Starting phenix.real_space_refine on Thu Nov 14 15:52:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvv_17973/11_2024/8pvv_17973.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvv_17973/11_2024/8pvv_17973.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvv_17973/11_2024/8pvv_17973.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvv_17973/11_2024/8pvv_17973.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvv_17973/11_2024/8pvv_17973.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvv_17973/11_2024/8pvv_17973.cif" } resolution = 2.81 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= 0.000 sd= 1.000 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 50 5.49 5 Mg 1 5.21 5 S 13 5.16 5 C 3979 2.51 5 N 1079 2.21 5 O 1355 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 6477 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3478 Classifications: {'peptide': 427} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 403} Chain: "C" Number of atoms: 1913 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 229, 1894 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 8, 'TRANS': 220} Conformer: "B" Number of residues, atoms: 229, 1894 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 8, 'TRANS': 220} bond proxies already assigned to first conformer: 1916 Chain: "R" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 549 Classifications: {'RNA': 25} Modifications used: {'p5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 18, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 23} Chain: "S" Number of atoms: 500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 500 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "R" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "S" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ALYS C 52 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS C 52 " occ=0.50 residue: pdb=" N AHIS C 137 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS C 137 " occ=0.50 Time building chain proxies: 5.33, per 1000 atoms: 0.82 Number of scatterers: 6477 At special positions: 0 Unit cell: (75.9, 83.6, 99, 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 13 16.00 P 50 15.00 Mg 1 11.99 O 1355 8.00 N 1079 7.00 C 3979 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: 2.25 Conformation dependent library (CDL) restraints added in 878.4 milliseconds 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1240 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 7 sheets defined 36.0% alpha, 30.8% beta 22 base pairs and 37 stacking pairs defined. Time for finding SS restraints: 2.66 Creating SS restraints... Processing helix chain 'A' and resid 25 through 37 Processing helix chain 'A' and resid 58 through 74 Processing helix chain 'A' and resid 92 through 107 Processing helix chain 'A' and resid 119 through 132 removed outlier: 3.961A pdb=" N TYR A 129 " --> pdb=" O LYS A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 147 Processing helix chain 'A' and resid 148 through 164 Processing helix chain 'A' and resid 221 through 241 Processing helix chain 'A' and resid 263 through 278 Processing helix chain 'A' and resid 303 through 307 Processing helix chain 'A' and resid 359 through 376 removed outlier: 3.705A pdb=" N LYS A 376 " --> pdb=" O TYR A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 407 Proline residue: A 394 - end of helix Processing helix chain 'A' and resid 417 through 423 removed outlier: 3.674A pdb=" N GLN A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 66 removed outlier: 3.601A pdb=" N ILE C 66 " --> pdb=" O GLY C 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 63 through 66' Processing helix chain 'C' and resid 77 through 93 removed outlier: 4.174A pdb=" N GLY C 81 " --> pdb=" O ASN C 77 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LYS C 82 " --> pdb=" O ALA C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 172 Processing helix chain 'C' and resid 172 through 187 Processing helix chain 'C' and resid 199 through 216 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 213 removed outlier: 5.566A pdb=" N TRP A 210 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N PHE A 202 " --> pdb=" O TRP A 210 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 208 through 213 removed outlier: 5.566A