Starting phenix.real_space_refine on Fri Dec 27 05:41:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xtx_38652/12_2024/8xtx_38652.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xtx_38652/12_2024/8xtx_38652.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xtx_38652/12_2024/8xtx_38652.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xtx_38652/12_2024/8xtx_38652.map" model { file = "/net/cci-nas-00/data/ceres_data/8xtx_38652/12_2024/8xtx_38652.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xtx_38652/12_2024/8xtx_38652.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.161 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 1912 2.51 5 N 458 2.21 5 O 489 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 2876 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 2876 Classifications: {'peptide': 382} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 357} Chain breaks: 2 Time building chain proxies: 2.81, per 1000 atoms: 0.98 Number of scatterers: 2876 At special positions: 0 Unit cell: (68.85, 72.25, 64.6, 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 489 8.00 N 458 7.00 C 1912 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: 0.74 Conformation dependent library (CDL) restraints added in 396.5 milliseconds 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 708 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 0 sheets defined 82.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 31 through 49 removed outlier: 4.121A pdb=" N VAL A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU A 49 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 121 through 129 removed outlier: 3.568A pdb=" N GLY A 125 " --> pdb=" O ASP A 121 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL A 126 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU A 127 " --> pdb=" O LYS A 123 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE A 128 " --> pdb=" O ILE A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 138 Processing helix chain 'A' and resid 138 through 147 Proline residue: A 144 - end of helix removed outlier: 3.955A pdb=" N ASP A 147 " --> pdb=" O GLY A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 167 Processing helix chain 'A' and resid 174 through 204 removed outlier: 4.576A pdb=" N THR A 194 " --> pdb=" O ALA A 190 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N SER A 195 " --> pdb=" O PHE A 191 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR A 204 " --> pdb=" O ILE A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 226 removed outlier: 3.678A pdb=" N ARG A 210 " --> pdb=" O GLU A 206 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N SER A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ARG A 212 " --> pdb=" O PRO A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 239 removed outlier: 4.330A pdb=" N PHE A 231 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE A 234 " --> pdb=" O PRO A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 263 Processing helix chain 'A' and resid 281 through 286 Processing helix chain 'A' and resid 288 through 302 removed outlier: 4.193A pdb=" N VAL A 293 " --> pdb=" O PRO A 289 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N VAL A 294 " --> pdb=" O TYR A 290 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 309 removed outlier: 3.747A pdb=" N GLU A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 317 Processing helix chain 'A' and resid 324 through 329 removed outlier: 4.128A pdb=" N GLY A 328 " --> pdb=" O GLU A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 334 removed outlier: 3.549A pdb=" N ALA A 334 " --> pdb=" O TRP A 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 331 through 334' Processing helix chain 'A' and resid 335 through 352 removed outlier: 3.705A pdb=" N ALA A 350 " --> pdb=" O VAL A 346 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 374 Processing helix chain 'A' and resid 379 through 412 removed outlier: 3.688A pdb=" N LEU A 383 " --> pdb=" O SER A 379 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA A 395 " --> pdb=" O CYS A 391 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU A 396 " --> pdb=" O PHE A 392 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL A 397 " --> pdb=" O GLY A 393 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA A 400 " --> pdb=" O LEU A 396 " (cutoff:3.500A) Proline residue: A 403 - end of helix removed outlier: 4.007A pdb=" N ALA A 406 " --> pdb=" O LEU A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 429 Processing helix chain 'A' and resid 430 through 447 Proline residue: A 436 - end of helix removed outlier: 5.594A pdb=" N GLY A 440 " --> pdb=" O PRO A 436 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N HIS A 441 " --> pdb=" O ILE A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 460 Processing helix chain 'A' and resid 464 through 468 removed outlier: 3.501A pdb=" N LEU A 468 " --> pdb=" O VAL A 465 " (cutoff:3.500A) 183 hydrogen bonds defined for protein. 