Starting phenix.real_space_refine on Thu Nov 14 00:38:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zms_60255/11_2024/8zms_60255.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zms_60255/11_2024/8zms_60255.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zms_60255/11_2024/8zms_60255.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zms_60255/11_2024/8zms_60255.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zms_60255/11_2024/8zms_60255.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zms_60255/11_2024/8zms_60255.cif" } resolution = 3.7 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= 0.020 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 1940 2.51 5 N 463 2.21 5 O 500 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 2920 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 2910 Classifications: {'peptide': 386} Link IDs: {'PTRANS': 24, 'TRANS': 361} Chain breaks: 2 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'ACH': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.54, per 1000 atoms: 0.87 Number of scatterers: 2920 At special positions: 0 Unit cell: (70.55, 59.76, 83.83, 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 500 8.00 N 463 7.00 C 1940 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 348.5 milliseconds 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 716 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 0 sheets defined 88.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 21 through 54 removed outlier: 3.608A pdb=" N VAL A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ILE A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL A 54 " --> pdb=" O TYR A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 61 removed outlier: 4.051A pdb=" N ILE A 61 " --> pdb=" O PRO A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 149 removed outlier: 3.577A pdb=" N ASN A 139 " --> pdb=" O GLN A 135 " (cutoff:3.500A) Proline residue: A 140 - end of helix Proline residue: A 144 - end of helix Processing helix chain 'A' and resid 151 through 171 removed outlier: 3.749A pdb=" N PHE A 171 " --> pdb=" O VAL A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 201 removed outlier: 4.660A pdb=" N THR A 194 " --> pdb=" O ALA A 190 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N SER A 195 " --> pdb=" O PHE A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 238 Proline residue: A 229 - end of helix removed outlier: 4.174A pdb=" N LEU A 235 " --> pdb=" O PHE A 231 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N PHE A 238 " --> pdb=" O ILE A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 264 removed outlier: 3.849A pdb=" N PHE A 245 " --> pdb=" O LYS A 241 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU A 246 " --> pdb=" O ARG A 242 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 307 Proline residue: A 304 - end of helix Processing helix chain 'A' and resid 311 through 319 removed outlier: 3.676A pdb=" N TRP A 315 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS A 317 " --> pdb=" O ALA A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 329 Processing helix chain 'A' and resid 331 through 334 removed outlier: 3.580A 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 351 Processing helix chain 'A' and resid 355 through 374 removed outlier: 3.529A pdb=" N TYR A 359 " --> pdb=" O LEU A 355 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL A 374 " --> pdb=" O SER A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 377 No H-bonds generated for 'chain 'A' and resid 375 through 377' Processing helix chain 'A' and resid 379 through 413 removed outlier: 3.900A pdb=" N LEU A 383 " --> pdb=" O SER A 379 " (cutoff:3.500A) Proline residue: A 403 - end of helix Processing helix chain 'A' and resid 418 through 446 removed outlier: 4.151A pdb=" N ALA A 431 " --> pdb=" O SER A 427 " (cutoff:3.500A) Proline residue: A 436 - end of helix removed outlier: 4.386A pdb=" N GLY A 440 " --> pdb=" O PRO A 436 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N HIS A 441 " --> pdb=" O ILE A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 463 Processing helix chain 'A' and resid 464 through 469 removed outlier: 3.774A pdb=" N LEU A 467 " --> pdb=" O PRO A 464 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 468 " --> pdb=" O VAL A 465 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU A 469 " --> pdb=" O LEU A 466 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 464 through 469' 229 hydrogen bonds defined for protein. 