Starting phenix.real_space_refine on Sat Apr 6 08:42:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8squ_40713/04_2024/8squ_40713_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8squ_40713/04_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_40713/04_2024/8squ_40713.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8squ_40713/04_2024/8squ_40713.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8squ_40713/04_2024/8squ_40713_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8squ_40713/04_2024/8squ_40713_neut.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 4.99, per 1000 atoms: 0.64 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 - 3.50 Amino acid : False - 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: 3.19 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 2.46 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: 2.57 Time building geometry restraints manager: 3.43 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: 98.93 - 105.96: 350 105.96 - 112.98: 4285 112.98 - 120.00: 2794 120.00 - 127.03: 3425 127.03 - 134.05: 179 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 2.440 nonbonded pdb=" OG SER B 291 " pdb=" O ASN B 293 " model vdw 2.167 2.440 ... (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 ========== 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: 0.960 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: 3.820 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 26.990 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.970 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 0.783 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: 0.2209 time to fit residues: 52.6431 Evaluate side-chains 90 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.814 ------------------------------------------------------------------------------- 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: 4.9990 chunk 65 optimal weight: 0.0770 chunk 36 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 44 optimal weight: 0.4980 chunk 35 optimal weight: 0.0970 chunk 68 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 41 optimal weight: 10.0000 chunk 50 optimal weight: 7.9990 chunk 79 optimal weight: 3.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- 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: 0.6240 moved from start: 0.2513 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= 0.181 Angle : 0.641 9.541 11033 Z= 0.328 Chirality : 0.045 0.359 1206 Planarity : 0.004 0.053 1244 Dihedral : 19.080 177.731 1453 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.07 % Allowed : 11.32 % Favored : 87.62 % 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: -0.37 (0.30), residues: 827 helix: 1.77 (0.33), residues: 283 sheet: -0.41 (0.46), residues: 140 loop : -1.74 (0.28), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 319 HIS 0.004 0.001 HIS B 329 PHE 0.016 0.002 PHE A 198 TYR 0.021 0.001 TYR A 416 ARG 0.005 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 115 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 107 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 396 LEU cc_start: 0.6969 (mt) cc_final: 0.5930 (mp) outliers start: 8 outliers final: 5 residues processed: 110 average time/residue: 0.1957 time to fit residues: 30.3016 Evaluate side-chains 85 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 80 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 476 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 43 optimal weight: 20.0000 chunk 24 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 79 optimal weight: 0.2980 chunk 85 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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: 0.6328 moved from start: 0.3130 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= 0.194 Angle : 0.615 9.514 11033 Z= 0.316 Chirality : 0.043 0.323 1206 Planarity : 0.004 0.051 1244 Dihedral : 19.182 177.976 1453 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 1.60 % Allowed : 13.72 % Favored : 84.69 % 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: -0.25 (0.29), residues: 827 helix: 1.87 (0.32), residues: 283 sheet: -0.37 (0.46), residues: 140 loop : -1.66 (0.28), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 319 HIS 0.015 0.001 HIS A 358 PHE 0.018 0.002 PHE A 410 TYR 0.017 0.001 TYR A 210 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 102 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 90 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 226 GLU cc_start: 0.6722 (OUTLIER) cc_final: 0.6427 (mt-10) REVERT: B 407 ARG cc_start: 0.6417 (ttt-90) cc_final: 0.6176 (ptp-110) outliers start: 12 outliers final: 7 residues processed: 98 average time/residue: 0.2335 time to fit residues: 31.8451 Evaluate side-chains 86 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 78 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 97 THR 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 Chi-restraints excluded: chain B residue 476 GLU 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: 0.8980 chunk 41 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 84 optimal weight: 5.9990 chunk 75 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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: 0.6326 moved from start: 0.3553 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= 0.178 Angle : 0.593 10.562 11033 Z= 0.301 Chirality : 0.042 0.229 1206 Planarity : 0.003 0.049 1244 Dihedral : 19.284 177.158 1453 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.73 % Allowed : 15.05 % Favored : 83.22 % 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: -0.12 (0.30), residues: 827 helix: 2.06 (0.32), residues: 285 sheet: -0.34 (0.44), residues: 151 loop : -1.68 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 86 HIS 0.011 0.001 HIS A 358 PHE 0.011 0.001 PHE A 380 TYR 0.020 0.001 TYR A 210 ARG 0.002 0.000 ARG A 361 *********************** 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 95 