Starting phenix.real_space_refine on Fri Nov 15 02:01:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8squ_40713/11_2024/8squ_40713_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8squ_40713/11_2024/8squ_40713.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/8squ_40713/11_2024/8squ_40713.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8squ_40713/11_2024/8squ_40713.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8squ_40713/11_2024/8squ_40713_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8squ_40713/11_2024/8squ_40713_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= 0.030 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 41 5.49 5 Mg 1 5.21 5 S 22 5.16 5 C 4876 2.51 5 N 1295 2.21 5 O 1526 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 7761 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 3120 Classifications: {'peptide': 372} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 360} Chain breaks: 4 Chain: "B" Number of atoms: 3787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3787 Classifications: {'peptide': 469} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 444} Chain breaks: 1 Chain: "C" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 442 Classifications: {'RNA': 21} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 9, 'rna3p_pyr': 10} Link IDs: {'rna2p': 1, 'rna3p': 19} Chain: "D" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 411 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.37, per 1000 atoms: 0.69 Number of scatterers: 7761 At special positions: 0 Unit cell: (81.7, 104.5, 120.65, 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 22 16.00 P 41 15.00 Mg 1 11.99 O 1526 8.00 N 1295 7.00 C 4876 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.27 Conformation dependent library (CDL) restraints added in 898.6 milliseconds 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1598 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 8 sheets defined 36.5% alpha, 15.7% beta 9 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 2.52 Creating SS restraints... Processing helix chain 'A' and resid 14 through 28 Processing helix chain 'A' and resid 46 through 56 Processing helix chain 'A' and resid 72 through 89 Processing helix chain 'A' and resid 123 through 138 removed outlier: 4.101A pdb=" N GLY A 127 " --> pdb=" O SER A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 158 Processing helix chain 'A' and resid 199 through 203 Processing helix chain 'A' and resid 234 through 238 removed outlier: 3.781A pdb=" N LYS A 237 " --> pdb=" O HIS A 234 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR A 238 " --> pdb=" O LYS A 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 234 through 238' Processing helix chain 'A' and resid 242 through 249 removed outlier: 3.872A pdb=" N ILE A 246 " --> pdb=" O PRO A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 280 Processing helix chain 'A' and resid 353 through 365 Processing helix chain 'A' and resid 369 through 384 removed outlier: 3.672A pdb=" N LEU A 384 " --> pdb=" O PHE A 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 17 No H-bonds generated for 'chain 'B' and resid 15 through 17' Processing helix chain 'B' and resid 22 through 31 removed outlier: 3.516A pdb=" N PHE B 30 " --> pdb=" O GLY B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 61 removed outlier: 3.794A pdb=" N GLN B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 83 Processing helix chain 'B' and resid 97 through 105 removed outlier: 3.702A pdb=" N PHE B 104 " --> pdb=" O ASP B 100 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU B 105 " --> pdb=" O ILE B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 131 removed outlier: 3.615A pdb=" N ARG B 113 " --> pdb=" O SER B 109 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS B 124 " --> pdb=" O LEU B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 150 removed outlier: 3.734A pdb=" N TYR B 148 " --> pdb=" O PRO B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 214 removed outlier: 4.082A pdb=" N GLN B 209 " --> pdb=" O GLN B 205 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU B 214 " --> pdb=" O PHE B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 230 Processing helix chain 'B' and resid 248 through 264 Processing helix chain 'B' and resid 331 through 350 Processing helix chain 'B' and resid 366 through 376 removed outlier: 4.034A pdb=" N VAL B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 462 Processing