540 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: 0.74 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 439 1.31 - 1.43: 765 1.43 - 1.56: 1714 1.56 - 1.69: 1 1.69 - 1.81: 28 Bond restraints: 2947 Sorted by residual: bond pdb=" C VAL A 52 " pdb=" O VAL A 52 " ideal model delta sigma weight residual 1.240 1.181 0.059 1.49e-02 4.50e+03 1.57e+01 bond pdb=" C LEU A 49 " pdb=" N TYR A 50 " ideal model delta sigma weight residual 1.333 1.285 0.048 1.47e-02 4.63e+03 1.07e+01 bond pdb=" C TYR A 50 " pdb=" O TYR A 50 " ideal model delta sigma weight residual 1.236 1.200 0.036 1.34e-02 5.57e+03 7.26e+00 bond pdb=" C MET A 51 " pdb=" O MET A 51 " ideal model delta sigma weight residual 1.235 1.196 0.039 1.48e-02 4.57e+03 6.99e+00 bond pdb=" N CYS A 301 " pdb=" CA CYS A 301 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.31e-02 5.83e+03 6.60e+00 ... (remaining 2942 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 3948 2.35 - 4.70: 68 4.70 - 7.05: 7 7.05 - 9.39: 4 9.39 - 11.74: 3 Bond angle restraints: 4030 Sorted by residual: angle pdb=" N TYR A 50 " pdb=" CA TYR A 50 " pdb=" C TYR A 50 " ideal model delta sigma weight residual 113.38 102.44 10.94 1.23e+00 6.61e-01 7.91e+01 angle pdb=" CA PRO A 58 " pdb=" N PRO A 58 " pdb=" CD PRO A 58 " ideal model delta sigma weight residual 112.00 100.26 11.74 1.40e+00 5.10e-01 7.04e+01 angle pdb=" N VAL A 52 " pdb=" CA VAL A 52 " pdb=" C VAL A 52 " ideal model delta sigma weight residual 112.90 106.53 6.37 9.60e-01 1.09e+00 4.41e+01 angle pdb=" C LEU A 49 " pdb=" N TYR A 50 " pdb=" CA TYR A 50 " ideal model delta sigma weight residual 122.26 113.42 8.84 1.73e+00 3.34e-01 2.61e+01 angle pdb=" CA TYR A 50 " pdb=" CB TYR A 50 " pdb=" CG TYR A 50 " ideal model delta sigma weight residual 113.90 122.36 -8.46 1.80e+00 3.09e-01 2.21e+01 ... (remaining 4025 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.61: 1423 15.61 - 31.21: 215 31.21 - 46.82: 71 46.82 - 62.43: 15 62.43 - 78.03: 5 Dihedral angle restraints: 1729 sinusoidal: 627 harmonic: 1102 Sorted by residual: dihedral pdb=" CA MET A 320 " pdb=" C MET A 320 " pdb=" N ALA A 321 " pdb=" CA ALA A 321 " ideal model delta harmonic sigma weight residual 180.00 157.04 22.96 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" CA MET A 149 " pdb=" C MET A 149 " pdb=" N SER A 150 " pdb=" CA SER A 150 " ideal model delta harmonic sigma weight residual 180.00 161.30 18.70 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA THR A 399 " pdb=" C THR A 399 " pdb=" N ALA A 400 " pdb=" CA ALA A 400 " ideal model delta harmonic sigma weight residual 180.00 162.01 17.99 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 1726 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 372 0.047 - 0.095: 108 0.095 - 0.142: 10 0.142 - 0.189: 2 0.189 - 0.236: 2 Chirality restraints: 494 Sorted by residual: chirality pdb=" CA GLN A 31 " pdb=" N GLN A 31 " pdb=" C GLN A 31 " pdb=" CB GLN A 31 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CB VAL A 52 " pdb=" CA VAL A 52 " pdb=" CG1 VAL A 52 " pdb=" CG2 VAL A 52 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA PRO A 58 " pdb=" N PRO A 58 " pdb=" C PRO A 58 " pdb=" CB PRO A 58 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.37e-01 ... (remaining 491 not shown) Planarity restraints: 495 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 57 " 0.076 5.00e-02 4.00e+02 1.07e-01 1.84e+01 pdb=" N PRO A 58 " -0.185 5.00e-02 4.00e+02 pdb=" CA PRO A 58 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 58 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 49 " 0.019 2.00e-02 2.50e+03 3.94e-02 1.55e+01 pdb=" C LEU A 49 " -0.068 2.00e-02 2.50e+03 pdb=" O LEU A 49 " 0.025 2.00e-02 2.50e+03 pdb=" N TYR A 50 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 