Starting phenix.real_space_refine on Thu Nov 14 01:12:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ex5_28651/11_2024/8ex5_28651.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ex5_28651/11_2024/8ex5_28651.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ex5_28651/11_2024/8ex5_28651.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ex5_28651/11_2024/8ex5_28651.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ex5_28651/11_2024/8ex5_28651.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ex5_28651/11_2024/8ex5_28651.cif" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.018 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: 4 Type Number sf(0) Gaussians S 17 5.16 5 C 2090 2.51 5 N 524 2.21 5 O 546 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 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: 3177 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3177 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 12, 'TRANS': 401} Chain breaks: 2 Time building chain proxies: 2.94, per 1000 atoms: 0.93 Number of scatterers: 3177 At special positions: 0 Unit cell: (70.092, 68.794, 79.827, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 17 16.00 O 546 8.00 N 524 7.00 C 2090 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: 0.84 Conformation dependent library (CDL) restraints added in 395.3 milliseconds 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 756 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 0 sheets defined 90.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 99 through 134 removed outlier: 3.628A pdb=" N ALA A 103 " --> pdb=" O GLU A 99 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N VAL A 122 " --> pdb=" O ASP A 118 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ALA A 123 " --> pdb=" O ARG A 119 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N LEU A 127 " --> pdb=" O ALA A 123 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N ASP A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 165 removed outlier: 3.726A pdb=" N ALA A 140 " --> pdb=" O LYS A 136 " (cutoff:3.500A) Proline residue: A 156 - end of helix removed outlier: 3.792A pdb=" N ARG A 164 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE A 165 " --> pdb=" O LEU A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 186 Processing helix chain 'A' and resid 193 through 222 Proline residue: A 215 - end of helix removed outlier: 3.820A pdb=" N PHE A 222 " --> pdb=" O ILE A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 256 removed outlier: 4.259A pdb=" N ILE A 238 " --> pdb=" O PHE A 234 " (cutoff:3.500A) Proline residue: A 239 - end of helix Processing helix chain 'A' and resid 265 through 281 removed outlier: 4.435A pdb=" N LEU A 269 " --> pdb=" O VAL A 265 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A 281 " --> pdb=" O ILE A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 312 Processing helix chain 'A' and resid 312 through 348 Proline residue: A 337 - end of helix Processing helix chain 'A' and resid 361 through 392 Processing helix chain 'A' and resid 394 through 417 removed outlier: 3.635A pdb=" N LEU A 398 " --> pdb=" O ARG A 394 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N CYS A 400 " --> pdb=" O ASP A 396 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE A 415 " --> pdb=" O ILE A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 438 removed outlier: 4.295A pdb=" N LEU A 435 " --> pdb=" O VAL A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 450 removed outlier: 3.583A pdb=" N ALA A 444 " --> pdb=" O TRP A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 454 No H-bonds generated for 'chain 'A' and resid 452 through 454' Processing helix chain 'A' and resid 455 through 470 Processing helix chain 'A' and resid 474 through 488 Processing helix chain 'A' and resid 493 through 538 removed outlier: 4.238A pdb=" N CYS A 508 " --> pdb=" O ALA A 504 " (cutoff:3.500A) Proline residue: A 509 - end of helix removed outlier: 5.161A pdb=" N VAL A 527 " --> pdb=" O ALA A 523 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N SER A 528 " --> pdb=" O LEU A 524 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN A 536 " --> pdb=" O ARG A 532 " (cutoff:3.500A) 274 hydrogen bonds defined for protein. 