helix chain 'B' and resid 477 through 480 Processing helix chain 'B' and resid 481 through 490 Processing sheet with id=AA1, first strand: chain 'A' and resid 170 through 171 Processing sheet with id=AA2, first strand: chain 'A' and resid 283 through 286 removed outlier: 6.542A pdb=" N THR A 291 " --> pdb=" O GLY A 325 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLY A 325 " --> pdb=" O THR A 291 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 283 through 286 removed outlier: 6.542A pdb=" N THR A 291 " --> pdb=" O GLY A 325 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLY A 325 " --> pdb=" O THR A 291 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU A 176 " --> pdb=" O LEU A 335 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N TRP A 175 " --> pdb=" O GLU A 406 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N GLU A 406 " --> pdb=" O TRP A 175 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N SER A 177 " --> pdb=" O SER A 404 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N PHE A 402 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL A 401 " --> pdb=" O LEU A 393 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A 403 " --> pdb=" O PHE A 391 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 208 through 210 Processing sheet with id=AA5, first strand: chain 'B' and resid 5 through 6 removed outlier: 3.598A pdb=" N VAL B 413 " --> pdb=" O SER B 417 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N SER B 417 " --> pdb=" O VAL B 413 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N GLY B 385 " --> pdb=" O ASN B 446 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N VAL B 357 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N VAL B 386 " --> pdb=" O VAL B 357 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ILE B 359 " --> pdb=" O VAL B 386 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ILE B 388 " --> pdb=" O ILE B 359 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ALA B 361 " --> pdb=" O ILE B 388 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 19 through 20 removed outlier: 3.503A pdb=" N LYS B 270 " --> pdb=" O LEU B 13 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 41 through 44 removed outlier: 5.835A pdb=" N GLY B 42 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ILE B 142 " --> pdb=" O GLY B 42 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ILE B 44 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N TRP B 139 " --> pdb=" O GLN B 222 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N PHE B 224 " --> pdb=" O TRP B 139 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N VAL B 141 " --> pdb=" O PHE B 224 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 302 through 304 removed outlier: 3.705A pdb=" N GLN B 302 " --> pdb=" O LYS B 314 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS B 314 " --> pdb=" O GLN B 302 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHE B 304 " --> pdb=" O VAL B 312 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL B 312 " --> pdb=" O PHE B 304 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 267 hydrogen bonds defined for protein. 750 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 23 hydrogen bonds 46 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 2.62 Time building geometry restraints manager: 2.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1819 1.33 - 1.45: 1869 1.45 - 1.57: 4234 1.57 - 1.69: 80 1.69 - 1.81: 33 Bond restraints: 8035 Sorted by residual: bond pdb=" O5' G C 20 " pdb=" C5' G C 20 " ideal model delta sigma weight residual 1.420 1.449 -0.029 1.50e-02 4.44e+03 3.72e+00 bond pdb=" O5' U C 21 " pdb=" C5' U C 21 " ideal model delta sigma weight residual 1.424 1.452 -0.028 1.50e-02 4.44e+03 3.50e+00 bond pdb=" O5' U C 10 " pdb=" C5' U C 10 " ideal model delta sigma weight residual 1.420 1.445 -0.025 1.50e-02 4.44e+03 2.85e+00 bond pdb=" O5' U C 13 " pdb=" C5' U C 13 " ideal model delta sigma weight residual 1.420 1.445 -0.025 1.50e-02 4.44e+03 2.76e+00 bond pdb=" P G C 20 " pdb=" OP2 G C 20 " ideal model delta sigma weight residual 1.485 1.518 -0.033 2.00e-02 2.50e+03 2.68e+00 ... (remaining 8030 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 10815 2.00 - 4.00: 179 4.00 - 5.99: 33 5.99 - 7.99: 5 7.99 - 9.99: 1 Bond angle restraints: 11033 Sorted by residual: angle pdb=" CA MET B 303 " pdb=" CB MET B 303 " pdb=" CG MET B 303 " ideal model delta sigma weight residual 114.10 120.87 -6.77 2.00e+00 2.50e-01 1.15e+01 