681 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: 0.73 Time building geometry restraints manager: 0.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 450 1.31 - 1.43: 765 1.43 - 1.56: 1746 1.56 - 1.68: 0 1.68 - 1.81: 28 Bond restraints: 2989 Sorted by residual: bond pdb=" C5 ACH A1001 " pdb=" O4 ACH A1001 " ideal model delta sigma weight residual 1.335 1.410 -0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" C2 ACH A1001 " pdb=" C3 ACH A1001 " ideal model delta sigma weight residual 1.509 1.553 -0.044 2.00e-02 2.50e+03 4.86e+00 bond pdb=" C5 ACH A1001 " pdb=" C6 ACH A1001 " ideal model delta sigma weight residual 1.497 1.541 -0.044 2.00e-02 2.50e+03 4.82e+00 bond pdb=" CA VAL A 336 " pdb=" C VAL A 336 " ideal model delta sigma weight residual 1.520 1.535 -0.015 8.80e-03 1.29e+04 3.04e+00 bond pdb=" C ILE A 303 " pdb=" N PRO A 304 " ideal model delta sigma weight residual 1.336 1.357 -0.021 1.23e-02 6.61e+03 2.99e+00 ... (remaining 2984 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 3867 2.14 - 4.29: 157 4.29 - 6.43: 37 6.43 - 8.58: 17 8.58 - 10.72: 4 Bond angle restraints: 4082 Sorted by residual: angle pdb=" C PHE A 335 " pdb=" N VAL A 336 " pdb=" CA VAL A 336 " ideal model delta sigma weight residual 120.24 123.54 -3.30 6.30e-01 2.52e+00 2.74e+01 angle pdb=" N PRO A 229 " pdb=" CA PRO A 229 " pdb=" C PRO A 229 " ideal model delta sigma weight residual 110.70 115.83 -5.13 1.22e+00 6.72e-01 1.77e+01 angle pdb=" CA PRO A 229 " pdb=" C PRO A 229 " pdb=" N PRO A 230 " ideal model delta sigma weight residual 117.93 122.77 -4.84 1.20e+00 6.94e-01 1.63e+01 angle pdb=" N VAL A 374 " pdb=" CA VAL A 374 " pdb=" C VAL A 374 " ideal model delta sigma weight residual 108.88 116.63 -7.75 2.16e+00 2.14e-01 1.29e+01 angle pdb=" C10 ACH A1001 " pdb=" N1 ACH A1001 " pdb=" C9 ACH A1001 " ideal model delta sigma weight residual 108.54 119.26 -10.72 3.00e+00 1.11e-01 1.28e+01 ... (remaining 4077 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.28: 1595 11.28 - 22.57: 128 22.57 - 33.85: 26 33.85 - 45.13: 10 45.13 - 56.42: 3 Dihedral angle restraints: 1762 sinusoidal: 648 harmonic: 1114 Sorted by residual: dihedral pdb=" CA SER A 379 " pdb=" C SER A 379 " pdb=" N PHE A 380 " pdb=" CA PHE A 380 " ideal model delta harmonic sigma weight residual -180.00 -161.18 -18.82 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA ASP A 288 " pdb=" C ASP A 288 " pdb=" N PRO A 289 " pdb=" CA PRO A 289 " ideal model delta harmonic sigma weight residual -180.00 -162.35 -17.65 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA GLU A 206 " pdb=" C GLU A 206 " pdb=" N GLU A 207 " pdb=" CA GLU A 207 " ideal model delta harmonic sigma weight residual -180.00 -162.46 -17.54 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 1759 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 341 0.049 - 0.098: 113 0.098 - 0.147: 36 0.147 - 0.195: 6 0.195 - 0.244: 1 Chirality restraints: 497 Sorted by residual: chirality pdb=" CB VAL A 54 " pdb=" CA VAL A 54 " pdb=" CG1 VAL A 54 " pdb=" CG2 VAL A 54 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CG LEU A 178 " pdb=" CB LEU A 178 " pdb=" CD1 LEU A 178 " pdb=" CD2 LEU A 178 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.55e-01 chirality pdb=" CA ASN A 139 " pdb=" N ASN A 139 " pdb=" C ASN A 139 " pdb=" CB ASN A 139 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.30e-01 ... (remaining 