pdb=" N TRP A 210 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N PHE A 202 " --> pdb=" O TRP A 210 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ILE A 181 " --> pdb=" O THR A 250 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N HIS A 252 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ILE A 183 " --> pdb=" O HIS A 252 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N GLU A 247 " --> pdb=" O LYS A 286 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N ALA A 288 " --> pdb=" O GLU A 247 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU A 249 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N LEU A 290 " --> pdb=" O LEU A 249 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU A 251 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N LEU A 292 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL A 253 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N TYR A 287 " --> pdb=" O ASP A 353 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ASP A 353 " --> pdb=" O TYR A 287 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE A 289 " --> pdb=" O VAL A 351 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N GLU A 3 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N MET A 2 " --> pdb=" O VAL C 242 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 20 through 22 removed outlier: 3.769A pdb=" N ILE A 170 " --> pdb=" O ARG A 14 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 87 removed outlier: 7.040A pdb=" N ILE A 49 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N PHE A 86 " --> pdb=" O ILE A 49 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N LEU A 51 " --> pdb=" O PHE A 86 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ALA A 50 " --> pdb=" O MET A 112 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N VAL A 114 " --> pdb=" O ALA A 50 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ILE A 52 " --> pdb=" O VAL A 114 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 101 through 105 removed outlier: 6.707A pdb=" N ARG C 110 " --> pdb=" O LYS C 103 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 105 removed outlier: 6.707A pdb=" N ARG C 110 " --> pdb=" O LYS C 103 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N PHE C 143 " --> pdb=" O ILE C 28 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN C 30 " --> pdb=" O LYS C 233 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 52 through 55 removed outlier: 3.551A pdb=" N ILE C 73 " --> pdb=" O ILE C 35 " (cutoff:3.500A) 271 hydrogen bonds defined for protein. 762 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 54 hydrogen bonds 104 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 37 stacking parallelities Total time for adding SS restraints: 2.43 Time building geometry restraints manager: 2.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1563 1.33 - 1.45: 1532 1.45 - 1.57: 3480 1.57 - 1.69: 98 1.69 - 1.80: 25 Bond restraints: 6698 Sorted by residual: bond pdb=" O3' C R 14 " pdb=" P U R 15 " ideal model delta sigma weight residual 1.607 1.652 -0.045 1.50e-02 4.44e+03 9.12e+00 bond pdb=" O3' G R 10 " pdb=" P A R 11 " ideal model delta sigma weight residual 1.607 1.642 -0.035 1.50e-02 4.44e+03 5.49e+00 bond pdb=" O3' A R 22 " pdb=" P A R 23 " ideal model delta sigma weight residual 1.607 1.642 -0.035 1.50e-02 4.44e+03 5.33e+00 bond pdb=" O3' A R 1 " pdb=" P G R 2 " ideal model delta sigma weight residual 1.607 1.581 0.026 1.50e-02 4.44e+03 3.12e+00 bond pdb=" O3' A R 4 " pdb=" P G R 5 " ideal model delta sigma weight residual 1.607 1.629 -0.022 1.50e-02 4.44e+03 2.22e+00 ... (remaining 6693 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 9099 1.83 - 3.67: 183 3.67 - 5.50: 18 5.50 - 7.34: 7 7.34 - 9.17: 1 Bond angle restraints: 9308 Sorted by residual: angle pdb=" C4' G R 12 " pdb=" C3' G R 12 " pdb=" O3' G R 12 " ideal model delta sigma weight residual 113.00 107.26 5.74 1.50e+00 4.44e-01 1.46e+01 angle pdb=" C GLU C 67 " pdb=" N ASN C 68 " pdb=" CA ASN C 68 " ideal model delta sigma weight residual 124.31 130.52 -6.21 1.67e+00 3.59e-01 1.38e+01 angle pdb=" O3' A R 1 " pdb=" C3' A R 1 " pdb=" C2' A R 1 " ideal model delta sigma weight residual 109.50 114.31 -4.81 1.50e+00 4.44e-01 1.03e+01 angle pdb=" C4' A R 1 " pdb=" C3' A R 1 " pdb=" O3' A R 1 " ideal model delta sigma weight residual 109.40 104.73 4.67 1.50e+00 4.44e-01 9.67e+00 angle pdb=" C LYS A 256 " pdb=" N ARG A 257 " pdb=" CA ARG A 257 " ideal model delta sigma weight residual 120.69 111.52 9.17 2.95e+00 1.15e-01 9.66e+00 ... (remaining 9303 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.05: 3375 17.05 - 34.09: 356 34.09 - 51.14: 138 51.14 - 68.18: 72 68.18 - 85.23: 9 Dihedral angle restraints: 3950 sinusoidal: 2012 harmonic: 1938 Sorted by residual: dihedral pdb=" CA ASP C 155 " pdb=" C ASP C 155 " pdb=" N ARG C 156 " pdb=" CA ARG C 156 " ideal model delta harmonic sigma weight residual -180.00 -160.87 -19.13 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA TYR C 22 " pdb=" C TYR C 22 " pdb=" N ILE C 23 " pdb=" CA ILE C 23 " ideal model delta harmonic sigma weight residual 180.00 -163.36 -16.64 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CB MET C 201 " pdb=" CG MET C 201 " pdb=" SD MET C 201 " pdb=" CE MET C 201 " ideal model delta sinusoidal sigma weight residual -60.00 -117.17 57.17 3 1.50e+01 4.44e-03 9.43e+00 ... (remaining 3947 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 801 0.050 - 0.100: 179 0.100 - 0.149: 56 0.149 - 0.199: 9 0.199 - 0.249: 2 Chirality restraints: 1047 Sorted by residual: chirality pdb=" C2' G R 12 " pdb=" C3' G R 12 " pdb=" O2' G R 12 " pdb=" C1' G R 12 " both_signs ideal model delta sigma weight residual False -2.75 -2.50 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" C3' G R 12 " pdb=" C4' G R 12 " pdb=" O3' G R 12 " pdb=" C2' G R 12 " both_signs ideal model delta sigma weight residual False -2.48 -2.70 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA ASN C 68 " pdb=" N ASN C 68 " pdb=" C ASN C 68 " pdb=" CB ASN C 68 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.83e-01 ... (remaining 1044 not shown) Planarity restraints: 995 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 423 " 0.051 5.00e-02 4.00e+02 7.84e-02 9.84e+00 pdb=" N PRO A 424 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO A 424 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 424 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 341 " 0.035 5.00e-02 4.00e+02 5.33e-02 4.55e+00 pdb=" N PRO A 342 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 342 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 342 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 134 " 0.032 5.00e-02 4.00e+02 4.85e-02 3.77e+00 pdb=" N PRO A 135 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 135 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 135 " 0.027 5.00e-02 4.00e+02 ... (remaining 992 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 12 2.35 - 2.98: 3172 2.98 - 3.62: 10221 3.62 - 4.26: 17559 4.26 - 4.90: 27536 Nonbonded interactions: 58500 Sorted by model distance: nonbonded pdb=" OP1 A R 1 " pdb="MG MG R 101 " model vdw 1.707 2.170 nonbonded pdb=" NE2 GLN A 159 " pdb="MG MG R 101 " model vdw 2.033 2.250 nonbonded pdb=" O THR C 191 " pdb=" O HOH C 301 " model vdw 2.242 3.040 nonbonded pdb=" O LEU A 427 " pdb="MG MG R 101 " model vdw 2.264 2.170 nonbonded pdb=" OD1 ASP C 57 " pdb=" O2' G R 18 " model vdw 2.268 3.040 ... (remaining 58495 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=0.50 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: 0.400 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: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 22.830 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.040 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:12.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 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 : 0.004 0.045 6698 Z= 0.231 Angle : 0.631 9.169 9308 Z= 0.358 Chirality : 0.049 0.249 1047 Planarity : 0.005 0.078 995 Dihedral : 18.006 85.227 2710 Min Nonbonded Distance : 1.707 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.33 % Allowed : 0.00 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.32), residues: 658 helix: 1.38 (0.35), residues: 216 sheet: 0.36 (0.44), residues: 157 loop : -0.33 (0.34), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 180 HIS 0.005 0.001 HIS C 187 PHE 0.027 0.002 PHE C 205 TYR 0.019 0.002 TYR C 197 ARG 0.004 0.001 ARG A 334 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.687 Fit side-chains REVERT: C 229 ASP