angle pdb=" CA ARG A 197 " pdb=" CB ARG A 197 " pdb=" CG ARG A 197 " ideal model delta sigma weight residual 114.10 120.56 -6.46 2.00e+00 2.50e-01 1.04e+01 angle pdb=" N GLU B 476 " pdb=" CA GLU B 476 " pdb=" C GLU B 476 " ideal model delta sigma weight residual 109.48 103.90 5.58 1.75e+00 3.27e-01 1.02e+01 angle pdb=" C3' A C 12 " pdb=" C2' A C 12 " pdb=" C1' A C 12 " ideal model delta sigma weight residual 101.30 104.36 -3.06 1.00e+00 1.00e+00 9.38e+00 angle pdb=" O5' U C 13 " pdb=" C5' U C 13 " pdb=" C4' U C 13 " ideal model delta sigma weight residual 111.50 106.95 4.55 1.50e+00 4.44e-01 9.20e+00 ... (remaining 11028 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.51: 4599 35.51 - 71.02: 160 71.02 - 106.53: 11 106.53 - 142.04: 2 142.04 - 177.55: 4 Dihedral angle restraints: 4776 sinusoidal: 2304 harmonic: 2472 Sorted by residual: dihedral pdb=" O4' U C 17 " pdb=" C1' U C 17 " pdb=" N1 U C 17 " pdb=" C2 U C 17 " ideal model delta sinusoidal sigma weight residual 200.00 45.61 154.39 1 1.50e+01 4.44e-03 8.11e+01 dihedral pdb=" O4' U C 13 " pdb=" C1' U C 13 " pdb=" N1 U C 13 " pdb=" C2 U C 13 " ideal model delta sinusoidal sigma weight residual 200.00 74.41 125.59 1 1.50e+01 4.44e-03 6.75e+01 dihedral pdb=" O4' U C 1 " pdb=" C1' U C 1 " pdb=" N1 U C 1 " pdb=" C2 U C 1 " ideal model delta sinusoidal sigma weight residual -128.00 49.55 -177.55 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 4773 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 1157 0.105 - 0.210: 43 0.210 - 0.315: 0 0.315 - 0.419: 3 0.419 - 0.524: 3 Chirality restraints: 1206 Sorted by residual: chirality pdb=" P U C 10 " pdb=" OP1 U C 10 " pdb=" OP2 U C 10 " pdb=" O5' U C 10 " both_signs ideal model delta sigma weight residual True 2.41 -2.93 -0.52 2.00e-01 2.50e+01 6.87e+00 chirality pdb=" P U C 21 " pdb=" OP1 U C 21 " pdb=" OP2 U C 21 " pdb=" O5' U C 21 " both_signs ideal model delta sigma weight residual True 2.41 -2.88 -0.47 2.00e-01 2.50e+01 5.63e+00 chirality pdb=" P G C 20 " pdb=" OP1 G C 20 " pdb=" OP2 G C 20 " pdb=" O5' G C 20 " both_signs ideal model delta sigma weight residual True 2.41 -2.86 -0.45 2.00e-01 2.50e+01 5.03e+00 ... (remaining 1203 not shown) Planarity restraints: 1244 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 331 " -0.037 5.00e-02 4.00e+02 5.67e-02 5.14e+00 pdb=" N PRO B 332 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO B 332 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 332 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 430 " -0.010 2.00e-02 2.50e+03 1.91e-02 3.64e+00 pdb=" C GLN B 430 " 0.033 2.00e-02 2.50e+03 pdb=" O GLN B 430 " -0.012 2.00e-02 2.50e+03 pdb=" N THR B 431 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 181 " -0.025 5.00e-02 4.00e+02 3.73e-02 2.22e+00 pdb=" N PRO A 182 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 182 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 182 " -0.021 5.00e-02 4.00e+02 ... (remaining 1241 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 53 2.55 - 3.14: 5763 3.14 - 3.73: 12155 3.73 - 4.31: 16269 4.31 - 4.90: 25918 Nonbonded interactions: 60158 Sorted by model distance: nonbonded pdb=" O TYR B 506 " pdb="MG MG B 601 " model vdw 1.967 2.170 nonbonded pdb=" OP2 U C 1 " pdb="MG MG B 601 " model vdw 1.976 2.170 nonbonded pdb=" OP1 U C 1 " pdb="MG MG B 601 " model vdw 2.087 2.170 nonbonded pdb=" O GLY B 487 " pdb=" OG1 THR B 491 " model vdw 2.117 3.040 nonbonded pdb=" OG SER B 291 " pdb=" O ASN B 293 " model vdw 2.167 3.040 ... (remaining 60153 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 23.550 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6180 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 : 0.003 0.046 8035 Z= 0.199 Angle : 0.625 9.991 11033 Z= 0.326 Chirality : 0.054 0.524 1206 Planarity : 0.004 0.057 1244 Dihedral : 18.098 177.551 3178 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.59 (0.30), residues: 827 helix: 1.71 (0.33), residues: 275 sheet: -0.53 (0.47), residues: 138 loop : -1.89 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 370 HIS 0.002 0.001 HIS B 329 PHE 0.020 0.002 PHE B 373 TYR 0.011 0.001 TYR A 293 ARG 0.002 0.000 ARG A 201 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.921 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: A 14 ASP cc_start: 0.8279 (m-30) cc_final: 0.7875 (m-30) REVERT: B 303 MET cc_start: 0.4240 (mmp) cc_final: 0.2824 (tpt) REVERT: B 396 LEU cc_start: 0.6911 (mt) cc_final: 0.6116 (mt) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.2372 