332 " -0.054 5.00e-02 4.00e+02 8.14e-02 1.06e+01 pdb=" N PRO A 333 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO A 333 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 333 " -0.046 5.00e-02 4.00e+02 ... (remaining 492 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 437 2.75 - 3.29: 2667 3.29 - 3.83: 4667 3.83 - 4.36: 4858 4.36 - 4.90: 8772 Nonbonded interactions: 21401 Sorted by model distance: nonbonded pdb=" O LEU A 305 " pdb=" OE1 GLU A 309 " model vdw 2.218 3.040 nonbonded pdb=" OD2 ASP A 410 " pdb=" OH TYR A 417 " model vdw 2.265 3.040 nonbonded pdb=" OE1 GLN A 135 " pdb=" OG SER A 429 " model vdw 2.290 3.040 nonbonded pdb=" N ASP A 147 " pdb=" OD1 ASP A 147 " model vdw 2.334 3.120 nonbonded pdb=" O GLY A 418 " pdb=" OG SER A 419 " model vdw 2.360 3.040 ... (remaining 21396 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.730 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.540 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: 16.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 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 0.112 2947 Z= 0.315 Angle : 0.774 11.743 4030 Z= 0.448 Chirality : 0.042 0.236 494 Planarity : 0.009 0.107 495 Dihedral : 17.361 78.032 1021 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 0.66 % Allowed : 33.99 % Favored : 65.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.04 (0.49), residues: 376 helix: 1.29 (0.35), residues: 290 sheet: None (None), residues: 0 loop : -4.62 (0.52), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 315 HIS 0.008 0.001 HIS A 441 PHE 0.010 0.001 PHE A 169 TYR 0.020 0.002 TYR A 50 ARG 0.004 0.000 ARG A 378 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 43 time to evaluate : 0.328 Fit side-chains REVERT: A 449 GLU cc_start: 0.7415 (mt-10) cc_final: 0.7140 (mm-30) outliers start: 2 outliers final: 1 residues processed: 44 average time/residue: 0.1279 time to fit residues: 7.1235 Evaluate side-chains 42 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 41 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 2.9990 chunk 28 optimal weight: 0.0470 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 29 optimal weight: 0.0970 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN A 441 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.0902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 2947 Z= 0.211 Angle : 0.597 5.724 4030 Z= 0.302 Chirality : 0.038 0.114 494 Planarity : 0.007 0.062 495 Dihedral : 4.658 29.669 411 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 3.30 % Allowed : 32.67 % Favored : 64.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.19 (0.49), residues: 376 helix: 1.44 (0.35), residues: 284 sheet: None (None), residues: 0 loop : -4.36 (0.51), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 315 HIS 0.005 0.001 HIS A 441 PHE 0.008 0.001 PHE A 335 TYR 0.005 0.001 TYR A 417 ARG 0.002 0.000 ARG A 378 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.288 Fit side-chains REVERT: A 147 ASP cc_start: 0.8226 (p0) cc_final: 0.8001 (p0) REVERT: A 173 GLU cc_start: 0.7732 (tm-30) cc_final: 0.7311 (tm-30) REVERT: A 461 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.7300 (tt) outliers start: 10 outliers final: 4 residues processed: 51 average time/residue: 0.1328 time to fit residues: 8.5534 Evaluate side-chains 48 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 356 GLN Chi-restraints excluded: chain A residue 461 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 3 optimal weight: 0.0170 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2947 Z= 0.192 Angle : 0.578 5.955 4030 Z= 0.287 Chirality : 0.037 0.110 494 Planarity : 0.006 0.061 495 Dihedral : 4.249 22.117 408 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 5.61 % Allowed : 30.69 % Favored : 63.