822 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.98 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 968 1.34 - 1.46: 631 1.46 - 1.58: 1626 1.58 - 1.69: 0 1.69 - 1.81: 26 Bond restraints: 3251 Sorted by residual: bond pdb=" C CYS A 508 " pdb=" N PRO A 509 " ideal model delta sigma weight residual 1.333 1.356 -0.023 1.44e-02 4.82e+03 2.55e+00 bond pdb=" C SER A 266 " pdb=" N PRO A 267 " ideal model delta sigma weight residual 1.334 1.368 -0.034 2.34e-02 1.83e+03 2.14e+00 bond pdb=" N LYS A 224 " pdb=" CA LYS A 224 " ideal model delta sigma weight residual 1.457 1.476 -0.018 1.29e-02 6.01e+03 2.00e+00 bond pdb=" CG LEU A 171 " pdb=" CD2 LEU A 171 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.25e+00 bond pdb=" CB ILE A 107 " pdb=" CG2 ILE A 107 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 9.99e-01 ... (remaining 3246 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 4132 1.27 - 2.55: 227 2.55 - 3.82: 35 3.82 - 5.10: 16 5.10 - 6.37: 6 Bond angle restraints: 4416 Sorted by residual: angle pdb=" N ILE A 188 " pdb=" CA ILE A 188 " pdb=" C ILE A 188 " ideal model delta sigma weight residual 108.95 112.36 -3.41 9.80e-01 1.04e+00 1.21e+01 angle pdb=" N VAL A 431 " pdb=" CA VAL A 431 " pdb=" C VAL A 431 " ideal model delta sigma weight residual 112.80 108.88 3.92 1.15e+00 7.56e-01 1.16e+01 angle pdb=" C PHE A 177 " pdb=" N TRP A 178 " pdb=" CA TRP A 178 " ideal model delta sigma weight residual 120.31 115.32 4.99 1.52e+00 4.33e-01 1.08e+01 angle pdb=" N TRP A 178 " pdb=" CA TRP A 178 " pdb=" CB TRP A 178 " ideal model delta sigma weight residual 110.28 115.08 -4.80 1.55e+00 4.16e-01 9.58e+00 angle pdb=" CA TRP A 178 " pdb=" CB TRP A 178 " pdb=" CG TRP A 178 " ideal model delta sigma weight residual 113.60 119.39 -5.79 1.90e+00 2.77e-01 9.28e+00 ... (remaining 4411 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.94: 1714 15.94 - 31.88: 125 31.88 - 47.82: 26 47.82 - 63.75: 6 63.75 - 79.69: 1 Dihedral angle restraints: 1872 sinusoidal: 692 harmonic: 1180 Sorted by residual: dihedral pdb=" CA THR A 223 " pdb=" C THR A 223 " pdb=" N LYS A 224 " pdb=" CA LYS A 224 " ideal model delta harmonic sigma weight residual 180.00 -156.37 -23.63 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA GLU A 207 " pdb=" C GLU A 207 " pdb=" N ALA A 208 " pdb=" CA ALA A 208 " ideal model delta harmonic sigma weight residual 180.00 162.16 17.84 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA LEU A 221 " pdb=" C LEU A 221 " pdb=" N PHE A 222 " pdb=" CA PHE A 222 " ideal model delta harmonic sigma weight residual 180.00 -162.50 -17.50 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 1869 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 313 0.031 - 0.061: 146 0.061 - 0.092: 39 0.092 - 0.123: 18 0.123 - 0.153: 5 Chirality restraints: 521 Sorted by residual: chirality pdb=" CA GLU A 207 " pdb=" N GLU A 207 " pdb=" C GLU A 207 " pdb=" CB GLU A 207 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.87e-01 chirality pdb=" CA PRO A 267 " pdb=" N PRO A 267 " pdb=" C PRO A 267 " pdb=" CB PRO A 267 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.52e-01 chirality pdb=" CA SER A 475 " pdb=" N SER A 475 " pdb=" C SER A 475 " pdb=" CB SER A 475 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.35e-01 ... (remaining 518 not shown) Planarity restraints: 539 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 178 " 0.025 2.00e-02 2.50e+03 2.10e-02 1.10e+01 pdb=" CG TRP A 178 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 TRP A 178 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP A 178 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP A 178 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 178 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 178 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 178 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 178 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 178 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS A 508 " -0.033 5.00e-02 4.00e+02 5.08e-02 4.13e+00 pdb=" N PRO A 509 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 509 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 509 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 223 " -0.007 2.00e-02 2.50e+03 1.45e-02 2.09e+00 pdb=" C THR A 223 " 0.025 2.00e-02 2.50e+03 pdb=" O THR A 223 " -0.010 2.00e-02 2.50e+03 pdb=" N LYS A 224 " -0.008 2.00e-02 2.50e+03 ... (remaining 536 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 52 2.69 - 3.24: 3428 3.24 - 3.80: 5240 3.80 - 4.35: 6680 4.35 - 4.90: 11130 Nonbonded interactions: 26530 Sorted by model distance: nonbonded pdb=" OG SER A 186 " pdb=" O LEU A 263 " model vdw 2.141 3.040 nonbonded pdb=" O GLY A 206 " pdb=" OG SER A 209 " model vdw 2.182 3.040 nonbonded pdb=" OD1 ASP A 118 " pdb=" OG SER A 266 " model vdw 2.290 3.040 nonbonded pdb=" O MET A 404 " pdb=" OG SER A 407 " model vdw 2.296 3.040 nonbonded pdb=" NH1 ARG A 167 " pdb=" OG1 THR A 216 " model vdw 2.368 3.120 ... (remaining 26525 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: 2.290 