time to fit residues: 56.2570 Evaluate side-chains 90 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 73 optimal weight: 3.9990 chunk 65 optimal weight: 0.0000 chunk 36 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 44 optimal weight: 0.0470 chunk 35 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 50 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 overall best weight: 0.9284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 GLN B 61 GLN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6292 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8035 Z= 0.213 Angle : 0.669 8.903 11033 Z= 0.344 Chirality : 0.046 0.372 1206 Planarity : 0.004 0.053 1244 Dihedral : 19.116 177.337 1453 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.93 % Allowed : 11.58 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.49 (0.29), residues: 827 helix: 1.69 (0.32), residues: 283 sheet: -0.55 (0.45), residues: 150 loop : -1.81 (0.28), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 319 HIS 0.003 0.001 HIS B 329 PHE 0.014 0.002 PHE B 82 TYR 0.021 0.001 TYR A 416 ARG 0.004 0.000 ARG A 374 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 101 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 396 LEU cc_start: 0.6964 (mt) cc_final: 0.6138 (mt) outliers start: 7 outliers final: 4 residues processed: 103 average time/residue: 0.1874 time to fit residues: 27.1047 Evaluate side-chains 82 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 78 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 431 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 43 optimal weight: 0.4980 chunk 24 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 53 optimal weight: 0.0170 chunk 21 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 78 optimal weight: 0.0040 chunk 26 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.4030 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6245 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8035 Z= 0.172 Angle : 0.624 9.382 11033 Z= 0.321 Chirality : 0.044 0.302 1206 Planarity : 0.004 0.049 1244 Dihedral : 19.239 177.663 1453 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.20 % Allowed : 13.45 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 (0.29), residues: 827 helix: 1.80 (0.32), residues: 283 sheet: -0.36 (0.45), residues: 148 loop : -1.76 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 370 HIS 0.008 0.001 HIS A 358 PHE 0.013 0.001 PHE A 321 TYR 0.013 0.001 TYR B 505 ARG 0.003 0.000 ARG A 374 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 226 GLU cc_start: 0.6683 (OUTLIER) cc_final: 0.6365 (mt-10) REVERT: B 396 LEU cc_start: 0.6983 (mt) cc_final: 0.5809 (mp) outliers start: 9 outliers final: 4 residues processed: 103 average time/residue: 0.1909 time to fit residues: 27.3565 Evaluate side-chains 81 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 431 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 78 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 41 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 84 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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: 0.6304 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8035 Z= 0.186 Angle : 0.619 10.548 11033 Z= 0.317 Chirality : 0.043 0.227 1206 Planarity : 0.004 0.049 1244 Dihedral : 19.282 179.565 1453 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.00 % Allowed : 13.72 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.23 (0.29), residues: 827 helix: 1.98 (0.32), residues: 283 sheet: -0.41 (0.45), residues: 148 loop : -1.72 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 319 HIS 0.007 0.001 HIS A 358 PHE 0.017 0.001 PHE A 410 TYR 0.013 0.001 TYR B 56 ARG 0.002 0.000 ARG A 374 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 8 residues processed: 91 average time/residue: 0.2001 time to fit residues: 25.6806 Evaluate side-chains 84 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 486 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 47 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 42 optimal weight: 4.9990 chunk 75 optimal weight: 0.0170 chunk 21 optimal weight: 6.9990 chunk 28 optimal weight: 0.5980 overall best weight: 2.3224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6530 moved from start: 0.4290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8035 Z= 0.305 Angle : 0.701 9.587 11033 Z= 0.363 Chirality : 0.047 0.258 1206 Planarity : 0.004 0.055 1244 