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.49), residues: 376 helix: 1.52 (0.35), residues: 284 sheet: None (None), residues: 0 loop : -4.46 (0.49), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 315 HIS 0.005 0.001 HIS A 441 PHE 0.008 0.001 PHE A 335 TYR 0.003 0.001 TYR A 50 ARG 0.003 0.000 ARG A 378 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 44 time to evaluate : 0.281 Fit side-chains REVERT: A 147 ASP cc_start: 0.8272 (p0) cc_final: 0.8038 (p0) REVERT: A 173 GLU cc_start: 0.7753 (tm-30) cc_final: 0.7324 (tm-30) REVERT: A 444 HIS cc_start: 0.7354 (t-90) cc_final: 0.7124 (t70) REVERT: A 453 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7453 (mm) REVERT: A 461 LEU cc_start: 0.7571 (OUTLIER) cc_final: 0.7254 (tt) outliers start: 17 outliers final: 8 residues processed: 56 average time/residue: 0.1260 time to fit residues: 8.8960 Evaluate side-chains 52 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 461 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 16 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 32 optimal weight: 0.4980 chunk 9 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 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 47 ASN A 441 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2947 Z= 0.211 Angle : 0.587 5.987 4030 Z= 0.290 Chirality : 0.037 0.113 494 Planarity : 0.006 0.060 495 Dihedral : 4.224 19.821 408 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 4.62 % Allowed : 31.68 % Favored : 63.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.32 (0.49), residues: 376 helix: 1.57 (0.35), residues: 284 sheet: None (None), residues: 0 loop : -4.44 (0.49), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 315 HIS 0.005 0.001 HIS A 441 PHE 0.008 0.001 PHE A 335 TYR 0.005 0.001 TYR A 417 ARG 0.002 0.000 ARG A 378 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 44 time to evaluate : 0.299 Fit side-chains REVERT: A 147 ASP cc_start: 0.8285 (p0) cc_final: 0.8018 (p0) REVERT: A 173 GLU cc_start: 0.7696 (tm-30) cc_final: 0.7299 (tm-30) REVERT: A 354 HIS cc_start: 0.7698 (OUTLIER) cc_final: 0.6961 (p-80) REVERT: A 444 HIS cc_start: 0.7355 (t-90) cc_final: 0.7138 (t70) REVERT: A 453 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7462 (mm) REVERT: A 461 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7279 (tt) outliers start: 14 outliers final: 9 residues processed: 54 average time/residue: 0.1176 time to fit residues: 8.1432 Evaluate side-chains 55 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 354 HIS Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 461 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 15 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.0980 chunk 0 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 32 optimal weight: 0.0870 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 21 optimal weight: 0.0470 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2947 Z= 0.194 Angle : 0.578 6.166 4030 Z= 0.285 Chirality : 0.037 0.110 494 Planarity : 0.005 0.061 495 Dihedral : 4.161 21.360 408 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 6.27 % Allowed : 30.36 % Favored : 63.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.46 (0.49), residues: 376 helix: 1.68 (0.35), residues: 284 sheet: None (None), residues: 0 loop : -4.41 (0.49), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 315 HIS 0.006 0.001 HIS A 441 PHE 0.008 0.001 PHE A 335 TYR 0.005 0.001 TYR A 417 ARG 0.002 0.000 ARG A 378 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 46 time to evaluate : 0.290 Fit side-chains REVERT: A 147 ASP cc_start: 0.8246 (p0) cc_final: 0.7952 (p0) REVERT: A 149 MET cc_start: 0.8064 (mtt) cc_final: 0.7785 (mtt) REVERT: A 173 GLU cc_start: 0.7685 (tm-30) cc_final: 0.7312 (tm-30) REVERT: A 354 HIS cc_start: 0.7695 (OUTLIER) cc_final: 0.7001 (p90) REVERT: A 444 HIS cc_start: 0.7356 (t-90) cc_final: 0.7151 (t70) REVERT: A 453 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7416 (mm) REVERT: A 461 LEU cc_start: 0.7556 (OUTLIER) cc_final: 0.7243 (tt) outliers start: 19 outliers final: 12 residues processed: 58 average time/residue: 0.1061 time to fit residues: 8.0689 Evaluate side-chains 59 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 44 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 354 HIS Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 461 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 3 optimal weight: 0.3980 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 26 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2947 Z= 0.226 Angle : 0.603 6.687 4030 Z= 0.296 Chirality : 0.038 0.115 494 Planarity : 0.005 0.061 495 Dihedral : 4.180 20.288 408 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 6.27 % Allowed : 31.02 % Favored : 62.