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 82 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 LYS cc_start: 0.6351 (pptt) cc_final: 0.6064 (ttpt) REVERT: B 303 MET cc_start: 0.5569 (mmm) cc_final: 0.5296 (mmm) outliers start: 13 outliers final: 11 residues processed: 87 average time/residue: 0.1985 time to fit residues: 24.0241 Evaluate side-chains 83 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 72 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain B residue 97 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 417 SER Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 476 GLU 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: 10.0000 chunk 1 optimal weight: 9.9990 chunk 62 optimal weight: 0.0980 chunk 34 optimal weight: 0.9990 chunk 71 optimal weight: 0.3980 chunk 58 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 7.9990 chunk 75 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6360 moved from start: 0.3853 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 : 0.589 11.463 11033 Z= 0.301 Chirality : 0.042 0.233 1206 Planarity : 0.004 0.047 1244 Dihedral : 19.365 176.707 1453 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.13 % Allowed : 15.45 % Favored : 82.42 % 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: -0.06 (0.30), residues: 827 helix: 2.16 (0.32), residues: 284 sheet: -0.27 (0.45), residues: 145 loop : -1.67 (0.28), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 370 HIS 0.015 0.001 HIS A 358 PHE 0.011 0.001 PHE A 332 TYR 0.027 0.001 TYR A 210 ARG 0.003 0.000 ARG A 361 *********************** 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 94 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 78 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 LYS cc_start: 0.6474 (pptt) cc_final: 0.6269 (ttpt) REVERT: B 407 ARG cc_start: 0.6459 (ttt-90) cc_final: 0.6050 (ptp-110) outliers start: 16 outliers final: 10 residues processed: 85 average time/residue: 0.1880 time to fit residues: 22.5482 Evaluate side-chains 81 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 71 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain B residue 97 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 431 THR 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: 0.0060 chunk 16 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 84 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 6 optimal weight: 50.0000 chunk 27 optimal weight: 2.9990 chunk 44 optimal weight: 0.0470 chunk 81 optimal weight: 0.8980 overall best weight: 0.5494 ------------------------------------------------------------------------------- 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: 0.6303 moved from start: 0.4129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 8035 Z= 0.157 Angle : 0.581 13.549 11033 Z= 0.293 Chirality : 0.041 0.229 1206 Planarity : 0.003 0.047 1244 Dihedral : 19.469 176.622 1453 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.60 % Allowed : 15.98 % Favored : 82.42 % 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: -0.01 (0.30), residues: 827 helix: 2.18 (0.32), residues: 285 sheet: -0.18 (0.45), residues: 143 loop : -1.66 (0.28), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 319 HIS 0.013 0.001 HIS A 358 PHE 0.009 0.001 PHE B 206 TYR 0.019 0.001 TYR A 210 ARG 0.002 0.000 ARG A 361 *********************** 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 96 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 84 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 LYS cc_start: 0.6343 (pptt) cc_final: 0.6123 (ttpt) outliers start: 12 outliers final: 9 residues processed: 90 average time/residue: 0.1954 time to fit residues: 24.6895 Evaluate side-chains 83 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 74 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain B residue 59 HIS Chi-restraints excluded: chain B residue 97 THR 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 431 THR Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 486 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 9 optimal weight: 4.9990 chunk 47 optimal weight: 20.0000 chunk 61 optimal weight: 0.8980 chunk 70 optimal weight: 0.7980 chunk 83 optimal weight: 8.9990 chunk 52 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 33 optimal weight: 0.0010 chunk 50 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6321 moved from start: 0.4336 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= 0.168 Angle : 0.603 14.725 11033 Z= 0.303 Chirality : 0.042 0.232 1206 Planarity : 0.003 0.045 1244 Dihedral : 19.510 177.088 1453 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.73 % Allowed : 17.04 % 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: 0.07 (0.30), residues: 827 helix: 2.29 (0.32), residues: 283 sheet: -0.18 (0.46), residues: 143 loop : -1.62 (0.28), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 319 HIS 0.007 0.001 HIS A 358 PHE 0.011 0.001 PHE A 332 TYR 0.021 0.001 TYR A 210 ARG 0.002 0.000 ARG A 361 *********************** 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 93 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 80 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 LYS cc_start: 0.6426 (pptt) cc_final: 0.6203 (ttpt) outliers start: 13 outliers final: 10 residues processed: 86 average time/residue: 0.1948 time to fit residues: 23.7139 Evaluate side-chains 87 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 77 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain B residue 97 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 431 THR 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: 0.9990 chunk 53 optimal weight: 8.9990 chunk 57 optimal weight: 0.0010 chunk 41 optimal weight: 9.9990 chunk 7 optimal weight: 20.0000 chunk 65 optimal weight: 4.9990 chunk 76 optimal weight: 0.6980 chunk 80 optimal weight: 7.9990 chunk 73 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 47 optimal weight: 9.9990 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6325 