Dihedral : 19.615 178.006 1453 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 2.66 % Allowed : 13.85 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.52 (0.29), residues: 827 helix: 1.67 (0.32), residues: 285 sheet: -0.66 (0.44), residues: 156 loop : -1.82 (0.28), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 319 HIS 0.003 0.001 HIS A 340 PHE 0.022 0.002 PHE A 223 TYR 0.017 0.002 TYR A 416 ARG 0.004 0.000 ARG B 213 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 83 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 ASN cc_start: 0.7798 (p0) cc_final: 0.7571 (p0) REVERT: B 303 MET cc_start: 0.5948 (mmm) cc_final: 0.5055 (mmt) outliers start: 20 outliers final: 11 residues processed: 91 average time/residue: 0.1905 time to fit residues: 24.4773 Evaluate side-chains 80 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 486 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 75 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 6 optimal weight: 50.0000 chunk 27 optimal weight: 2.9990 chunk 44 optimal weight: 0.2980 chunk 81 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 HIS B 439 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6389 moved from start: 0.4477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8035 Z= 0.179 Angle : 0.618 9.497 11033 Z= 0.319 Chirality : 0.043 0.230 1206 Planarity : 0.004 0.058 1244 Dihedral : 19.649 177.244 1453 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.73 % Allowed : 15.98 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 (0.29), residues: 827 helix: 1.88 (0.32), residues: 285 sheet: -0.49 (0.45), residues: 151 loop : -1.73 (0.28), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 319 HIS 0.003 0.000 HIS A 358 PHE 0.012 0.001 PHE A 380 TYR 0.010 0.001 TYR B 56 ARG 0.002 0.000 ARG A 276 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 6 residues processed: 86 average time/residue: 0.1847 time to fit residues: 22.4616 Evaluate side-chains 78 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 HIS Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 439 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 9 optimal weight: 8.9990 chunk 47 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 83 optimal weight: 8.9990 chunk 52 optimal weight: 7.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 33 optimal weight: 0.0670 chunk 50 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 overall best weight: 1.3122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 360 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6444 moved from start: 0.4678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8035 Z= 0.213 Angle : 0.661 12.763 11033 Z= 0.339 Chirality : 0.043 0.240 1206 Planarity : 0.004 0.058 1244 Dihedral : 19.718 178.624 1453 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 1.86 % Allowed : 17.31 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 (0.29), residues: 827 helix: 1.87 (0.32), residues: 286 sheet: -0.56 (0.44), residues: 151 loop : -1.72 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 319 HIS 0.009 0.001 HIS A 358 PHE 0.014 0.002 PHE B 304 TYR 0.011 0.001 TYR A 392 ARG 0.002 0.000 ARG B 213 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 303 MET cc_start: 0.5628 (mmm) cc_final: 0.4226 (mmt) outliers start: 14 outliers final: 10 residues processed: 81 average time/residue: 0.1945 time to fit residues: 22.4898 Evaluate side-chains 82 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 439 ASN Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 486 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 16 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 chunk 57 optimal weight: 7.9990 chunk 41 optimal weight: 8.9990 chunk 7 optimal weight: 0.9990 chunk 65 optimal weight: 0.0980 chunk 76 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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: 0.6483 moved from start: 0.4946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8035 Z= 0.230 Angle : 0.666 11.613 11033 Z= 0.342 Chirality : 0.044 0.250 1206 Planarity : 0.004 0.062 1244 Dihedral : 19.777 178.110 1453 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 1.20 % Allowed : 17.58 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 (0.29), residues: 827 helix: 1.79 (0.32), residues: 286 sheet: -0.51 (0.45), residues: 145 loop : -1.76 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 319 HIS 0.008 0.001 HIS A 358 PHE 0.014 0.002 PHE A 223 TYR 0.011 0.001 TYR A 392 ARG 