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.46 (0.49), residues: 376 helix: 1.69 (0.35), residues: 284 sheet: None (None), residues: 0 loop : -4.42 (0.49), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 315 HIS 0.006 0.001 HIS A 441 PHE 0.009 0.001 PHE A 335 TYR 0.005 0.001 TYR A 421 ARG 0.003 0.000 ARG A 378 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 40 time to evaluate : 0.324 Fit side-chains REVERT: A 147 ASP cc_start: 0.8196 (p0) cc_final: 0.7911 (p0) REVERT: A 173 GLU cc_start: 0.7649 (tm-30) cc_final: 0.7280 (tm-30) REVERT: A 354 HIS cc_start: 0.7720 (OUTLIER) cc_final: 0.6994 (p-80) REVERT: A 453 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7425 (mm) REVERT: A 461 LEU cc_start: 0.7552 (OUTLIER) cc_final: 0.7241 (tt) outliers start: 19 outliers final: 13 residues processed: 53 average time/residue: 0.1153 time to fit residues: 7.9748 Evaluate side-chains 56 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 40 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 354 HIS Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 461 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 20 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 22 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 0.4980 chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 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 441 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2947 Z= 0.201 Angle : 0.590 6.256 4030 Z= 0.290 Chirality : 0.038 0.117 494 Planarity : 0.005 0.062 495 Dihedral : 4.218 21.349 408 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 5.61 % Allowed : 32.34 % Favored : 62.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.54 (0.49), residues: 376 helix: 1.74 (0.35), residues: 284 sheet: None (None), residues: 0 loop : -4.38 (0.49), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 315 HIS 0.006 0.001 HIS A 441 PHE 0.009 0.001 PHE A 335 TYR 0.005 0.001 TYR A 417 ARG 0.003 0.000 ARG A 378 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 43 time to evaluate : 0.339 Fit side-chains REVERT: A 46 ASP cc_start: 0.8743 (t0) cc_final: 0.8477 (t0) REVERT: A 147 ASP cc_start: 0.8229 (p0) cc_final: 0.7998 (p0) REVERT: A 173 GLU cc_start: 0.7647 (tm-30) cc_final: 0.7088 (tm-30) REVERT: A 354 HIS cc_start: 0.7709 (OUTLIER) cc_final: 0.6983 (p-80) REVERT: A 453 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7426 (mm) REVERT: A 461 LEU cc_start: 0.7537 (OUTLIER) cc_final: 0.7229 (tt) outliers start: 17 outliers final: 12 residues processed: 57 average time/residue: 0.1087 time to fit residues: 8.0283 Evaluate side-chains 55 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 40 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 354 HIS Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 461 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 18 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2947 Z= 0.216 Angle : 0.610 9.707 4030 Z= 0.296 Chirality : 0.038 0.120 494 Planarity : 0.005 0.062 495 Dihedral : 4.167 20.746 408 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 5.94 % Allowed : 33.00 % Favored : 61.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.49), residues: 376 helix: 1.76 (0.35), residues: 284 sheet: None (None), residues: 0 loop : -4.32 (0.51), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 315 HIS 0.007 0.001 HIS A 441 PHE 0.009 0.001 PHE A 335 TYR 0.006 0.001 TYR A 417 ARG 0.003 0.000 ARG A 378 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 42 time to evaluate : 0.318 Fit side-chains REVERT: A 147 ASP cc_start: 0.8210 (p0) cc_final: 0.8001 (p0) REVERT: A 173 GLU cc_start: 0.7538 (tm-30) cc_final: 0.7019 (tm-30) REVERT: A 354 HIS cc_start: 0.7722 (OUTLIER) cc_final: 0.6990 (p-80) REVERT: A 453 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7428 (mm) REVERT: A 461 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.7259 (tt) outliers start: 18 outliers final: 12 residues processed: 55 average time/residue: 0.1160 time to fit residues: 8.2158 Evaluate side-chains 56 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 41 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 354 HIS Chi-restraints excluded: chain A residue 356 GLN Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 461 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 30 optimal weight: 0.2980 chunk 32 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 22 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2947 Z= 0.209 Angle : 0.604 8.627 4030 Z= 0.295 Chirality : 0.038 0.118 494 Planarity : 0.005 0.062 495 Dihedral : 4.244 21.247 408 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 5.61 % Allowed : 32.34 % Favored : 62.