 chunk 8 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 overall best weight: 2.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4511 moved from start: 0.6530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9403 Z= 0.287 Angle : 0.664 6.708 13534 Z= 0.362 Chirality : 0.038 0.175 1597 Planarity : 0.006 0.051 1055 Dihedral : 24.944 179.027 3245 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.91 % Allowed : 13.82 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.43 (0.35), residues: 604 helix: 1.14 (0.29), residues: 317 sheet: -1.73 (0.69), residues: 53 loop : -0.27 (0.43), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 335 HIS 0.007 0.001 HIS P 68 PHE 0.019 0.002 PHE P 260 TYR 0.016 0.002 TYR P 105 ARG 0.004 0.001 ARG P 602 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 5 ARG cc_start: 0.7050 (OUTLIER) cc_final: 0.6705 (mtt90) outliers start: 16 outliers final: 13 residues processed: 74 average time/residue: 0.5062 time to fit residues: 49.8795 Evaluate side-chains 72 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 5 ARG Chi-restraints excluded: chain P residue 43 SER Chi-restraints excluded: chain P residue 96 ASP Chi-restraints excluded: chain P residue 263 SER Chi-restraints excluded: chain P residue 290 LYS Chi-restraints excluded: chain P residue 432 ASP Chi-restraints excluded: chain P residue 464 LEU Chi-restraints excluded: chain P residue 489 HIS Chi-restraints excluded: chain P residue 499 SER Chi-restraints excluded: chain P residue 522 LEU Chi-restraints excluded: chain P residue 538 VAL Chi-restraints excluded: chain P residue 654 TRP Chi-restraints excluded: chain P residue 655 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 47 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4471 moved from start: 0.6794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9403 Z= 0.236 Angle : 0.624 6.388 13534 Z= 0.340 Chirality : 0.037 0.165 1597 Planarity : 0.005 0.048 1055 Dihedral : 24.822 179.589 3245 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.18 % Allowed : 14.91 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.64 (0.35), residues: 604 helix: 1.40 (0.29), residues: 317 sheet: -1.80 (0.67), residues: 53 loop : -0.26 (0.43), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 335 HIS 0.005 0.001 HIS P 68 PHE 0.014 0.002 PHE P 260 TYR 0.014 0.002 TYR P 105 ARG 0.004 0.000 ARG P 325 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 5 ARG cc_start: 0.6984 (OUTLIER) cc_final: 0.6438 (mpt180) outliers start: 12 outliers final: 11 residues processed: 72 average time/residue: 0.5330 time to fit residues: 50.7113 Evaluate side-chains 70 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 5 ARG Chi-restraints excluded: chain P residue 43 SER Chi-restraints excluded: chain P residue 96 ASP Chi-restraints excluded: chain P residue 281 MET Chi-restraints excluded: chain P residue 290 LYS Chi-restraints excluded: chain P residue 432 ASP Chi-restraints excluded: chain P residue 464 LEU Chi-restraints excluded: chain P residue 489 HIS Chi-restraints excluded: chain P residue 499 SER Chi-restraints excluded: chain P residue 538 VAL Chi-restraints excluded: chain P residue 638 MET Chi-restraints excluded: chain P residue 654 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 59 optimal weight: 10.0000 chunk 68 optimal weight: 5.9990 chunk 72 optimal weight: 20.0000 chunk 65 optimal weight: 9.9990 chunk 70 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 647 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4496 moved from start: 0.6965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9403 Z= 0.253 Angle : 0.628 6.181 13534 Z= 0.343 Chirality : 0.037 0.166 1597 Planarity : 0.005 0.050 1055 Dihedral : 24.819 179.078 3245 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.18 % Allowed : 14.73 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.58 (0.35), residues: 604 helix: 1.35 (0.29), residues: 317 sheet: -1.81 (0.68), residues: 53 loop : -0.31 (0.43), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 335 HIS 0.003 0.001 HIS P 68 PHE 0.016 0.002 PHE P 260 TYR 0.014 0.002 TYR P 105 ARG 0.002 0.000 ARG P 270 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 5 ARG cc_start: 0.7017 (OUTLIER) cc_final: 0.6507 (mpt180) outliers start: 12 outliers final: 10 residues processed: 74 average time/residue: 0.5188 time to fit residues: 50.8696 Evaluate side-chains 72 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 5 ARG Chi-restraints excluded: chain P residue 43 SER Chi-restraints excluded: chain P residue 96 ASP Chi-restraints excluded: chain P residue 263 SER Chi-restraints excluded: chain P residue 290 LYS Chi-restraints excluded: chain P residue 432 ASP Chi-restraints excluded: chain P residue 464 LEU Chi-restraints excluded: chain P residue 489 HIS Chi-restraints excluded: chain P residue 499 SER Chi-restraints excluded: chain P residue 538 VAL Chi-restraints excluded: chain P residue 654 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 74 optimal weight: 30.0000 chunk 45 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 118 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4486 moved from start: 0.7219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9403 Z= 0.243 Angle : 0.617 6.226 13534 Z= 0.336 Chirality : 0.037 0.165 1597 Planarity : 0.005 0.050 1055 Dihedral : 24.794 179.605 3245 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.36 % Allowed : 14.73 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.76 (0.36), residues: 604 helix: 1.55 (0.29), residues: 311 sheet: -1.78 (0.70), residues: 53 loop : -0.24 (0.43), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 335 HIS 0.004 0.001 HIS P 68 PHE 0.014 0.002 PHE P 260 TYR 0.021 0.002 TYR P 475 ARG 0.007 0.000 ARG P 553 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 5 ARG cc_start: 0.6993 (OUTLIER) cc_final: 0.6498 (mpt180) outliers start: 13 outliers final: 10 residues processed: 71 average time/residue: 0.5776 time to fit residues: 54.0252 Evaluate side-chains 70 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 5 ARG Chi-restraints excluded: chain P residue 43 SER Chi-restraints excluded: chain P residue 96 ASP Chi-restraints excluded: chain P residue 290 LYS Chi-restraints excluded: chain P residue 334 MET Chi-restraints excluded: chain P residue 432 ASP Chi-restraints excluded: chain P residue 464 LEU Chi-restraints excluded: chain P residue 489 HIS Chi-restraints excluded: chain P residue 499 SER Chi-restraints excluded: chain P residue 538 VAL Chi-restraints excluded: chain P residue 654 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 47 optimal weight: 0.4980 chunk 37 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 65 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 57 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4499 moved from start: 0.7378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9403 Z= 0.248 Angle : 0.622 6.306 13534 Z= 0.338 Chirality : 0.037 0.166 1597 Planarity : 0.005 0.052 1055 Dihedral : 24.829 179.562 3245 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.36 % Allowed : 14.91 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.63 (0.35), residues: 604 helix: 1.44 (0.29), residues: 316 sheet: -1.87 (0.68), residues: 53 loop : -0.33 (0.43), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 335 HIS 0.004 0.001 HIS P 68 PHE 0.015 0.002 PHE P 260 TYR 0.014 0.002 TYR P 105 ARG 0.004 0.000 ARG P 325 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 5 ARG cc_start: 0.7009 (OUTLIER) cc_final: 0.6528 (mpt180) REVERT: P 492 MET cc_start: 0.6770 (mmp) cc_final: 0.6475 (mmm) outliers start: 13 outliers final: 12 residues processed: 73 average time/residue: 0.5932 time to fit residues: 56.2792 Evaluate side-chains 72 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 5 ARG Chi-restraints excluded: chain P residue 43 SER Chi-restraints excluded: chain P residue 96 ASP Chi-restraints excluded: chain P residue 263 SER Chi-restraints excluded: chain P residue 290 LYS Chi-restraints excluded: chain P residue 334 MET Chi-restraints excluded: chain P residue 432 ASP Chi-restraints excluded: chain P residue 464 LEU Chi-restraints excluded: chain P residue 489 HIS Chi-restraints excluded: chain P residue 499 SER Chi-restraints excluded: chain P residue 538 VAL Chi-restraints excluded: chain P residue 654 TRP Chi-restraints excluded: chain P residue 667 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 0.6980 chunk 61 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 44 optimal weight: 7.9990 chunk 70 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4819 r_free = 0.4819 target = 0.230962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.192682 restraints weight = 33904.792| |-----------------------------------------------------------------------------| r_work (start): 0.4419 rms_B_bonded: 2.79 r_work: 0.3981 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.7545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9403 Z= 0.177 Angle : 0.577 6.107 13534 Z= 0.313 Chirality : 0.035 0.161 1597 Planarity : 0.004 0.045 1055 Dihedral : 24.768 179.998 3245 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.18 % Allowed : 15.09 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.99 (0.36), residues: 604 helix: 1.79 (0.30), residues: 316 sheet: -1.78 (0.68), residues: 53 loop : -0.23 (0.43), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 335 HIS 0.005 0.001 HIS P 68 PHE 0.012 0.001 PHE P 663 TYR 0.010 0.001 TYR P 105 ARG 0.002 0.000 ARG P 270 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4858.56 seconds wall clock time: 87 minutes 4.57 seconds (5224.57 seconds total)