Starting phenix.real_space_refine on Fri Aug 22 13:14:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z7r_39825/08_2025/8z7r_39825.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z7r_39825/08_2025/8z7r_39825.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z7r_39825/08_2025/8z7r_39825.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z7r_39825/08_2025/8z7r_39825.map" model { file = "/net/cci-nas-00/data/ceres_data/8z7r_39825/08_2025/8z7r_39825.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z7r_39825/08_2025/8z7r_39825.cif" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= -0.000 sd= 0.102 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 15 5.16 5 C 2091 2.51 5 N 463 2.21 5 O 529 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3098 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3098 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 13, 'TRANS': 373} Chain breaks: 1 Time building chain proxies: 0.87, per 1000 atoms: 0.28 Number of scatterers: 3098 At special positions: 0 Unit cell: (64, 68, 67, 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 15 16.00 O 529 8.00 N 463 7.00 C 2091 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: 0.16 Conformation dependent library (CDL) restraints added in 110.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 734 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 0 sheets defined 86.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 12 through 28 Processing helix chain 'A' and resid 34 through 39 Processing helix chain 'A' and resid 47 through 54 removed outlier: 3.535A pdb=" N ILE A 51 " --> pdb=" O THR A 47 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR A 52 " --> pdb=" O SER A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 74 removed outlier: 3.756A pdb=" N TRP A 59 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR A 60 " --> pdb=" O PHE A 56 " (cutoff:3.500A) Proline residue: A 69 - end of helix Processing helix chain 'A' and resid 79 through 99 removed outlier: 3.636A pdb=" N ILE A 83 " --> pdb=" O TYR A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 131 removed outlier: 3.923A pdb=" N ALA A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ILE A 127 " --> pdb=" O TYR A 123 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N TYR A 128 " --> pdb=" O TYR A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 134 No H-bonds generated for 'chain 'A' and resid 132 through 134' Processing helix chain 'A' and resid 135 through 164 Processing helix chain 'A' and resid 168 through 189 removed outlier: 3.572A pdb=" N PHE A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 273 removed outlier: 3.638A pdb=" N PHE A 266 " --> pdb=" O PHE A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 306 removed outlier: 4.126A pdb=" N ALA A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN A 294 " --> pdb=" O ALA A 290 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLN A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ILE A 301 " --> pdb=" O ASN A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 337 Processing helix chain 'A' and resid 340 through 366 removed outlier: 5.482A pdb=" N GLU A 346 " --> pdb=" O ASP A 342 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LEU A 347 " --> pdb=" O LEU A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 397 Processing helix chain 'A' and resid 402 through 426 Processing helix chain 'A' and resid 434 through 460 removed outlier: 3.504A pdb=" N SER A 457 " --> pdb=" O PHE A 453 " (cutoff:3.500A) 251 hydrogen bonds defined for protein. 753 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: 0.38 Time building geometry restraints manager: 0.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 868 1.34 - 1.46: 715 1.46 - 1.58: 1582 1.58 - 1.70: 0 1.70 - 1.82: 26 Bond restraints: 3191 Sorted by residual: bond pdb=" N ILE A 314 " pdb=" CA ILE A 314 " ideal model delta sigma weight residual 1.462 1.495 -0.033 1.14e-02 7.69e+03 8.43e+00 bond pdb=" N ASN A 397 " pdb=" CA ASN A 397 " ideal model delta sigma weight residual 1.455 1.490 -0.035 1.25e-02 6.40e+03 7.71e+00 bond pdb=" N SER A 312 " pdb=" CA SER A 312 " ideal model delta sigma weight residual 1.453 1.488 -0.035 1.27e-02 6.20e+03 7.43e+00 bond pdb=" N GLU A 320 " pdb=" CA GLU A 320 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.23e-02 6.61e+03 6.37e+00 bond pdb=" N ASN A 316 " pdb=" CA ASN A 316 " ideal model delta sigma weight residual 1.463 1.489 -0.026 1.08e-02 8.57e+03 6.00e+00 ... (remaining 3186 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 4073 1.41 - 2.81: 231 2.81 - 4.22: 39 4.22 - 5.62: 16 5.62 - 7.03: 3 Bond angle restraints: 4362 Sorted by residual: angle pdb=" CA TYR A 336 " pdb=" C TYR A 336 " pdb=" N VAL A 337 " ideal model delta sigma weight residual 118.14 123.56 -5.42 1.56e+00 4.11e-01 1.21e+01 angle pdb=" N ILE A 460 " pdb=" CA ILE A 460 " pdb=" C ILE A 460 " ideal model delta sigma weight residual 111.77 108.51 3.26 1.04e+00 9.25e-01 9.83e+00 angle pdb=" CA ASP A 311 " pdb=" C