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.49), residues: 376 helix: 1.77 (0.35), residues: 284 sheet: None (None), residues: 0 loop : -4.23 (0.52), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 315 HIS 0.004 0.001 HIS A 441 PHE 0.009 0.001 PHE A 335 TYR 0.006 0.001 TYR A 417 ARG 0.003 0.000 ARG A 378 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 42 time to evaluate : 0.318 Fit side-chains REVERT: A 46 ASP cc_start: 0.8649 (t0) cc_final: 0.8379 (t0) REVERT: A 147 ASP cc_start: 0.8237 (p0) cc_final: 0.8037 (p0) REVERT: A 149 MET cc_start: 0.8199 (mtt) cc_final: 0.7986 (mtm) REVERT: A 162 MET cc_start: 0.7823 (tpp) cc_final: 0.7537 (ttp) REVERT: A 173 GLU cc_start: 0.7529 (tm-30) cc_final: 0.7012 (tm-30) REVERT: A 354 HIS cc_start: 0.7723 (OUTLIER) cc_final: 0.7009 (p90) REVERT: A 453 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7461 (mm) REVERT: A 461 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.7254 (tt) outliers start: 17 outliers final: 13 residues processed: 55 average time/residue: 0.1184 time to fit residues: 8.4427 Evaluate side-chains 57 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 41 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 354 HIS Chi-restraints excluded: chain A residue 356 GLN Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 461 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 23 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 3 optimal weight: 0.0270 chunk 5 optimal weight: 0.2980 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2947 Z= 0.186 Angle : 0.589 8.546 4030 Z= 0.288 Chirality : 0.037 0.118 494 Planarity : 0.005 0.062 495 Dihedral : 4.128 21.513 408 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 5.61 % Allowed : 32.34 % Favored : 62.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.78 (0.49), residues: 376 helix: 1.88 (0.35), residues: 284 sheet: None (None), residues: 0 loop : -4.15 (0.52), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 315 HIS 0.004 0.001 HIS A 441 PHE 0.009 0.001 PHE A 335 TYR 0.006 0.001 TYR A 417 ARG 0.004 0.000 ARG A 378 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 45 time to evaluate : 0.347 Fit side-chains REVERT: A 46 ASP cc_start: 0.8681 (t0) cc_final: 0.8378 (t0) REVERT: A 149 MET cc_start: 0.8094 (mtt) cc_final: 0.7758 (mtm) REVERT: A 162 MET cc_start: 0.7813 (tpp) cc_final: 0.7541 (ttp) REVERT: A 173 GLU cc_start: 0.7361 (tm-30) cc_final: 0.6830 (tm-30) REVERT: A 354 HIS cc_start: 0.7711 (OUTLIER) cc_final: 0.7002 (p90) REVERT: A 453 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7442 (mm) REVERT: A 461 LEU cc_start: 0.7521 (OUTLIER) cc_final: 0.7234 (tt) outliers start: 17 outliers final: 12 residues processed: 57 average time/residue: 0.1106 time to fit residues: 8.2267 Evaluate side-chains 57 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 42 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 354 HIS Chi-restraints excluded: chain A residue 356 GLN Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 461 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 26 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 25 optimal weight: 0.0070 chunk 24 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 14 optimal weight: 0.0980 chunk 37 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.152241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.126526 restraints weight = 3865.829| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.80 r_work: 0.3331 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2947 Z= 0.188 Angle : 0.593 8.196 4030 Z= 0.290 Chirality : 0.037 0.115 494 Planarity : 0.005 0.062 495 Dihedral : 4.128 20.992 408 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 4.95 % Allowed : 33.33 % Favored : 61.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.82 (0.49), residues: 376 helix: 1.89 (0.35), residues: 284 sheet: None (None), residues: 0 loop : -4.10 (0.53), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 315 HIS 0.004 0.001 HIS A 441 PHE 0.008 0.001 PHE A 335 TYR 0.003 0.001 TYR A 417 ARG 0.004 0.000 ARG A 378 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1019.35 seconds wall clock time: 19 minutes 16.55 seconds (1156.55 seconds total)