0.003 0.000 ARG B 213 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.866 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 8 residues processed: 81 average time/residue: 0.1638 time to fit residues: 19.8030 Evaluate side-chains 79 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 486 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 34 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 70 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 51 optimal weight: 0.4980 chunk 82 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6413 moved from start: 0.5107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8035 Z= 0.188 Angle : 0.654 11.549 11033 Z= 0.334 Chirality : 0.043 0.242 1206 Planarity : 0.004 0.061 1244 Dihedral : 19.820 178.941 1453 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 0.80 % Allowed : 18.51 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 (0.29), residues: 827 helix: 1.87 (0.32), residues: 287 sheet: -0.53 (0.45), residues: 145 loop : -1.70 (0.28), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP A 319 HIS 0.007 0.001 HIS A 358 PHE 0.014 0.001 PHE B 304 TYR 0.022 0.001 TYR A 416 ARG 0.002 0.000 ARG B 481 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.782 Fit side-chains revert: symmetry clash REVERT: B 303 MET cc_start: 0.5385 (mmm) cc_final: 0.4039 (mmt) REVERT: B 316 GLU cc_start: 0.7247 (OUTLIER) cc_final: 0.6932 (pp20) outliers start: 6 outliers final: 5 residues processed: 76 average time/residue: 0.1703 time to fit residues: 19.2917 Evaluate side-chains 74 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 486 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 86 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 7 optimal weight: 8.9990 chunk 53 optimal weight: 5.9990 chunk 42 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 chunk 73 optimal weight: 8.9990 chunk 21 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6540 moved from start: 0.5308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8035 Z= 0.287 Angle : 0.723 11.729 11033 Z= 0.372 Chirality : 0.045 0.268 1206 Planarity : 0.004 0.065 1244 Dihedral : 19.874 179.165 1453 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 16.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 1.60 % Allowed : 17.84 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.44 (0.30), residues: 827 helix: 1.77 (0.32), residues: 286 sheet: -0.69 (0.45), residues: 145 loop : -1.76 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 319 HIS 0.009 0.001 HIS A 358 PHE 0.017 0.002 PHE A 223 TYR 0.020 0.002 TYR A 416 ARG 0.003 0.000 ARG B 213 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.813 Fit side-chains REVERT: B 74 MET cc_start: 0.3628 (tpp) cc_final: 0.3367 (tpt) REVERT: B 303 MET cc_start: 0.5946 (mmm) cc_final: 0.4618 (mmt) REVERT: B 316 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.6977 (pp20) outliers start: 12 outliers final: 9 residues processed: 75 average time/residue: 0.1647 time to fit residues: 18.8844 Evaluate side-chains 75 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 486 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 19 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 8 optimal weight: 0.0970 chunk 12 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 chunk 49 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 209 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 = 0.4541 r_free = 0.4541 target = 0.148968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.115152 restraints weight = 21809.750| |-----------------------------------------------------------------------------| r_work (start): 0.4053 rms_B_bonded: 6.55 r_work (final): 0.4053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 moved from start: 0.5448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8035 Z= 0.190 Angle : 0.674 11.787 11033 Z= 0.344 Chirality : 0.043 0.245 1206 Planarity : 0.004 0.060 1244 Dihedral : 19.895 179.936 1453 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.20 % Allowed : 17.98 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 (0.30), residues: 827 helix: 1.85 (0.32), residues: 287 sheet: -0.55 (0.45), residues: 145 loop : -1.68 (0.29), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 319 HIS 0.006 0.001 HIS A 358 PHE 0.023 0.001 PHE A 273 TYR 0.020 0.001 TYR A 416 ARG 0.003 0.000 ARG B 481 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1879.66 seconds wall clock time: 34 minutes 58.41 seconds (2098.41 seconds total)