494 not shown) Planarity restraints: 501 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 309 " 0.044 5.00e-02 4.00e+02 6.63e-02 7.04e+00 pdb=" N PRO A 310 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 310 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 310 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 224 " -0.012 2.00e-02 2.50e+03 2.38e-02 5.69e+00 pdb=" C GLY A 224 " 0.041 2.00e-02 2.50e+03 pdb=" O GLY A 224 " -0.015 2.00e-02 2.50e+03 pdb=" N SER A 225 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 228 " 0.037 5.00e-02 4.00e+02 5.48e-02 4.81e+00 pdb=" N PRO A 229 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 229 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 229 " 0.031 5.00e-02 4.00e+02 ... (remaining 498 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 931 2.86 - 3.37: 2895 3.37 - 3.88: 4862 3.88 - 4.39: 5087 4.39 - 4.90: 8758 Nonbonded interactions: 22533 Sorted by model distance: nonbonded pdb=" O LEU A 127 " pdb=" OG SER A 130 " model vdw 2.349 3.040 nonbonded pdb=" O ASP A 174 " pdb=" OG1 THR A 177 " model vdw 2.358 3.040 nonbonded pdb=" OD2 ASP A 147 " pdb=" OG SER A 419 " model vdw 2.359 3.040 nonbonded pdb=" ND2 ASN A 139 " pdb=" OD2 ASP A 425 " model vdw 2.390 3.120 nonbonded pdb=" O GLN A 135 " pdb=" ND2 ASN A 139 " model vdw 2.412 3.120 ... (remaining 22528 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.430 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: 0.030 Process input model: 11.790 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 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 : 0.007 0.075 2989 Z= 0.437 Angle : 1.147 10.721 4082 Z= 0.589 Chirality : 0.055 0.244 497 Planarity : 0.010 0.066 501 Dihedral : 9.676 56.418 1046 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % 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: -3.71 (0.32), residues: 380 helix: -2.04 (0.21), residues: 301 sheet: None (None), residues: 0 loop : -3.30 (0.64), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 325 HIS 0.005 0.001 HIS A 338 PHE 0.019 0.003 PHE A 238 TYR 0.014 0.002 TYR A 50 ARG 0.002 0.001 ARG A 378 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.304 Fit side-chains REVERT: A 21 GLU cc_start: 0.7771 (tt0) cc_final: 0.7280 (pm20) REVERT: A 254 PHE cc_start: 0.7232 (t80) cc_final: 0.7026 (m-80) REVERT: A 286 MET cc_start: 0.5604 (mmp) cc_final: 0.4183 (ttm) REVERT: A 305 LEU cc_start: 0.8372 (mt) cc_final: 0.8097 (mt) REVERT: A 429 SER cc_start: 0.8595 (m) cc_final: 0.8097 (p) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.1351 time to fit residues: 14.7555 Evaluate side-chains 65 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 29 optimal weight: 0.2980 chunk 11 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 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 : 0.004 0.037 2989 Z= 0.241 Angle : 0.732 7.254 4082 Z= 0.359 Chirality : 0.042 0.129 497 Planarity : 0.006 0.048 501 Dihedral : 5.859 47.252 415 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.63 % Allowed : 12.75 % Favored : 85.62 % 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: -1.06 (0.41), residues: 380 helix: -0.10 (0.28), residues: 318 sheet: None (None), residues: 0 loop : -3.34 (0.68), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 315 HIS 0.002 0.000 HIS A 283 PHE 0.027 0.002 PHE A 169 TYR 0.011 0.002 TYR A 352 ARG 0.001 0.000 ARG A 470 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.285 Fit side-chains REVERT: A 21 GLU cc_start: 0.7719 (tt0) cc_final: 0.7238 (pm20) REVERT: A 286 MET cc_start: 0.5542 (mmp) cc_final: 0.4061 (ttp) outliers start: 5 outliers final: 3 residues processed: 71 average time/residue: 0.0930 time to fit residues: 8.8072 Evaluate side-chains 63 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 60 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 278 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 0.7980 chunk 23 optimal weight: 0.4980 