cc_start: 0.7901 (m-30) cc_final: 0.7633 (m-30) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 1.1913 time to fit residues: 103.1225 Evaluate side-chains 59 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 57 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 28 optimal weight: 0.4980 chunk 17 optimal weight: 9.9990 chunk 34 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 39 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN C 136 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6698 Z= 0.239 Angle : 0.604 6.970 9308 Z= 0.327 Chirality : 0.046 0.192 1047 Planarity : 0.005 0.051 995 Dihedral : 19.134 91.545 1357 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.99 % Allowed : 9.26 % Favored : 89.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.32), residues: 658 helix: 1.61 (0.35), residues: 218 sheet: 0.45 (0.43), residues: 157 loop : -0.30 (0.34), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 180 HIS 0.004 0.001 HIS C 187 PHE 0.013 0.001 PHE C 205 TYR 0.015 0.002 TYR C 197 ARG 0.002 0.000 ARG A 189 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 67 time to evaluate : 1.500 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 68 average time/residue: 1.5277 time to fit residues: 111.7190 Evaluate side-chains 61 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 60 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 34 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 17 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 55 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6698 Z= 0.206 Angle : 0.546 6.159 9308 Z= 0.299 Chirality : 0.044 0.190 1047 Planarity : 0.005 0.048 995 Dihedral : 18.930 92.094 1357 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.65 % Allowed : 12.07 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.32), residues: 658 helix: 1.67 (0.35), residues: 218 sheet: 0.53 (0.43), residues: 157 loop : -0.24 (0.35), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 180 HIS 0.004 0.001 HIS C 187 PHE 0.010 0.001 PHE A 426 TYR 0.014 0.001 TYR A 124 ARG 0.002 0.000 ARG A 189 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.749 Fit side-chains REVERT: A 260 MET cc_start: 0.7348 (OUTLIER) cc_final: 0.6474 (ppp) REVERT: A 278 GLN cc_start: 0.7386 (mp10) cc_final: 0.7141 (mp-120) outliers start: 8 outliers final: 2 residues processed: 76 average time/residue: 1.1910 time to fit residues: 95.8772 Evaluate side-chains 65 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain C residue 107 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 32 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 62 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN A 99 GLN C 137 HIS B Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.074 6698 Z= 0.491 Angle : 0.692 6.298 9308 Z= 0.371 Chirality : 0.050 0.195 1047 Planarity : 0.006 0.050 995 Dihedral : 19.008 87.070 1357 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.31 % Allowed : 14.21 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.32), residues: 658 helix: 1.25 (0.33), residues: 223 sheet: 0.22 (0.43), residues: 159 loop : -0.51 (0.34), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 180 HIS 0.006 0.002 HIS C 187 PHE 0.019 0.003 PHE C 216 TYR 0.019 0.003 TYR A 124 ARG 0.005 0.001 ARG C 85 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.666 Fit side-chains REVERT: A 63 GLN cc_start: 0.7446 (OUTLIER) cc_final: 0.6888 (mp10) REVERT: A 99 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.7552 (mp-120) REVERT: A 260 MET cc_start: 0.7519 (OUTLIER) cc_final: 0.6692 (ppp) REVERT: A 278 GLN cc_start: 0.7608 (mp10) cc_final: 0.7341 (mp10) outliers start: 12 outliers final: 3 residues processed: 64 average time/residue: 1.2550 time to fit residues: 85.0883 Evaluate side-chains 58 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 107 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 56 optimal weight: 0.3980 chunk 45 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 58 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN A 25 ASN A 99 GLN A 211 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6698 Z= 0.193 Angle : 0.537 6.054 9308 Z= 0.297 Chirality : 0.044 0.188 1047 Planarity : 0.005 0.050 995 Dihedral : 18.966 93.470 1357 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.98 % Allowed : 15.70 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.32), residues: 658 helix: 1.62 (0.35), residues: 217 sheet: 0.55 (0.44), residues: 157 loop : -0.37 (0.34), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 100 HIS 0.003 0.001 HIS C 187 PHE 0.010 0.001 PHE A 426 TYR 0.019 0.001 TYR A 124 ARG 0.003 0.000 ARG A 383 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.688 Fit side-chains REVERT: A 260 MET cc_start: 0.7388 (OUTLIER) cc_final: 0.6558 (ppp) REVERT: A 278 GLN cc_start: 0.7434 (mp10) cc_final: 0.7162 (mp-120) REVERT: A 421 GLN cc_start: 0.8187 (mp10) cc_final: 0.7987 (mp10) outliers start: 10 outliers final: 3 residues processed: 76 average time/residue: 1.0881 time to fit residues: 87.7773 Evaluate side-chains 69 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 201 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 38 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN A 99 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6698 Z= 0.289 Angle : 0.574 6.077 9308 Z= 0.314 Chirality : 0.045 0.189 1047 Planarity : 0.005 0.049 995 Dihedral : 18.908 90.624 1357 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.31 % Allowed : 15.87 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.32), residues: 658 helix: 1.60 (0.34), residues: 217 sheet: 0.59 (0.44), residues: 157 loop : -0.40 (0.34), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 180 HIS 0.003 0.001 HIS C 187 PHE 0.012 0.002 PHE C 205 TYR 0.015 0.002 TYR C 62 ARG 0.003 0.000 ARG A 383 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.543 Fit side-chains REVERT: A 260 MET cc_start: 0.7430 (OUTLIER) cc_final: 0.6585 (ppp) REVERT: A 278 GLN cc_start: 0.7447 (mp10) cc_final: 0.7206 (mp10) REVERT: A 421 GLN cc_start: 0.8243 (mp10) cc_final: 0.7996 (mp10) outliers start: 12 outliers final: 7 residues processed: 69 average time/residue: 1.1370 time to fit residues: 83.3173 Evaluate side-chains 67 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 365 HIS Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 201 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 39 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6698 Z= 0.200 Angle : 0.532 5.958 9308 Z= 0.293 Chirality : 0.044 0.206 1047 Planarity : 0.004 0.049 995 Dihedral : 18.834 92.666 1357 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.31 % Allowed : 15.87 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.32), residues: 658 helix: 1.71 (0.35), residues: 217 sheet: 0.74 (0.44), residues: 157 loop : -0.37 (0.34), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 180 HIS 0.003 0.001 HIS C 187 PHE 0.010 0.001 PHE A 426 TYR 0.022 0.002 TYR A 124 ARG 0.002 0.000 ARG A 383 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.695 Fit side-chains REVERT: A 260 MET cc_start: 0.7350 (OUTLIER) cc_final: 0.6566 (ppp) REVERT: A 278 GLN cc_start: 0.7396 (mp10) cc_final: 0.7115 (mp-120) REVERT: A 421 GLN cc_start: 0.8242 (mp10) cc_final: 0.7974 (mp10) outliers start: 12 outliers final: 5 residues processed: 69 average time/residue: 1.2138 time to fit residues: 88.5475 Evaluate side-chains 66 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 365 HIS Chi-restraints excluded: chain C residue 201 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 12 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 44 optimal weight: 0.0770 chunk 32 optimal weight: 4.9990 chunk 6 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 overall best weight: 0.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN A 194 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6698 Z= 0.219 Angle : 0.540 5.960 9308 Z= 0.297 Chirality : 0.044 0.209 1047 Planarity : 0.004 0.047 995 Dihedral : 18.723 91.564 1357 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.98 % Allowed : 15.54 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.32), residues: 658 helix: 1.76 (0.34), residues: 218 sheet: 0.72 (0.43), residues: 162 loop : -0.32 (0.34), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 180 HIS 0.003 0.001 HIS C 187 PHE 0.010 0.001 PHE A 426 TYR 0.012 0.002 TYR A 13 ARG 0.002 0.000 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.755 Fit side-chains REVERT: A 260 MET cc_start: 0.7342 (OUTLIER) cc_final: 0.6546 (ppp) REVERT: A 278 GLN