Starting phenix.real_space_refine on Thu Jul 18 18:39:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zms_60255/07_2024/8zms_60255.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zms_60255/07_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_60255/07_2024/8zms_60255.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zms_60255/07_2024/8zms_60255.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zms_60255/07_2024/8zms_60255.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zms_60255/07_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 Residue "A ARG 284": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 3.08, per 1000 atoms: 1.05 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.18 Conformation dependent library (CDL) restraints added in 735.9 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: 0.32 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: 0.76 Time building geometry restraints manager: 1.20 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: 99.98 - 107.00: 127 107.00 - 114.02: 1714 114.02 - 121.04: 1556 121.04 - 128.06: 651 128.06 - 135.09: 34 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 2.440 nonbonded pdb=" O ASP A 174 " pdb=" OG1 THR A 177 " model vdw 2.358 2.440 nonbonded pdb=" OD2 ASP A 147 " pdb=" OG SER A 419 " model vdw 2.359 2.440 nonbonded pdb=" ND2 ASN A 139 " pdb=" OD2 ASP A 425 " model vdw 2.390 2.520 nonbonded pdb=" O GLN A 135 " pdb=" ND2 ASN A 139 " model vdw 2.412 2.520 ... (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: 1.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 14.170 Find NCS groups from input model: 0.020 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.510 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.318 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: 0.1382 time to fit residues: 15.1278 Evaluate side-chains 65 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.328 ------------------------------------------------------------------------------- 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: 0.8980 chunk 28 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 9 optimal weight: 0.0980 chunk 19 optimal weight: 0.3980 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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: 0.7408 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 2989 Z= 0.237 Angle : 0.724 7.237 4082 Z= 0.355 Chirality : 0.041 0.126 497 Planarity : 0.006 0.047 501 Dihedral : 5.849 47.287 415 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.96 % Allowed : 12.09 % Favored : 85.95 % 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: -1.03 (0.41), residues: 380 helix: -0.09 (0.28), residues: 318 sheet: None (None), residues: 0 loop : -3.30 (0.69), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 315 HIS 0.002 0.000 HIS A 283 PHE 0.026 0.002 PHE A 169 TYR 0.011 0.002 TYR A 428 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 76 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 70 time to evaluate : 0.322 Fit side-chains REVERT: A 21 GLU cc_start: 0.7715 (tt0) cc_final: 0.7236 (pm20) REVERT: A 286 MET cc_start: 0.5680 (mmp) cc_final: 0.4189 (ttp) outliers start: 6 outliers final: 4 residues processed: 73 average time/residue: 0.0980 time to fit residues: 9.4284 Evaluate side-chains 68 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 64 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 Chi-restraints excluded: chain A residue 427 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 2989 Z= 0.272 Angle : 0.731 7.209 4082 Z= 0.359 Chirality : 0.042 0.122 497 Planarity : 0.005 0.040 501 Dihedral : 5.576 42.647 415 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.90 % Allowed : 13.40 % 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: 0.04 (0.44), residues: 380 helix: 0.72 (0.30), residues: 311 sheet: None (None), residues: 0 loop : -3.01 (0.69), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 325 HIS 0.002 0.001 HIS A 283 PHE 0.022 0.002 PHE A 169 TYR 0.012 0.002 TYR A 432 ARG 0.002 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 78 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 63 time to evaluate : 0.287 Fit side-chains REVERT: A 21 GLU cc_start: 0.7831 (tt0) cc_final: 0.7284 (pm20) REVERT: A 286 MET cc_start: 0.5901 (mmp) cc_final: 0.4304 (ttp) REVERT: A 299 THR cc_start: 0.8640 (OUTLIER) cc_final: 0.8322 (m) REVERT: A 410 ASP cc_start: 0.8018 (m-30) cc_final: 0.7767 (m-30) outliers start: 15 outliers final: 11 residues processed: 70 average time/residue: 0.0786 time to fit residues: 7.5654 Evaluate side-chains 75 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 63 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 135 GLN 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 299 THR Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 427 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 16 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 32 optimal weight: 0.0980 chunk 9 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.2595 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= 0.248 Angle : 0.691 6.985 4082 Z= 0.339 Chirality : 0.041 0.118 497 Planarity : 0.005 0.036 501 Dihedral : 5.451 44.417 415 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 5.23 % Allowed : 15.03 % Favored : 79.74 % 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: 0.54 (0.45), residues: 380 helix: 1.08 (0.30), residues: 310 sheet: None (None), residues: 0 loop : -2.90 (0.71), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 325 HIS 0.002 0.001 HIS A 283 PHE 0.019 0.002 PHE A 169 TYR 0.011 0.002 TYR A 432 ARG 0.002 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 73 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 57 time to evaluate : 0.293 Fit side-chains REVERT: A 21 GLU cc_start: 0.7785 (tt0) cc_final: 0.7290 (pm20) REVERT: A 286 MET cc_start: 0.5984 (mmp) cc_final: 0.4301 (ttp) REVERT: A 410 ASP cc_start: 0.8071 (m-30) cc_final: 0.7816 (m-30) outliers start: 16 outliers final: 13 residues processed: 64 average time/residue: 0.0761 time to fit residues: 6.7771 Evaluate side-chains 68 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 55 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 135 GLN Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 225 SER 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 Chi-restraints excluded: chain A residue 427 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 15 optimal weight: 0.0770 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 0.3980 chunk 12 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2989 Z= 0.221 Angle : 0.674 6.874 4082 Z= 0.328 Chirality : 0.040 0.117 497 Planarity : 0.005 0.037 501 Dihedral : 5.319 43.663 415 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 4.90 % Allowed : 15.36 % Favored : 79.74 % 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: 0.80 (0.45), residues: 380 helix: 1.16 (0.30), residues: 319 sheet: None (None), residues: 0 loop : -2.74 (0.83), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 357 HIS 0.002 0.000 HIS A 283 PHE 0.020 0.002 PHE A 169 TYR 0.010 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 75 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 60 time to evaluate : 0.264 Fit side-chains REVERT: A 21 GLU cc_start: 0.7788 (tt0) cc_final: 0.7306 (pm20) REVERT: A 286 MET cc_start: 0.5984 (mmp) cc_final: 0.4273 (ttp) REVERT: A 410 ASP cc_start: 0.8130 (m-30) cc_final: 0.7885 (m-30) outliers start: 15 outliers final: 11 residues processed: 68 average time/residue: 0.0831 time to fit residues: 7.8409 Evaluate side-chains 68 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 57 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 51 MET 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 278 VAL Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 427 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 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: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 2989 Z= 0.261 Angle : 0.705 6.854 4082 Z= 0.343 Chirality : 0.042 0.137 497 Planarity : 0.005 0.035 501 Dihedral : 5.379 44.534 415 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 5.56 % Allowed : 16.67 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.45), residues: 380 helix: 1.12 (0.30), residues: 320 sheet: None (None), residues: 0 loop : -2.60 (0.86), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 357 HIS 0.002 0.001 HIS A 283 PHE 0.017 0.002 PHE A 169 TYR 0.013 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 77 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 60 time to evaluate : 0.317 Fit side-chains REVERT: A 21 GLU cc_start: 0.7823 (tt0) cc_final: 0.7299 (pm20) REVERT: A 286 MET cc_start: 0.5990 (mmp) cc_final: 0.4180 (ttp) REVERT: A 299 THR cc_start: 0.8578 (OUTLIER) cc_final: 0.8272 (m) REVERT: A 316 MET cc_start: 0.7653 (mmt) cc_final: 0.7435 (mmt) REVERT: A 410 ASP cc_start: 0.8192 (m-30) cc_final: 0.7936 (m-30) outliers start: 17 outliers final: 13 residues processed: 69 average time/residue: 0.0768 time to fit residues: 7.4088 Evaluate side-chains 72 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 58 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 46 ASP 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 124 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 278 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 427 SER 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: 0.9980 chunk 36 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2989 Z= 0.264 Angle : 0.720 8.701 4082 Z= 0.347 Chirality : 0.043 0.139 497 Planarity : 0.005 0.035 501 Dihedral : 5.400 44.757 415 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 5.56 % Allowed : 16.99 % Favored : 77.45 % 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: 1.14 (0.30), residues: 319 sheet: None (None), residues: 0 loop : -2.55 (0.86), residues: 61 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 0.016 0.002 PHE A 169 TYR 0.012 0.002 TYR A 432 ARG 0.002 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 76 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 59 time to evaluate : 0.332 Fit side-chains REVERT: A 21 GLU cc_start: 0.7830 (tt0) cc_final: 0.7303 (pm20) REVERT: A 286 MET cc_start: 0.5993 (mmp) cc_final: 0.4413 (ttt) REVERT: A 316 MET cc_start: 0.7679 (mmt) cc_final: 0.7449 (mmt) REVERT: A 410 ASP cc_start: 0.8211 (m-30) cc_final: 0.7960 (m-30) outliers start: 17 outliers final: 15 residues processed: 67 average time/residue: 0.0757 time to fit residues: 7.2112 Evaluate side-chains 72 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 57 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 46 ASP 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 124 ILE Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 225 SER 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 Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 427 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 0.0050 chunk 28 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 14 optimal weight: 0.0670 chunk 26 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 overall best weight: 0.4332 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2989 Z= 0.201 Angle : 0.679 10.222 4082 Z= 0.324 Chirality : 0.040 0.137 497 Planarity : 0.005 0.037 501 Dihedral : 5.370 48.813 415 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.90 % Allowed : 16.99 % Favored : 78.10 % 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 (0.46), residues: 380 helix: 1.32 (0.30), residues: 318 sheet: None (None), residues: 0 loop : -2.48 (0.87), residues: 62 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 