ASP A 311 " pdb=" O ASP A 311 " ideal model delta sigma weight residual 122.45 118.40 4.05 1.30e+00 5.92e-01 9.70e+00 angle pdb=" N GLN A 86 " pdb=" CA GLN A 86 " pdb=" C GLN A 86 " ideal model delta sigma weight residual 111.36 108.02 3.34 1.09e+00 8.42e-01 9.39e+00 angle pdb=" N VAL A 435 " pdb=" CA VAL A 435 " pdb=" C VAL A 435 " ideal model delta sigma weight residual 110.42 113.36 -2.94 9.60e-01 1.09e+00 9.35e+00 ... (remaining 4357 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.34: 1527 16.34 - 32.68: 213 32.68 - 49.02: 51 49.02 - 65.36: 13 65.36 - 81.70: 4 Dihedral angle restraints: 1808 sinusoidal: 659 harmonic: 1149 Sorted by residual: dihedral pdb=" CA ARG A 78 " pdb=" C ARG A 78 " pdb=" N TYR A 79 " pdb=" CA TYR A 79 " ideal model delta harmonic sigma weight residual 180.00 159.79 20.21 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA PRO A 434 " pdb=" C PRO A 434 " pdb=" N VAL A 435 " pdb=" CA VAL A 435 " ideal model delta harmonic sigma weight residual -180.00 -162.80 -17.20 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA VAL A 425 " pdb=" C VAL A 425 " pdb=" N VAL A 426 " pdb=" CA VAL A 426 " ideal model delta harmonic sigma weight residual -180.00 -163.90 -16.10 0 5.00e+00 4.00e-02 1.04e+01 ... (remaining 1805 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 342 0.039 - 0.079: 124 0.079 - 0.118: 33 0.118 - 0.158: 4 0.158 - 0.197: 2 Chirality restraints: 505 Sorted by residual: chirality pdb=" CA GLN A 310 " pdb=" N GLN A 310 " pdb=" C GLN A 310 " pdb=" CB GLN A 310 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.71e-01 chirality pdb=" CA ILE A 314 " pdb=" N ILE A 314 " pdb=" C ILE A 314 " pdb=" CB ILE A 314 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.47e-01 chirality pdb=" CA VAL A 400 " pdb=" N VAL A 400 " pdb=" C VAL A 400 " pdb=" CB VAL A 400 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.90e-01 ... (remaining 502 not shown) Planarity restraints: 523 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 319 " 0.011 2.00e-02 2.50e+03 2.20e-02 4.82e+00 pdb=" C VAL A 319 " -0.038 2.00e-02 2.50e+03 pdb=" O VAL A 319 " 0.014 2.00e-02 2.50e+03 pdb=" N GLU A 320 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 144 " 0.011 2.00e-02 2.50e+03 2.15e-02 4.64e+00 pdb=" C ARG A 144 " -0.037 2.00e-02 2.50e+03 pdb=" O ARG A 144 " 0.014 2.00e-02 2.50e+03 pdb=" N SER A 145 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 154 " 0.011 2.00e-02 2.50e+03 2.12e-02 4.49e+00 pdb=" C GLY A 154 " -0.037 2.00e-02 2.50e+03 pdb=" O GLY A 154 " 0.014 2.00e-02 2.50e+03 pdb=" N SER A 155 " 0.012 2.00e-02 2.50e+03 ... (remaining 520 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 474 2.75 - 3.29: 3331 3.29 - 3.83: 5497 3.83 - 4.36: 6441 4.36 - 4.90: 10967 Nonbonded interactions: 26710 Sorted by model distance: nonbonded pdb=" OH TYR A 128 " pdb=" OG SER A 140 " model vdw 2.214 3.040 nonbonded pdb=" OD1 ASP A 75 " pdb=" OH TYR A 79 " model vdw 2.295 3.040 nonbonded pdb=" O SER A 89 " pdb=" OG1 THR A 93 " model vdw 2.355 3.040 nonbonded pdb=" O PHE A 287 " pdb=" OH TYR A 445 " model vdw 2.357 3.040 nonbonded pdb=" OE1 GLU A 320 " pdb=" OH TYR A 376 " model vdw 2.368 3.040 ... (remaining 26705 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.980 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: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.110 Find NCS groups from input model: 0.000 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:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 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 : 0.005 0.042 3191 Z= 0.291 Angle : 0.773 7.031 4362 Z= 0.494 Chirality : 0.044 0.197 505 Planarity : 0.006 0.038 523 Dihedral : 16.633 81.698 1074 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.60 % Allowed : 22.52 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.42), residues: 383 helix: -0.14 (0.28), residues: 319 sheet: None (None), residues: 0 loop : 0.16 (0.90), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 138 TYR 0.019 0.002 TYR A 383 PHE 0.024 0.002 PHE A 71 TRP 0.012 0.002 TRP A 94 HIS 0.001 0.001 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00492 ( 3191) covalent geometry : angle 0.77301 ( 4362) hydrogen bonds : bond 0.20196 ( 251) hydrogen bonds : angle 7.87831 ( 753) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 48 time to evaluate : 0.065 Fit side-chains REVERT: A 270 LYS cc_start: 0.8005 (mtpt) cc_final: 0.6875 (mmmt) REVERT: A 315 TYR cc_start: 0.7492 (OUTLIER) cc_final: 0.6953 (t80) outliers start: 2 outliers final: 0 residues processed: 49 average time/residue: 0.0520 time to fit residues: 3.1147 Evaluate side-chains 48 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 24 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.0020 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 0.4980 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.151763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.125792 restraints weight = 3650.872| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.85 