cc_start: 0.7392 (mp10) cc_final: 0.7140 (mp-120) REVERT: A 421 GLN cc_start: 0.8271 (mp10) cc_final: 0.7969 (mp10) outliers start: 16 outliers final: 8 residues processed: 73 average time/residue: 1.1174 time to fit residues: 86.6310 Evaluate side-chains 72 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 365 HIS Chi-restraints excluded: chain C residue 201 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 26 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 55 optimal weight: 0.1980 chunk 57 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6698 Z= 0.191 Angle : 0.528 5.939 9308 Z= 0.290 Chirality : 0.043 0.185 1047 Planarity : 0.004 0.048 995 Dihedral : 18.614 91.386 1357 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.31 % Allowed : 16.69 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.32), residues: 658 helix: 1.85 (0.35), residues: 216 sheet: 0.81 (0.43), residues: 162 loop : -0.31 (0.34), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 76 HIS 0.003 0.001 HIS C 187 PHE 0.010 0.001 PHE A 426 TYR 0.015 0.001 TYR A 13 ARG 0.002 0.000 ARG A 383 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.717 Fit side-chains REVERT: A 260 MET cc_start: 0.7318 (OUTLIER) cc_final: 0.6507 (ppp) REVERT: A 421 GLN cc_start: 0.8279 (mp10) cc_final: 0.8060 (mp10) outliers start: 12 outliers final: 6 residues processed: 76 average time/residue: 1.1200 time to fit residues: 90.3937 Evaluate side-chains 68 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 365 HIS Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 201 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 67 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 chunk 41 optimal weight: 0.9980 chunk 33 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 7 optimal weight: 5.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 6698 Z= 0.436 Angle : 0.665 6.390 9308 Z= 0.356 Chirality : 0.049 0.190 1047 Planarity : 0.005 0.049 995 Dihedral : 18.574 83.916 1357 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.98 % Allowed : 17.36 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.31), residues: 658 helix: 1.40 (0.34), residues: 217 sheet: 0.47 (0.42), residues: 162 loop : -0.46 (0.33), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 180 HIS 0.005 0.001 HIS C 136 PHE 0.019 0.002 PHE A 138 TYR 0.026 0.003 TYR A 124 ARG 0.010 0.001 ARG A 147 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.703 Fit side-chains REVERT: A 260 MET cc_start: 0.7443 (OUTLIER) cc_final: 0.6614 (ppp) REVERT: A 332 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7795 (pp) REVERT: A 421 GLN cc_start: 0.8138 (mp10) cc_final: 0.7881 (mp10) outliers start: 10 outliers final: 5 residues processed: 61 average time/residue: 1.2656 time to fit residues: 81.7835 Evaluate side-chains 62 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 201 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 14 optimal weight: 0.0980 chunk 54 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 47 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 39 optimal weight: 0.0870 chunk 61 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.137877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.115208 restraints weight = 23837.891| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.58 r_work: 0.3443 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3427 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3427 r_free = 0.3427 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3427 r_free = 0.3427 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3427 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6698 Z= 0.182 Angle : 0.547 5.816 9308 Z= 0.300 Chirality : 0.043 0.185 1047 Planarity : 0.005 0.048 995 Dihedral : 18.455 85.430 1357 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.98 % Allowed : 17.36 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.32), residues: 658 helix: 1.88 (0.35), residues: 217 sheet: 0.79 (0.44), residues: 157 loop : -0.37 (0.33), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 244 HIS 0.002 0.001 HIS C 187 PHE 0.010 0.001 PHE A 426 TYR 0.015 0.002 TYR A 13 ARG 0.006 0.000 ARG A 147 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2269.18 seconds wall clock time: 41 minutes 56.74 seconds (2516.74 seconds total)