Starting phenix.real_space_refine on Mon Feb 10 23:55:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c03_16354/02_2025/8c03_16354.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c03_16354/02_2025/8c03_16354.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8c03_16354/02_2025/8c03_16354.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c03_16354/02_2025/8c03_16354.map" model { file = "/net/cci-nas-00/data/ceres_data/8c03_16354/02_2025/8c03_16354.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c03_16354/02_2025/8c03_16354.cif" } resolution = 3.89 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= 0.028 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: 5 Type Number sf(0) Gaussians S 26 5.16 5 C 2187 2.51 5 N 542 2.21 5 O 574 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3330 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3300 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 9, 'TRANS': 419} Chain breaks: 2 Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'SZU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.73, per 1000 atoms: 0.82 Number of scatterers: 3330 At special positions: 0 Unit cell: (78.12, 67.704, 84.63, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 26 16.00 F 1 9.00 O 574 8.00 N 542 7.00 C 2187 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: 0.89 Conformation dependent library (CDL) restraints added in 400.3 milliseconds 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 788 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 0 sheets defined 92.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 23 through 54 removed outlier: 3.767A pdb=" N GLY A 38 " --> pdb=" O LEU A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 86 removed outlier: 3.634A pdb=" N GLY A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER A 71 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP A 84 " --> pdb=" O GLY A 80 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 116 removed outlier: 3.782A pdb=" N ALA A 92 " --> pdb=" O ARG A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 121 removed outlier: 3.723A pdb=" N LEU A 121 " --> pdb=" O LYS A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 156 removed outlier: 3.826A pdb=" N LEU A 129 " --> pdb=" O HIS A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 164 Processing helix chain 'A' and resid 166 through 199 Proline residue: A 189 - end of helix Processing helix chain 'A' and resid 200 through 230 removed outlier: 3.742A pdb=" N GLY A 206 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE A 208 " --> pdb=" O GLY A 204 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER A 209 " --> pdb=" O CYS A 205 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR A 230 " --> pdb=" O VAL A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 234 Processing helix chain 'A' and resid 288 through 305 Processing helix chain 'A' and resid 307 through 319 Processing helix chain 'A' and resid 325 through 336 Processing helix chain 'A' and resid 338 through 367 Processing helix chain 'A' and resid 369 through 393 Processing helix chain 'A' and resid 451 through 483 Processing helix chain 'A' and resid 485 through 487 No H-bonds generated for 'chain 'A' and resid 485 through 487' Processing helix chain 'A' and resid 488 through 514 removed outlier: 3.815A pdb=" N ASN A 493 " --> pdb=" O ARG A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 546 removed outlier: 4.118A pdb=" N LEU A 523 " --> pdb=" O ALA A 519 " (cutoff:3.500A) 308 hydrogen bonds defined for protein. 921 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: 1.07 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1028 1.34 - 1.46: 824 1.46 - 1.58: 1505 1.58 - 1.70: 0 1.70 - 1.82: 44 Bond restraints: 3401 Sorted by residual: bond pdb=" C1 SZU A 601 " pdb=" C8 SZU A 601 " ideal model delta sigma weight residual 1.476 1.325 0.151 2.00e-02 2.50e+03 5.66e+01 bond pdb=" C2 SZU A 601 " pdb=" C3 SZU A 601 " ideal model delta sigma weight residual 1.517 1.377 0.140 2.00e-02 2.50e+03 4.92e+01 bond pdb=" C16 SZU A 601 " pdb=" C21 SZU A 601 " ideal model delta sigma weight residual 1.413 1.335 0.078 2.00e-02 2.50e+03 1.51e+01 bond pdb=" C8 SZU A 601 " pdb=" N6 SZU A 601 " ideal model delta sigma weight residual 1.396 1.329 0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" C20 SZU A 601 " pdb=" C21 SZU A 601 " ideal model delta sigma weight residual 1.395 1.328 0.067 2.00e-02 2.50e+03 1.11e+01 ... (remaining 3396 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 