moved from start: 0.4532 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= 0.170 Angle : 0.600 15.288 11033 Z= 0.301 Chirality : 0.042 0.233 1206 Planarity : 0.004 0.044 1244 Dihedral : 19.562 177.129 1453 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 1.33 % Allowed : 17.04 % Favored : 81.62 % 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: 0.07 (0.30), residues: 827 helix: 2.25 (0.32), residues: 283 sheet: -0.15 (0.46), residues: 143 loop : -1.59 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 319 HIS 0.007 0.001 HIS A 358 PHE 0.010 0.001 PHE A 332 TYR 0.019 0.001 TYR A 210 ARG 0.002 0.000 ARG A 361 *********************** 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 89 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 79 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 LYS cc_start: 0.6448 (pptt) cc_final: 0.6236 (ttpt) outliers start: 10 outliers final: 10 residues processed: 84 average time/residue: 0.1867 time to fit residues: 22.0756 Evaluate side-chains 83 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 73 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain B residue 97 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 431 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: 0.4980 chunk 61 optimal weight: 0.7980 chunk 23 optimal weight: 6.9990 chunk 70 optimal weight: 0.4980 chunk 73 optimal weight: 0.9990 chunk 77 optimal weight: 0.2980 chunk 51 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 50 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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: 0.6295 moved from start: 0.4756 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= 0.167 Angle : 0.619 16.530 11033 Z= 0.309 Chirality : 0.041 0.231 1206 Planarity : 0.004 0.047 1244 Dihedral : 19.599 177.617 1453 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.33 % Allowed : 17.58 % Favored : 81.09 % 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: 0.10 (0.30), residues: 827 helix: 2.29 (0.32), residues: 283 sheet: -0.10 (0.46), residues: 143 loop : -1.59 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 319 HIS 0.006 0.001 HIS A 358 PHE 0.018 0.001 PHE A 273 TYR 0.021 0.001 TYR A 210 ARG 0.001 0.000 ARG A 361 *********************** 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 83 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 73 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 LYS cc_start: 0.6528 (pptt) cc_final: 0.6284 (ttpt) REVERT: B 303 MET cc_start: 0.5094 (mmm) cc_final: 0.4710 (mmm) outliers start: 10 outliers final: 8 residues processed: 79 average time/residue: 0.1932 time to fit residues: 21.7172 Evaluate side-chains 78 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 70 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain B residue 97 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 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 86 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 7 optimal weight: 20.0000 chunk 53 optimal weight: 4.9990 chunk 42 optimal weight: 8.9990 chunk 54 optimal weight: 0.8980 chunk 73 optimal weight: 0.0170 chunk 21 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 overall best weight: 1.1824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6388 moved from start: 0.4890 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= 0.202 Angle : 0.643 16.392 11033 Z= 0.322 Chirality : 0.042 0.242 1206 Planarity : 0.003 0.043 1244 Dihedral : 19.607 177.216 1453 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % 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: 0.06 (0.30), residues: 827 helix: 2.25 (0.32), residues: 283 sheet: -0.13 (0.45), residues: 143 loop : -1.61 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A 319 HIS 0.006 0.001 HIS A 358 PHE 0.022 0.002 PHE A 198 TYR 0.023 0.001 TYR A 210 ARG 0.002 0.000 ARG A 361 ********************** 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 fitting. rotamer outliers: 9 poor density : 72 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 LYS cc_start: 0.6723 (pptt) cc_final: 0.6465 (pttm) REVERT: B 82 PHE cc_start: 0.5916 (m-10) cc_final: 0.5354 (m-80) REVERT: B 303 MET cc_start: 0.5177 (mmm) cc_final: 0.4832 (mmm) outliers start: 9 outliers final: 8 residues processed: 78 average time/residue: 0.1765 time to fit residues: 19.9615 Evaluate side-chains 79 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 71 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain B residue 97 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 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: 0.8980 chunk 69 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 8 optimal weight: 0.4980 chunk 12 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 3 optimal weight: 40.0000 chunk 49 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 chunk 46 optimal weight: 9.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.151200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.118120 restraints weight = 21587.128| |-----------------------------------------------------------------------------| r_work (start): 0.4065 rms_B_bonded: 6.70 r_work (final): 0.4065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.5056 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= 0.185 Angle : 0.638 16.855 11033 Z= 0.320 Chirality : 0.042 0.234 1206 Planarity : 0.004 0.050 1244 Dihedral : 19.630 177.106 1453 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.07 % Allowed : 18.38 % 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: 0.08 (0.30), residues: 827 helix: 2.20 (0.32), residues: 285 sheet: -0.16 (0.45), residues: 145 loop : -1.55 (0.29), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 319 HIS 0.006 0.001 HIS A 358 PHE 0.016 0.001 PHE A 273 TYR 0.021 0.001 TYR A 210 ARG 0.002 0.000 ARG A 361 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1923.20 seconds wall clock time: 36 minutes 1.49 seconds (2161.49 seconds total)