0.016 0.001 PHE A 169 TYR 0.009 0.001 TYR A 359 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 75 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 60 time to evaluate : 0.319 Fit side-chains REVERT: A 21 GLU cc_start: 0.7780 (tt0) cc_final: 0.7306 (pm20) REVERT: A 51 MET cc_start: 0.7551 (OUTLIER) cc_final: 0.7336 (mmm) REVERT: A 286 MET cc_start: 0.6080 (mmp) cc_final: 0.4275 (ttp) REVERT: A 299 THR cc_start: 0.8560 (OUTLIER) cc_final: 0.8258 (m) REVERT: A 316 MET cc_start: 0.7619 (mmt) cc_final: 0.7373 (mmt) REVERT: A 410 ASP cc_start: 0.8223 (m-30) cc_final: 0.7956 (m-30) outliers start: 15 outliers final: 11 residues processed: 69 average time/residue: 0.0972 time to fit residues: 8.7861 Evaluate side-chains 70 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 57 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 225 SER 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 299 THR Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 427 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 30 optimal weight: 0.8980 chunk 32 optimal weight: 0.1980 chunk 34 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 37 optimal weight: 0.0670 chunk 3 optimal weight: 1.9990 chunk 23 optimal weight: 0.0170 chunk 18 optimal weight: 1.9990 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2989 Z= 0.197 Angle : 0.677 9.688 4082 Z= 0.321 Chirality : 0.040 0.114 497 Planarity : 0.005 0.037 501 Dihedral : 5.266 46.496 415 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.25 % Allowed : 18.30 % Favored : 77.45 % 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: 1.11 (0.45), residues: 380 helix: 1.34 (0.30), residues: 318 sheet: None (None), residues: 0 loop : -2.36 (0.87), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 357 HIS 0.002 0.000 HIS A 283 PHE 0.015 0.001 PHE A 169 TYR 0.009 0.001 TYR A 359 ARG 0.001 0.000 ARG A 212 *********************** 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 71 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 58 time to evaluate : 0.318 Fit side-chains REVERT: A 21 GLU cc_start: 0.7762 (tt0) cc_final: 0.7307 (pm20) REVERT: A 51 MET cc_start: 0.7522 (OUTLIER) cc_final: 0.7295 (mmm) REVERT: A 286 MET cc_start: 0.6097 (mmp) cc_final: 0.4278 (ttp) REVERT: A 299 THR cc_start: 0.8520 (OUTLIER) cc_final: 0.8255 (m) REVERT: A 316 MET cc_start: 0.7579 (mmt) cc_final: 0.7333 (mmt) REVERT: A 332 LEU cc_start: 0.8443 (tt) cc_final: 0.8143 (tp) REVERT: A 410 ASP cc_start: 0.8188 (m-30) cc_final: 0.7911 (m-30) outliers start: 13 outliers final: 8 residues processed: 66 average time/residue: 0.0795 time to fit residues: 7.3211 Evaluate side-chains 67 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 57 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 427 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 23 optimal weight: 3.9990 chunk 32 optimal weight: 0.0980 chunk 9 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 4 optimal weight: 0.4980 chunk 8 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 31 optimal weight: 0.0370 chunk 3 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 overall best weight: 0.3658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.3489 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= 0.193 Angle : 0.680 9.445 4082 Z= 0.323 Chirality : 0.040 0.120 497 Planarity : 0.005 0.037 501 Dihedral : 5.209 46.353 415 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.94 % Allowed : 19.28 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.46), residues: 380 helix: 1.34 (0.30), residues: 317 sheet: None (None), residues: 0 loop : -2.44 (0.85), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 357 HIS 0.001 0.000 HIS A 283 PHE 0.015 0.001 PHE A 169 TYR 0.012 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 64 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 55 time to evaluate : 0.311 Fit side-chains REVERT: A 21 GLU cc_start: 0.7805 (tt0) cc_final: 0.7344 (pm20) REVERT: A 286 MET cc_start: 0.6029 (mmp) cc_final: 0.4474 (ttt) REVERT: A 299 THR cc_start: 0.8517 (OUTLIER) cc_final: 0.8256 (m) REVERT: A 316 MET cc_start: 0.7564 (mmt) cc_final: 0.7327 (mmt) REVERT: A 332 LEU cc_start: 0.8447 (tt) cc_final: 0.8137 (tp) REVERT: A 410 ASP cc_start: 0.8180 (m-30) cc_final: 0.7905 (m-30) outliers start: 9 outliers final: 6 residues processed: 61 average time/residue: 0.0784 time to fit residues: 6.7345 Evaluate side-chains 61 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 54 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 427 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 26 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 23 optimal weight: 7.9990 chunk 14 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 ASN ** 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 = 0.4055 r_free = 0.4055 target = 0.177302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.162083 restraints weight = 4646.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.165924 restraints weight = 2513.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.168470 restraints weight = 1557.606| |-----------------------------------------------------------------------------| r_work (final): 0.3962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 2989 Z= 0.244 Angle : 0.721 9.523 4082 Z= 0.341 Chirality : 0.042 0.138 497 Planarity : 0.005 0.032 501 Dihedral : 5.326 45.418 415 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.94 % Allowed : 19.28 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.45), residues: 380 helix: 1.27 (0.30), residues: 318 sheet: None (None), residues: 0 loop : -2.45 (0.85), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 357 HIS 0.002 0.001 HIS A 283 PHE 0.014 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: 1051.66 seconds wall clock time: 21 minutes 5.33 seconds (1265.33 seconds total)