4565 2.51 - 5.03: 58 5.03 - 7.54: 2 7.54 - 10.06: 1 10.06 - 12.57: 1 Bond angle restraints: 4627 Sorted by residual: angle pdb=" C3 SZU A 601 " pdb=" C2 SZU A 601 " pdb=" N1 SZU A 601 " ideal model delta sigma weight residual 113.72 101.15 12.57 3.00e+00 1.11e-01 1.76e+01 angle pdb=" N GLN A 496 " pdb=" CA GLN A 496 " pdb=" C GLN A 496 " ideal model delta sigma weight residual 111.36 106.91 4.45 1.09e+00 8.42e-01 1.67e+01 angle pdb=" N LEU A 59 " pdb=" CA LEU A 59 " pdb=" C LEU A 59 " ideal model delta sigma weight residual 111.11 106.50 4.61 1.20e+00 6.94e-01 1.48e+01 angle pdb=" CA THR A 334 " pdb=" C THR A 334 " pdb=" O THR A 334 " ideal model delta sigma weight residual 120.90 117.00 3.90 1.03e+00 9.43e-01 1.43e+01 angle pdb=" N PHE A 324 " pdb=" CA PHE A 324 " pdb=" C PHE A 324 " ideal model delta sigma weight residual 111.71 106.79 4.92 1.34e+00 5.57e-01 1.35e+01 ... (remaining 4622 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.30: 1769 14.30 - 28.61: 130 28.61 - 42.91: 44 42.91 - 57.21: 17 57.21 - 71.52: 6 Dihedral angle restraints: 1966 sinusoidal: 737 harmonic: 1229 Sorted by residual: dihedral pdb=" N GLU A 518 " pdb=" CA GLU A 518 " pdb=" CB GLU A 518 " pdb=" CG GLU A 518 " ideal model delta sinusoidal sigma weight residual -60.00 -119.88 59.88 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA ILE A 186 " pdb=" CB ILE A 186 " pdb=" CG1 ILE A 186 " pdb=" CD1 ILE A 186 " ideal model delta sinusoidal sigma weight residual 180.00 123.89 56.11 3 1.50e+01 4.44e-03 9.38e+00 dihedral pdb=" N ILE A 78 " pdb=" CA ILE A 78 " pdb=" CB ILE A 78 " pdb=" CG1 ILE A 78 " ideal model delta sinusoidal sigma weight residual -60.00 -114.35 54.35 3 1.50e+01 4.44e-03 9.28e+00 ... (remaining 1963 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 473 0.052 - 0.104: 74 0.104 - 0.156: 9 0.156 - 0.208: 3 0.208 - 0.260: 1 Chirality restraints: 560 Sorted by residual: chirality pdb=" CA LEU A 59 " pdb=" N LEU A 59 " pdb=" C LEU A 59 " pdb=" CB LEU A 59 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA TYR A 333 " pdb=" N TYR A 333 " pdb=" C TYR A 333 " pdb=" CB TYR A 333 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.91e-01 chirality pdb=" CA PHE A 324 " pdb=" N PHE A 324 " pdb=" C PHE A 324 " pdb=" CB PHE A 324 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.98e-01 ... (remaining 557 not shown) Planarity restraints: 556 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 53 " -0.008 2.00e-02 2.50e+03 1.69e-02 2.86e+00 pdb=" C LEU A 53 " 0.029 2.00e-02 2.50e+03 pdb=" O LEU A 53 " -0.011 2.00e-02 2.50e+03 pdb=" N TYR A 54 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 324 " 0.008 2.00e-02 2.50e+03 1.66e-02 2.75e+00 pdb=" C PHE A 324 " -0.029 2.00e-02 2.50e+03 pdb=" O PHE A 324 " 0.011 2.00e-02 2.50e+03 pdb=" N ASP A 325 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 SZU A 601 " -0.004 2.00e-02 2.50e+03 1.42e-02 2.53e+00 pdb=" C2 SZU A 601 " 0.016 2.00e-02 2.50e+03 pdb=" C8 SZU A 601 " 0.013 2.00e-02 2.50e+03 pdb=" N1 SZU A 601 " -0.023 2.00e-02 2.50e+03 pdb=" O1 SZU A 601 " -0.002 2.00e-02 2.50e+03 ... (remaining 553 not shown) Histogram of nonbonded interaction distances: 1.23 - 1.97: 1 1.97 - 2.70: 81 2.70 - 3.43: 5414 3.43 - 4.17: 7309 4.17 - 4.90: 13846 Nonbonded interactions: 26651 Sorted by model distance: nonbonded pdb=" OH TYR A 302 " pdb=" OE1 GLN A 496 " model vdw 1.232 3.040 nonbonded pdb=" CD1 LEU A 469 " pdb=" F1 SZU A 601 " model vdw 2.141 3.410 nonbonded pdb=" O TYR A 20 " pdb=" OG SER A 23 " model vdw 2.205 3.040 nonbonded pdb=" O ASN A 86 " pdb=" NZ LYS A 236 " model vdw 2.209 3.120 nonbonded pdb=" O LEU A 369 " pdb=" OG1 THR A 372 " model vdw 2.260 3.040 ... (remaining 26646 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: 0.390 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.620 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 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 : 0.006 0.151 3401 Z= 0.430 Angle : 0.670 12.575 4627 Z= 0.403 Chirality : 0.040 0.260 560 Planarity : 0.003 0.017 556 Dihedral : 13.116 71.516 1178 Min Nonbonded Distance : 1.232 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.06 % Allowed : 8.08 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.75 (0.41), residues: 423 helix: 2.29 (0.26), residues: 357 sheet: None (None), residues: 0 loop : -0.88 (0.85), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 470 HIS 0.003 0.001 HIS A 32 PHE 0.008 0.001 PHE A 508 TYR 0.006 0.001 TYR A 220 ARG 0.001 0.000 ARG A 88 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 