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.700 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6687 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 0.040 3251 Z= 0.287 Angle : 0.714 6.370 4416 Z= 0.423 Chirality : 0.041 0.153 521 Planarity : 0.005 0.051 539 Dihedral : 12.108 79.692 1116 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.88 (0.42), residues: 408 helix: 1.13 (0.27), residues: 353 sheet: None (None), residues: 0 loop : -2.78 (0.82), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.003 TRP A 178 HIS 0.001 0.001 HIS A 260 PHE 0.023 0.002 PHE A 465 TYR 0.018 0.002 TYR A 426 ARG 0.005 0.001 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.340 Fit side-chains REVERT: A 182 THR cc_start: 0.7787 (m) cc_final: 0.6251 (t) REVERT: A 447 LEU cc_start: 0.8555 (tt) cc_final: 0.8258 (tp) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.1200 time to fit residues: 6.2213 Evaluate side-chains 35 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 0.0970 chunk 37 optimal weight: 0.8980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6652 moved from start: 0.0767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3251 Z= 0.226 Angle : 0.599 6.231 4416 Z= 0.323 Chirality : 0.042 0.154 521 Planarity : 0.004 0.049 539 Dihedral : 4.961 20.893 444 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.30 % Allowed : 6.87 % Favored : 92.84 % 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: 1.43 (0.41), residues: 408 helix: 1.50 (0.27), residues: 353 sheet: None (None), residues: 0 loop : -2.64 (0.77), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 178 HIS 0.002 0.001 HIS A 468 PHE 0.014 0.002 PHE A 327 TYR 0.016 0.002 TYR A 426 ARG 0.004 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 41 time to evaluate : 0.333 Fit side-chains REVERT: A 182 THR cc_start: 0.7768 (m) cc_final: 0.6235 (t) REVERT: A 264 ARG cc_start: 0.4355 (mtp85) cc_final: 0.3541 (mtp-110) REVERT: A 447 LEU cc_start: 0.8519 (tt) cc_final: 0.8240 (tp) outliers start: 1 outliers final: 1 residues processed: 41 average time/residue: 0.1391 time to fit residues: 7.3275 Evaluate side-chains 40 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 GLN A 535 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6670 moved from start: 0.1046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3251 Z= 0.236 Angle : 0.584 6.312 4416 Z= 0.315 Chirality : 0.042 0.144 521 Planarity : 0.004 0.049 539 Dihedral : 4.858 21.252 444 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.90 % Allowed : 10.15 % Favored : 88.96 % 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: 1.51 (0.41), residues: 408 helix: 1.53 (0.27), residues: 356 sheet: None (None), residues: 0 loop : -2.63 (0.81), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 178 HIS 0.002 0.001 HIS A 468 PHE 0.015 0.002 PHE A 327 TYR 0.015 0.002 TYR A 426 ARG 0.003 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.354 Fit side-chains REVERT: A 182 THR cc_start: 0.7768 (m) cc_final: 0.6266 (t) REVERT: A 264 ARG cc_start: 0.4280 (mtp85) cc_final: 0.3358 (mtp-110) REVERT: A 447 LEU cc_start: 0.8514 (tt) cc_final: 0.8237 (tp) outliers start: 3 outliers final: 1 residues processed: 43 average time/residue: 0.1479 time to fit residues: 8.1604 Evaluate side-chains 41 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 40 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 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 344 GLN A 535 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6668 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3251 Z= 0.228 Angle : 0.570 6.381 4416 Z= 0.307 Chirality : 0.041 0.141 521 Planarity : 0.004 0.049 539 Dihedral : 4.801 20.850 444 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.19 % Allowed : 11.64 % Favored : 87.16 % 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: 1.68 (0.41), residues: 408 helix: 1.64 (0.27), residues: 356 sheet: None (None), residues: 0 loop : -2.54 (0.81), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 178 HIS 0.002 0.001 HIS A 468 PHE 0.014 0.002 PHE A 327 TYR 0.016 0.002 TYR A 426 ARG 0.004 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.365 Fit side-chains REVERT: A 182 THR cc_start: 0.7780 (m) cc_final: 0.6298 (t) REVERT: A 264 ARG cc_start: 0.4388 (mtp85) cc_final: 0.3253 (mtp-110) REVERT: A 439 ASN cc_start: 0.7021 (p0) cc_final: 0.6414 (m-40) REVERT: A 447 LEU cc_start: 0.8521 (tt) cc_final: 0.8267 (tp) outliers start: 4 outliers final: 3 residues processed: 44 average time/residue: 0.1316 time to fit residues: 7.4415 Evaluate side-chains 42 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 248 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 