chunk 9 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 chunk 11 optimal weight: 0.1980 chunk 27 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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: 0.7410 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2989 Z= 0.222 Angle : 0.695 7.191 4082 Z= 0.339 Chirality : 0.041 0.117 497 Planarity : 0.005 0.040 501 Dihedral : 5.496 42.688 415 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.27 % Allowed : 15.03 % Favored : 81.70 % 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: 0.06 (0.44), residues: 380 helix: 0.73 (0.30), residues: 312 sheet: None (None), residues: 0 loop : -3.02 (0.67), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 325 HIS 0.002 0.000 HIS A 283 PHE 0.025 0.002 PHE A 169 TYR 0.009 0.001 TYR A 428 ARG 0.001 0.000 ARG A 470 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.310 Fit side-chains REVERT: A 21 GLU cc_start: 0.7713 (tt0) cc_final: 0.7225 (pm20) REVERT: A 286 MET cc_start: 0.5659 (mmp) cc_final: 0.4116 (ttp) REVERT: A 410 ASP cc_start: 0.8275 (m-30) cc_final: 0.7956 (m-30) outliers start: 10 outliers final: 7 residues processed: 68 average time/residue: 0.0788 time to fit residues: 7.5235 Evaluate side-chains 66 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 372 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 16 optimal weight: 0.0570 chunk 23 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 32 optimal weight: 0.2980 chunk 9 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2989 Z= 0.201 Angle : 0.656 6.985 4082 Z= 0.321 Chirality : 0.040 0.124 497 Planarity : 0.005 0.038 501 Dihedral : 5.237 41.924 415 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.59 % Allowed : 15.69 % Favored : 80.72 % 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: 0.66 (0.45), residues: 380 helix: 1.17 (0.31), residues: 311 sheet: None (None), residues: 0 loop : -2.91 (0.70), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 357 HIS 0.002 0.000 HIS A 283 PHE 0.021 0.002 PHE A 169 TYR 0.009 0.001 TYR A 359 ARG 0.001 0.000 ARG A 470 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.249 Fit side-chains REVERT: A 21 GLU cc_start: 0.7682 (tt0) cc_final: 0.7260 (pm20) REVERT: A 286 MET cc_start: 0.5747 (mmp) cc_final: 0.4185 (ttp) REVERT: A 311 THR cc_start: 0.9239 (m) cc_final: 0.8807 (t) REVERT: A 410 ASP cc_start: 0.8316 (m-30) cc_final: 0.7985 (m-30) outliers start: 11 outliers final: 7 residues processed: 65 average time/residue: 0.0817 time to fit residues: 7.5093 Evaluate side-chains 63 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 372 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 15 optimal weight: 0.0570 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2989 Z= 0.223 Angle : 0.691 8.611 4082 Z= 0.334 Chirality : 0.041 0.148 497 Planarity : 0.005 0.037 501 Dihedral : 5.214 41.458 415 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.27 % Allowed : 16.01 % Favored : 80.72 % 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: 0.75 (0.45), residues: 380 helix: 1.16 (0.30), residues: 316 sheet: None (None), residues: 0 loop : -2.75 (0.75), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 357 HIS 0.002 0.001 HIS A 283 PHE 0.019 0.001 PHE A 169 TYR 0.009 0.001 TYR A 432 ARG 0.001 0.000 ARG A 470 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.270 Fit side-chains REVERT: A 21 GLU cc_start: 0.7708 (tt0) cc_final: 0.7263 (pm20) REVERT: A 286 MET cc_start: 0.5732 (mmp) cc_final: 0.4161 (ttp) REVERT: A 410 ASP cc_start: 0.8355 (m-30) cc_final: 0.8016 (m-30) outliers start: 10 outliers final: 8 residues processed: 64 average time/residue: 0.0826 time to fit residues: 7.4842 Evaluate side-chains 63 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 385 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 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: 0.7441 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2989 Z= 0.249 Angle : 0.709 9.016 4082 Z= 0.344 Chirality : 0.042 0.131 497 Planarity : 0.005 0.039 501 Dihedral : 5.288 41.767 415 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 4.58 % Allowed : 16.67 % Favored : 78.76 % 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: 0.78 (0.45), residues: 380 helix: 1.15 (0.30), residues: 316 sheet: None (None), residues: 0 loop : -2.54 (0.77), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 357 HIS 0.002 0.001 HIS A 283 PHE 0.017 0.002 PHE A 169 TYR 0.011 0.002 TYR A 432 ARG 0.002 0.000 ARG A 470 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.316 Fit side-chains REVERT: A 21 GLU cc_start: 0.7801 (tt0) cc_final: 0.7298 (pm20) REVERT: A 51 MET cc_start: 0.7701 (OUTLIER) cc_final: 0.7483 (mmm) REVERT: A 286 MET cc_start: 0.5978 (mmp) cc_final: 0.4254 (ttp) REVERT: A 410 ASP cc_start: 0.8436 (m-30) cc_final: 0.8082 (m-30) outliers start: 14 outliers final: 8 residues processed: 65 average time/residue: 0.0834 time to fit residues: 7.4949 Evaluate side-chains 64 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 385 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.7432 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2989 Z= 0.232 Angle : 0.698 8.304 4082 Z= 0.338 Chirality : 0.042 0.141 497 Planarity : 0.005 0.035 501 Dihedral : 5.228 41.191 415 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.92 % Allowed : 16.99 % Favored : 79.08 % 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: 0.81 (0.45), residues: 380 helix: 1.16 (0.30), residues: 317 sheet: None (None), residues: 0 loop : -2.54 (0.81), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 357 HIS 0.002 0.001 HIS A 283 PHE 0.017 0.002 PHE A 169 TYR 0.010 0.002 TYR A 50 ARG 0.001 0.000 ARG A 470 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.351 Fit side-chains REVERT: A 21 GLU cc_start: 0.7802 (tt0) cc_final: 0.7319 (pm20) REVERT: A 286 MET cc_start: 0.6037 (mmp) cc_final: 0.4233 (ttp) REVERT: A 316 MET cc_start: 0.7609 (mmt) cc_final: 0.7396 (mmt) REVERT: A 410 ASP cc_start: 0.8435 (m-30) cc_final: 0.8071 (m-30) outliers start: 12 outliers final: 8 residues processed: 64 average time/residue: 0.0831 time to fit residues: 7.4249 Evaluate side-chains 63 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 385 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 18 optimal weight: 0.0980 chunk 3 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2989 Z= 0.216 Angle : 0.705 7.812 4082 Z= 0.338 Chirality : 0.041 0.139 497 Planarity : 0.005 0.035 501 Dihedral : 5.321 45.712 415 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.27 % Allowed : 17.32 % Favored : 79.41 % 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: 0.91 (0.45), residues: 380 helix: 1.20 (0.30), residues: 317 sheet: None (None), residues: 0 loop : -2.36 (0.82), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 357 HIS 0.002 0.000 HIS A 283 PHE 0.014 0.001 PHE A 169 TYR 0.013 0.001 TYR A 50 ARG 0.001 0.000 ARG A 470 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.335 Fit side-chains REVERT: A 21 GLU cc_start: 0.7775 (tt0) cc_final: 0.7321 (pm20) REVERT: A 51 MET cc_start: 0.7998 (mmm) cc_final: 0.7270 (mmt) REVERT: A 286 MET cc_start: 0.5980 (mmp) cc_final: 0.4194 (ttp) REVERT: A 316 MET cc_start: 0.7554 (mmt) cc_final: 0.7338 (mmt) REVERT: A 410 ASP cc_start: 0.8450 (m-30) cc_final: 0.8079 (m-30) outliers start: 10 outliers final: 8 residues processed: 66 average time/residue: 0.0989 time to fit residues: 8.6360 Evaluate side-chains 65 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 385 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 30 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 0.3980 chunk 3 optimal weight: 0.2980 chunk 23 optimal weight: 0.9990 chunk 18 optimal weight: 0.0070 overall best weight: 0.