132 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: A 90 LYS cc_start: 0.7974 (tptt) cc_final: 0.7485 (tppt) REVERT: A 100 ASN cc_start: 0.7632 (m-40) cc_final: 0.6460 (m-40) REVERT: A 216 MET cc_start: 0.8280 (tpt) cc_final: 0.7925 (tpp) REVERT: A 319 MET cc_start: 0.7296 (ttt) cc_final: 0.6959 (tmm) outliers start: 11 outliers final: 3 residues processed: 138 average time/residue: 0.1344 time to fit residues: 22.7574 Evaluate side-chains 104 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 101 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 174 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 10 optimal weight: 0.1980 chunk 21 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 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 43 HIS A 125 HIS A 194 GLN ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.177418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.142673 restraints weight = 4819.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.147238 restraints weight = 3040.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.150348 restraints weight = 2315.377| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3401 Z= 0.227 Angle : 0.580 6.753 4627 Z= 0.300 Chirality : 0.039 0.135 560 Planarity : 0.004 0.028 556 Dihedral : 7.431 75.543 476 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.62 % Allowed : 18.11 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.07 (0.40), residues: 423 helix: 2.31 (0.25), residues: 371 sheet: None (None), residues: 0 loop : -0.08 (1.04), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 299 HIS 0.003 0.001 HIS A 32 PHE 0.026 0.002 PHE A 308 TYR 0.013 0.002 TYR A 29 ARG 0.008 0.001 ARG A 293 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.338 Fit side-chains REVERT: A 90 LYS cc_start: 0.8024 (tptt) cc_final: 0.7469 (tppt) REVERT: A 166 ASP cc_start: 0.8219 (t0) cc_final: 0.7825 (t0) REVERT: A 173 MET cc_start: 0.7646 (ttm) cc_final: 0.7309 (ttm) REVERT: A 319 MET cc_start: 0.7576 (ttt) cc_final: 0.7152 (tmm) REVERT: A 366 LYS cc_start: 0.8336 (tptt) cc_final: 0.7850 (mmmt) REVERT: A 469 LEU cc_start: 0.8933 (tp) cc_final: 0.8670 (tp) outliers start: 13 outliers final: 4 residues processed: 113 average time/residue: 0.1356 time to fit residues: 18.9804 Evaluate side-chains 105 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 101 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 221 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 17 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 36 optimal weight: 0.0980 chunk 38 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.175073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.139849 restraints weight = 4658.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.144505 restraints weight = 2951.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.147637 restraints weight = 2235.844| |-----------------------------------------------------------------------------| r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3401 Z= 0.213 Angle : 0.583 6.754 4627 Z= 0.301 Chirality : 0.039 0.158 560 Planarity : 0.003 0.028 556 Dihedral : 6.932 73.884 470 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.79 % Allowed : 20.89 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.93 (0.40), residues: 423 helix: 2.24 (0.25), residues: 371 sheet: None (None), residues: 0 loop : -0.26 (1.04), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 470 HIS 0.004 0.001 HIS A 43 PHE 0.023 0.002 PHE A 308 TYR 0.020 0.002 TYR A 29 ARG 0.002 0.000 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 104 time to evaluate : 0.359 Fit side-chains REVERT: A 57 SER cc_start: 0.8312 (m) cc_final: 0.7940 (p) REVERT: A 166 ASP cc_start: 0.8152 (t0) cc_final: 0.7676 (t0) REVERT: A 319 MET cc_start: 0.7715 (ttt) cc_final: 0.7235 (tmm) REVERT: A 366 LYS cc_start: 0.8400 (tptt) cc_final: 0.7931 (mmmt) REVERT: A 457 LEU cc_start: 0.7849 (tp) cc_final: 0.7632 (tp) REVERT: A 543 GLN cc_start: 0.7979 (mm110) cc_final: 0.7622 (mm-40) outliers start: 10 outliers final: 7 residues processed: 109 average time/residue: 0.1186 time to fit residues: 16.3825 Evaluate side-chains 105 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 98 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 222 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 5 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 27 optimal weight: 7.9990 chunk 20 optimal weight: 0.5980 chunk 13 optimal weight: 0.0980 chunk 35 optimal weight: 0.9980 chunk 39 optimal weight: 0.0170 chunk 10 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.176040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.141287 restraints weight = 4761.