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 344 GLN A 535 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6658 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3251 Z= 0.216 Angle : 0.563 6.262 4416 Z= 0.302 Chirality : 0.041 0.139 521 Planarity : 0.004 0.049 539 Dihedral : 4.760 21.073 444 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.19 % Allowed : 12.84 % Favored : 85.97 % 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: 1.88 (0.41), residues: 408 helix: 1.75 (0.27), residues: 356 sheet: None (None), residues: 0 loop : -2.31 (0.83), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 178 HIS 0.002 0.001 HIS A 468 PHE 0.014 0.002 PHE A 327 TYR 0.016 0.002 TYR A 426 ARG 0.003 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.346 Fit side-chains REVERT: A 182 THR cc_start: 0.7768 (m) cc_final: 0.6292 (t) REVERT: A 264 ARG cc_start: 0.4334 (mtp85) cc_final: 0.3146 (mtp-110) REVERT: A 439 ASN cc_start: 0.6887 (p0) cc_final: 0.6534 (m-40) REVERT: A 447 LEU cc_start: 0.8520 (tt) cc_final: 0.8273 (tp) outliers start: 4 outliers final: 4 residues processed: 43 average time/residue: 0.1413 time to fit residues: 7.8565 Evaluate side-chains 43 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 385 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.8980 chunk 9 optimal weight: 0.0770 chunk 39 optimal weight: 0.8980 chunk 32 optimal weight: 0.2980 chunk 18 optimal weight: 0.8980 chunk 3 optimal weight: 0.1980 chunk 13 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 overall best weight: 0.3738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 GLN A 535 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6587 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3251 Z= 0.169 Angle : 0.521 5.825 4416 Z= 0.280 Chirality : 0.040 0.133 521 Planarity : 0.004 0.049 539 Dihedral : 4.589 20.308 444 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.90 % Allowed : 12.84 % Favored : 86.27 % 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: 2.33 (0.42), residues: 408 helix: 1.98 (0.27), residues: 358 sheet: None (None), residues: 0 loop : -1.73 (0.88), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 178 HIS 0.001 0.000 HIS A 468 PHE 0.011 0.001 PHE A 327 TYR 0.015 0.001 TYR A 426 ARG 0.002 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.359 Fit side-chains REVERT: A 182 THR cc_start: 0.7682 (m) cc_final: 0.6174 (t) REVERT: A 264 ARG cc_start: 0.4410 (mtp85) cc_final: 0.3290 (mtm180) REVERT: A 447 LEU cc_start: 0.8446 (tt) cc_final: 0.8194 (tp) REVERT: A 455 ARG cc_start: 0.6226 (mtm180) cc_final: 0.5968 (mtm180) REVERT: A 517 MET cc_start: 0.4804 (ttt) cc_final: 0.4527 (ttm) outliers start: 3 outliers final: 2 residues processed: 40 average time/residue: 0.1425 time to fit residues: 7.3148 Evaluate side-chains 37 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 178 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 GLN A 535 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6666 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3251 Z= 0.242 Angle : 0.581 6.283 4416 Z= 0.311 Chirality : 0.041 0.140 521 Planarity : 0.004 0.050 539 Dihedral : 4.681 20.107 444 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.49 % Allowed : 12.54 % Favored : 85.97 % 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: 2.06 (0.42), residues: 408 helix: 1.79 (0.27), residues: 358 sheet: None (None), residues: 0 loop : -1.68 (0.90), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 178 HIS 0.002 0.001 HIS A 468 PHE 0.015 0.002 PHE A 327 TYR 0.015 0.002 TYR A 426 ARG 0.003 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.335 Fit side-chains REVERT: A 182 THR cc_start: 0.7794 (m) cc_final: 0.6343 (t) REVERT: A 264 ARG cc_start: 0.4452 (mtp85) cc_final: 0.3265 (mtm110) REVERT: A 517 MET cc_start: 0.4829 (ttt) cc_final: 0.4513 (ttm) REVERT: A 535 GLN cc_start: 0.5956 (mt0) cc_final: 0.5711 (mt0) outliers start: 5 outliers final: 4 residues processed: 43 average time/residue: 0.1157 time to fit residues: 6.6750 Evaluate side-chains 40 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 248 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.4980 chunk 19 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 36 optimal weight: 0.4980 chunk 22 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6631 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3251 Z= 0.205 Angle : 0.554 6.310 4416 Z= 0.297 Chirality : 0.041 0.148 521 Planarity : 0.004 0.049 539 Dihedral : 4.593 19.574 444 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.19 % Allowed : 13.13 % Favored : 85.67 % 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: 2.22 (0.42), residues: 