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2989 Z= 0.197 Angle : 0.693 7.574 4082 Z= 0.331 Chirality : 0.040 0.133 497 Planarity : 0.005 0.036 501 Dihedral : 5.168 43.025 415 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.94 % Allowed : 16.99 % Favored : 80.07 % 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: 0.99 (0.45), residues: 380 helix: 1.31 (0.30), residues: 314 sheet: None (None), residues: 0 loop : -2.46 (0.80), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 357 HIS 0.001 0.000 HIS A 283 PHE 0.014 0.001 PHE A 169 TYR 0.014 0.001 TYR A 50 ARG 0.001 0.000 ARG A 378 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.324 Fit side-chains REVERT: A 21 GLU cc_start: 0.7794 (tt0) cc_final: 0.7376 (pm20) REVERT: A 284 ARG cc_start: 0.7271 (ttm170) cc_final: 0.7003 (mpt180) REVERT: A 286 MET cc_start: 0.6019 (mmp) cc_final: 0.4265 (ttp) REVERT: A 316 MET cc_start: 0.7480 (mmt) cc_final: 0.7273 (mmt) REVERT: A 332 LEU cc_start: 0.8368 (tt) cc_final: 0.8101 (tp) REVERT: A 410 ASP cc_start: 0.8443 (m-30) cc_final: 0.8076 (m-30) outliers start: 9 outliers final: 7 residues processed: 66 average time/residue: 0.0963 time to fit residues: 8.5760 Evaluate side-chains 64 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 385 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 23 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 12 optimal weight: 0.0270 chunk 31 optimal weight: 0.2980 chunk 3 optimal weight: 0.1980 chunk 5 optimal weight: 1.9990 overall best weight: 0.3638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2989 Z= 0.198 Angle : 0.741 15.980 4082 Z= 0.346 Chirality : 0.041 0.140 497 Planarity : 0.005 0.036 501 Dihedral : 5.135 42.370 415 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.29 % Allowed : 18.63 % Favored : 79.08 % 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: 1.02 (0.45), residues: 380 helix: 1.33 (0.30), residues: 314 sheet: None (None), residues: 0 loop : -2.45 (0.81), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 357 HIS 0.001 0.000 HIS A 283 PHE 0.013 0.001 PHE A 169 TYR 0.015 0.001 TYR A 50 ARG 0.001 0.000 ARG A 378 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.325 Fit side-chains REVERT: A 21 GLU cc_start: 0.7768 (tt0) cc_final: 0.7382 (pm20) REVERT: A 284 ARG cc_start: 0.7258 (ttm170) cc_final: 0.6988 (mpt180) REVERT: A 286 MET cc_start: 0.6024 (mmp) cc_final: 0.4307 (ttp) REVERT: A 316 MET cc_start: 0.7479 (mmt) cc_final: 0.7263 (mmt) REVERT: A 332 LEU cc_start: 0.8402 (tt) cc_final: 0.8075 (tp) REVERT: A 410 ASP cc_start: 0.8430 (m-30) cc_final: 0.8071 (m-30) outliers start: 7 outliers final: 5 residues processed: 65 average time/residue: 0.0960 time to fit residues: 8.3396 Evaluate side-chains 66 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 385 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 26 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 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 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.181249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.165685 restraints weight = 4626.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.169525 restraints weight = 2523.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.172176 restraints weight = 1590.922| |-----------------------------------------------------------------------------| r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 2989 Z= 0.241 Angle : 0.762 14.067 4082 Z= 0.357 Chirality : 0.042 0.145 497 Planarity : 0.005 0.035 501 Dihedral : 5.221 41.205 415 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.63 % Allowed : 19.93 % Favored : 78.43 % 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: 0.91 (0.45), residues: 380 helix: 1.25 (0.30), residues: 314 sheet: None (None), residues: 0 loop : -2.45 (0.79), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 357 HIS 0.002 0.000 HIS A 283 PHE 0.013 0.002 PHE A 169 TYR 0.010 0.001 TYR A 50 ARG 0.002 0.000 ARG A 470 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1036.87 seconds wall clock time: 19 minutes 34.62 seconds (1174.62 seconds total)