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.146068 restraints weight = 3007.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.149199 restraints weight = 2274.409| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3401 Z= 0.197 Angle : 0.576 6.208 4627 Z= 0.296 Chirality : 0.039 0.149 560 Planarity : 0.003 0.033 556 Dihedral : 6.823 74.017 470 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.62 % Allowed : 21.45 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.97 (0.40), residues: 423 helix: 2.27 (0.25), residues: 371 sheet: None (None), residues: 0 loop : -0.33 (1.01), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 42 HIS 0.007 0.002 HIS A 535 PHE 0.037 0.002 PHE A 308 TYR 0.026 0.002 TYR A 29 ARG 0.002 0.000 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.372 Fit side-chains REVERT: A 166 ASP cc_start: 0.8108 (t0) cc_final: 0.7638 (t0) REVERT: A 319 MET cc_start: 0.7634 (ttt) cc_final: 0.7195 (tmm) REVERT: A 366 LYS cc_start: 0.8392 (tptt) cc_final: 0.7955 (mmmt) REVERT: A 543 GLN cc_start: 0.8085 (mm110) cc_final: 0.7705 (mm-40) outliers start: 13 outliers final: 9 residues processed: 107 average time/residue: 0.1269 time to fit residues: 17.0449 Evaluate side-chains 104 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 458 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 37 optimal weight: 0.2980 chunk 30 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 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 43 HIS A 125 HIS A 212 ASN ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.176394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.141495 restraints weight = 4846.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.146136 restraints weight = 3066.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.149203 restraints weight = 2325.848| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3401 Z= 0.241 Angle : 0.621 7.449 4627 Z= 0.313 Chirality : 0.039 0.182 560 Planarity : 0.003 0.033 556 Dihedral : 6.736 72.931 470 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 5.85 % Allowed : 22.01 % Favored : 72.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.86 (0.40), residues: 423 helix: 2.19 (0.25), residues: 373 sheet: None (None), residues: 0 loop : -0.37 (1.02), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 470 HIS 0.004 0.001 HIS A 535 PHE 0.031 0.002 PHE A 308 TYR 0.020 0.002 TYR A 29 ARG 0.002 0.000 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.351 Fit side-chains REVERT: A 166 ASP cc_start: 0.8061 (t0) cc_final: 0.7577 (t0) REVERT: A 319 MET cc_start: 0.7695 (ttt) cc_final: 0.7187 (tmm) REVERT: A 366 LYS cc_start: 0.8430 (tptt) cc_final: 0.8076 (tptt) REVERT: A 504 ASP cc_start: 0.7994 (t70) cc_final: 0.7623 (t0) REVERT: A 543 GLN cc_start: 0.8091 (mm110) cc_final: 0.7673 (mm-40) outliers start: 21 outliers final: 16 residues processed: 107 average time/residue: 0.1226 time to fit residues: 16.6428 Evaluate side-chains 110 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 174 ASN Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 212 ASN Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 475 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 34 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 6 optimal weight: 0.4980 chunk 31 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS A 212 ASN ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.176392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.141353 restraints weight = 4851.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.145834 restraints weight = 3071.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.148898 restraints weight = 2345.092| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3401 Z= 0.242 Angle : 0.628 8.158 4627 Z= 0.316 Chirality : 0.040 0.184 560 Planarity : 0.003 0.033 556 Dihedral : 6.640 71.586 470 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 5.29 % Allowed : 23.12 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.94 (0.40), residues: 423 helix: 2.23 (0.26), residues: 373 sheet: None (None), residues: 0 loop : -0.24 (1.02), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 470 HIS 0.004 0.001 HIS A 535 PHE 0.027 0.002 PHE A 308 TYR 0.022 0.002 TYR A 29 ARG 0.002 0.000 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.384 Fit side-chains REVERT: A 166 ASP cc_start: 0.8121 (t0) cc_final: 0.7645 (t0) REVERT: A 319 MET cc_start: 0.7785 (ttt) cc_final: 0.7264 (tmm) REVERT: A 366 LYS cc_start: 0.8414 (tptt) cc_final: 0.8205 (tptt) REVERT: A 392 PHE cc_start: 0.8318 (t80) cc_final: 0.8004 (t80) REVERT: A 504 ASP cc_start: 0.8014 (t70) cc_final: 0.7641 (t0) outliers start: 19 outliers final: 17 residues processed: 104 average time/residue: 0.1272 time to fit residues: 16.7655 Evaluate side-chains 109 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 174 ASN Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 476 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 12 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 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 43 HIS ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.174934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.139740 restraints weight = 4795.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.144265 restraints weight = 3042.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.147258 restraints weight = 2321.865| |-----------------------------------------------------------------------------| r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3401 Z= 0.251 Angle : 0.624 8.988 4627 Z= 0.316 Chirality : 0.040 0.187 560 Planarity : 0.003 0.032 556 Dihedral : 6.562 70.043 470 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 5.57 % Allowed : 23.40 % Favored : 71.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.95 (0.40), residues: 423 helix: 2.24 (0.26), residues: 373 sheet: None (None), residues: 0 loop : -0.23 (1.02), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 82 HIS 0.004 0.001 HIS A 32 PHE 0.026 0.002 PHE A 308 TYR 0.020 0.002 TYR A 29 ARG 0.001 0.000 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.374 Fit side-chains REVERT: A 145 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8390 (mp) REVERT: A 202 VAL cc_start: 0.8573 (m) cc_final: 0.8333 (p) REVERT: A 319 MET cc_start: 0.7798 (ttt) cc_final: 0.7279 (tmm) REVERT: A 366 LYS cc_start: 0.8514 (tptt) cc_final: 0.8285 (tptt) REVERT: A 392 PHE cc_start: 0.8314 (t80) cc_final: 0.7997 (t80) REVERT: A 504 ASP cc_start: 0.8036 (t70) cc_final: 0.7669 (t0) REVERT: A 543 GLN cc_start: 0.8046 (mm110) cc_final: 0.7688 (mm-40) outliers start: 20 outliers final: 17 residues processed: 110 average time/residue: 0.1256 time to fit residues: 17.6602 Evaluate side-chains 111 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 174 ASN Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 476 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 0.0770 chunk 34 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 40 optimal weight: 0.0980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.176806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.142161 restraints weight = 4697.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.146633 restraints weight = 3002.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.149667 restraints weight = 2294.763| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3401 Z= 0.208 Angle : 0.621 9.735 4627 Z= 0.313 Chirality : 0.040 0.187 560 Planarity : 0.003 0.032 556 Dihedral : 6.482 69.342 470 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 4.46 % Allowed : 25.63 % Favored : 69.92 % 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: 3.06 (0.40), residues: 423 helix: 2.33 (0.26), residues: 373 sheet: None (None), residues: 0 loop : -0.36 (0.99), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 82 HIS 0.003 0.001 HIS A 535 PHE 0.027 0.002 PHE A 308 TYR 0.022 0.001 TYR A 29 ARG 0.001 0.000 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.376 Fit side-chains REVERT: A 166 ASP cc_start: 0.8148 (t0) cc_final: 0.7791 (t0) REVERT: A 202 VAL cc_start: 0.8494 (m) cc_final: 0.8253 (p) REVERT: A 319 MET cc_start: 0.7796 (ttt) cc_final: 0.7294 (tmm) REVERT: A 324 PHE cc_start: 0.8413 (m-80) cc_final: 0.8160 (m-80) REVERT: A 392 PHE cc_start: 0.8175 (t80) cc_final: 0.7892 (t80) REVERT: A 504 ASP cc_start: 0.7989 (t70) cc_final: 0.7620 (t0) outliers start: 16 outliers final: 13 residues processed: 105 average time/residue: 0.1189 time to fit residues: 16.0122 Evaluate side-chains 107 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 475 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.175832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.140592 restraints weight = 4759.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.145077 restraints weight = 3075.