408 helix: 1.89 (0.27), residues: 358 sheet: None (None), residues: 0 loop : -1.59 (0.93), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 178 HIS 0.001 0.001 HIS A 468 PHE 0.013 0.001 PHE A 327 TYR 0.015 0.001 TYR A 426 ARG 0.002 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.336 Fit side-chains REVERT: A 182 THR cc_start: 0.7739 (m) cc_final: 0.6278 (t) REVERT: A 264 ARG cc_start: 0.4481 (mtp85) cc_final: 0.3277 (mtm180) REVERT: A 447 LEU cc_start: 0.8483 (tt) cc_final: 0.8240 (tp) REVERT: A 517 MET cc_start: 0.4782 (ttt) cc_final: 0.4514 (ttm) outliers start: 4 outliers final: 2 residues processed: 40 average time/residue: 0.1199 time to fit residues: 6.3943 Evaluate side-chains 39 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 37 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 178 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 18 optimal weight: 0.0770 chunk 27 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 GLN A 535 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6627 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 : 0.003 0.032 3251 Z= 0.202 Angle : 0.552 6.192 4416 Z= 0.296 Chirality : 0.041 0.149 521 Planarity : 0.004 0.049 539 Dihedral : 4.584 19.184 444 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.49 % Allowed : 13.73 % Favored : 84.78 % 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: 2.29 (0.42), residues: 408 helix: 1.93 (0.27), residues: 358 sheet: None (None), residues: 0 loop : -1.54 (0.90), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 178 HIS 0.001 0.001 HIS A 468 PHE 0.019 0.002 PHE A 465 TYR 0.015 0.001 TYR A 426 ARG 0.002 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.338 Fit side-chains REVERT: A 182 THR cc_start: 0.7720 (m) cc_final: 0.6217 (t) REVERT: A 447 LEU cc_start: 0.8479 (tt) cc_final: 0.8233 (tp) REVERT: A 517 MET cc_start: 0.4769 (ttt) cc_final: 0.4497 (ttm) outliers start: 5 outliers final: 4 residues processed: 38 average time/residue: 0.0932 time to fit residues: 5.0951 Evaluate side-chains 37 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 248 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 9 optimal weight: 0.0170 chunk 29 optimal weight: 0.0270 chunk 4 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6580 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3251 Z= 0.175 Angle : 0.524 6.069 4416 Z= 0.281 Chirality : 0.040 0.145 521 Planarity : 0.004 0.049 539 Dihedral : 4.480 19.104 444 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.90 % Allowed : 14.63 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.42), residues: 408 helix: 2.08 (0.27), residues: 358 sheet: None (None), residues: 0 loop : -1.53 (0.88), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 178 HIS 0.001 0.000 HIS A 468 PHE 0.019 0.001 PHE A 465 TYR 0.015 0.001 TYR A 426 ARG 0.002 0.000 ARG A 264 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.301 Fit side-chains REVERT: A 182 THR cc_start: 0.7695 (m) cc_final: 0.6204 (t) REVERT: A 264 ARG cc_start: 0.4488 (mtp85) cc_final: 0.3312 (mtm180) REVERT: A 447 LEU cc_start: 0.8442 (tt) cc_final: 0.8188 (tp) REVERT: A 517 MET cc_start: 0.4784 (ttt) cc_final: 0.4515 (ttm) outliers start: 3 outliers final: 3 residues processed: 38 average time/residue: 0.1230 time to fit residues: 6.2144 Evaluate side-chains 38 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 226 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 27 optimal weight: 0.3980 chunk 26 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 40 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 GLN A 535 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.234916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.213153 restraints weight = 3585.036| |-----------------------------------------------------------------------------| r_work (start): 0.4370 rms_B_bonded: 1.51 r_work: 0.4195 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.4195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3251 Z= 0.218 Angle : 0.560 6.284 4416 Z= 0.300 Chirality : 0.041 0.144 521 Planarity : 0.004 0.050 539 Dihedral : 4.565 18.031 444 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.19 % Allowed : 15.52 % Favored : 83.28 % 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: 2.31 (0.42), residues: 408 helix: 1.99 (0.27), residues: 356 sheet: None (None), residues: 0 loop : -1.80 (0.83), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 178 HIS 0.002 0.001 HIS A 468 PHE 0.018 0.002 PHE A 465 TYR 0.015 0.001 TYR A 426 ARG 0.002 0.000 ARG A 264 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1170.44 seconds wall clock time: 21 minutes 58.21 seconds (1318.21 seconds total)