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.148062 restraints weight = 2359.697| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3401 Z= 0.264 Angle : 0.670 10.414 4627 Z= 0.337 Chirality : 0.041 0.190 560 Planarity : 0.004 0.032 556 Dihedral : 6.467 67.870 470 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 4.74 % Allowed : 25.35 % Favored : 69.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.94 (0.40), residues: 423 helix: 2.25 (0.26), residues: 373 sheet: None (None), residues: 0 loop : -0.38 (0.99), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 82 HIS 0.004 0.001 HIS A 32 PHE 0.025 0.002 PHE A 308 TYR 0.023 0.002 TYR A 29 ARG 0.002 0.000 ARG A 365 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.304 Fit side-chains REVERT: A 177 ILE cc_start: 0.7240 (OUTLIER) cc_final: 0.6967 (mt) REVERT: A 202 VAL cc_start: 0.8448 (m) cc_final: 0.8246 (p) REVERT: A 216 MET cc_start: 0.8594 (tpt) cc_final: 0.8360 (tpt) REVERT: A 319 MET cc_start: 0.7672 (ttt) cc_final: 0.7230 (tmm) REVERT: A 324 PHE cc_start: 0.8450 (m-80) cc_final: 0.8080 (m-80) REVERT: A 366 LYS cc_start: 0.8396 (tptt) cc_final: 0.8128 (mmmt) REVERT: A 392 PHE cc_start: 0.8206 (t80) cc_final: 0.7929 (t80) REVERT: A 504 ASP cc_start: 0.8037 (t70) cc_final: 0.7652 (t0) outliers start: 17 outliers final: 15 residues processed: 103 average time/residue: 0.1261 time to fit residues: 16.5764 Evaluate side-chains 106 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 174 ASN Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 475 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 38 optimal weight: 0.4980 chunk 30 optimal weight: 0.0770 chunk 2 optimal weight: 0.4980 chunk 29 optimal weight: 0.6980 chunk 14 optimal weight: 0.4980 chunk 40 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.178360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.143340 restraints weight = 4755.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.147985 restraints weight = 3036.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.151015 restraints weight = 2314.012| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3401 Z= 0.224 Angle : 0.667 10.957 4627 Z= 0.332 Chirality : 0.041 0.190 560 Planarity : 0.004 0.033 556 Dihedral : 6.411 67.191 470 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 4.18 % Allowed : 26.74 % Favored : 69.08 % 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: 2.93 (0.40), residues: 423 helix: 2.23 (0.26), residues: 374 sheet: None (None), residues: 0 loop : -0.37 (0.99), residues: 49 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 470 HIS 0.005 0.001 HIS A 43 PHE 0.029 0.002 PHE A 308 TYR 0.011 0.001 TYR A 29 ARG 0.001 0.000 ARG A 40 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.369 Fit side-chains REVERT: A 42 TRP cc_start: 0.8196 (t60) cc_final: 0.7983 (t60) REVERT: A 202 VAL cc_start: 0.8340 (m) cc_final: 0.8125 (p) REVERT: A 319 MET cc_start: 0.7540 (ttt) cc_final: 0.7051 (tmm) REVERT: A 392 PHE cc_start: 0.8197 (t80) cc_final: 0.7919 (t80) REVERT: A 504 ASP cc_start: 0.7991 (t70) cc_final: 0.7617 (t0) outliers start: 15 outliers final: 15 residues processed: 100 average time/residue: 0.1203 time to fit residues: 15.1490 Evaluate side-chains 104 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 174 ASN Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 475 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 6 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 9 optimal weight: 0.3980 chunk 37 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.177726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.142940 restraints weight = 4786.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.147459 restraints weight = 3084.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.150165 restraints weight = 2358.000| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3401 Z= 0.243 Angle : 0.666 11.024 4627 Z= 0.332 Chirality : 0.041 0.187 560 Planarity : 0.004 0.032 556 Dihedral : 6.427 65.908 470 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 4.46 % Allowed : 27.02 % Favored : 68.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.85 (0.40), residues: 423 helix: 2.19 (0.26), residues: 373 sheet: None (None), residues: 0 loop : -0.44 (0.97), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 82 HIS 0.003 0.001 HIS A 32 PHE 0.027 0.002 PHE A 308 TYR 0.009 0.001 TYR A 29 ARG 0.001 0.000 ARG A 40 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1327.24 seconds wall clock time: 24 minutes 47.15 seconds (1487.15 seconds total)