r_work: 0.3305 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3191 Z= 0.168 Angle : 0.646 8.596 4362 Z= 0.345 Chirality : 0.044 0.196 505 Planarity : 0.004 0.032 523 Dihedral : 5.211 53.347 425 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.30 % Allowed : 20.72 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.41), residues: 383 helix: 0.74 (0.27), residues: 315 sheet: None (None), residues: 0 loop : -0.53 (0.82), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 277 TYR 0.016 0.002 TYR A 280 PHE 0.021 0.001 PHE A 71 TRP 0.014 0.002 TRP A 94 HIS 0.002 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 3191) covalent geometry : angle 0.64586 ( 4362) hydrogen bonds : bond 0.06143 ( 251) hydrogen bonds : angle 5.05176 ( 753) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.110 Fit side-chains revert: symmetry clash REVERT: A 181 SER cc_start: 0.8467 (t) cc_final: 0.8190 (p) REVERT: A 270 LYS cc_start: 0.8042 (OUTLIER) cc_final: 0.7104 (tptt) REVERT: A 315 TYR cc_start: 0.7749 (OUTLIER) cc_final: 0.7226 (t80) outliers start: 11 outliers final: 7 residues processed: 59 average time/residue: 0.0362 time to fit residues: 2.8388 Evaluate side-chains 55 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 439 PHE Chi-restraints excluded: chain A residue 441 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 26 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 35 optimal weight: 0.0980 chunk 8 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.151222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.125048 restraints weight = 3689.781| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.87 r_work: 0.3225 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3191 Z= 0.158 Angle : 0.605 7.131 4362 Z= 0.322 Chirality : 0.043 0.192 505 Planarity : 0.004 0.032 523 Dihedral : 5.132 54.373 425 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.90 % Allowed : 19.52 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.41), residues: 383 helix: 1.03 (0.27), residues: 319 sheet: None (None), residues: 0 loop : -0.06 (0.85), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 138 TYR 0.019 0.002 TYR A 280 PHE 0.021 0.001 PHE A 71 TRP 0.012 0.002 TRP A 284 HIS 0.002 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 3191) covalent geometry : angle 0.60529 ( 4362) hydrogen bonds : bond 0.05573 ( 251) hydrogen bonds : angle 4.69255 ( 753) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.069 Fit side-chains revert: symmetry clash REVERT: A 164 LEU cc_start: 0.7726 (mt) cc_final: 0.7488 (mp) REVERT: A 181 SER cc_start: 0.8434 (t) cc_final: 0.8126 (p) REVERT: A 270 LYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7128 (tptp) REVERT: A 315 TYR cc_start: 0.7691 (OUTLIER) cc_final: 0.7179 (t80) REVERT: A 455 MET cc_start: 0.6691 (tmm) cc_final: 0.6438 (tmm) outliers start: 13 outliers final: 8 residues processed: 62 average time/residue: 0.0315 time to fit residues: 2.6385 Evaluate side-chains 56 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 439 PHE Chi-restraints excluded: chain A residue 441 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 27 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 18 optimal weight: 0.1980 chunk 28 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.148967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.122982 restraints weight = 3604.211| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.83 r_work: 0.3115 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3191 Z= 0.158 Angle : 0.593 6.775 4362 Z= 0.316 Chirality : 0.042 0.189 505 Planarity : 0.004 0.032 523 Dihedral : 5.103 55.008 425 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 5.71 % Allowed : 17.12 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.42), residues: 383 helix: 1.14 (0.27), residues: 325 sheet: None (None), residues: 0 loop : 0.33 (0.90), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 138 TYR 0.019 0.002 TYR A 280 PHE 0.020 0.001 PHE A 71 TRP 0.012 0.001 TRP A 284 HIS 0.003 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 3191) covalent geometry : angle 0.59325 ( 4362) hydrogen bonds : bond 0.05358 ( 251) hydrogen bonds : angle 4.54794 ( 753) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 49 time to evaluate : 0.065 Fit side-chains revert: symmetry clash REVERT: A 164 LEU cc_start: 0.7745 (mt) cc_final: 0.7534 (mp) REVERT: A 181 SER cc_start: 0.8202 (t) cc_final: 0.7842 (p) REVERT: A 270 LYS cc_start: 0.7807 (OUTLIER) cc_final: 0.6948 (tptp) REVERT: A 296 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8184 (mp) REVERT: A 315 TYR cc_start: 0.7329 (OUTLIER) cc_final: 0.6824 (t80) REVERT: A 322 ILE cc_start: 0.7307 (pt) cc_final: 0.6967 (mm) REVERT: A 365 TYR cc_start: 0.8114 (m-10) cc_final: 0.7781 (m-10) REVERT: A 427 ASP cc_start: 0.7969 (OUTLIER) cc_final: 0.7643 (m-30) REVERT: A 455 MET cc_start: 0.6469 (tmm) cc_final: 0.6205 (tmm) outliers start: 19 outliers final: 13 residues processed: 65 average time/residue: 0.0344 time to fit residues: 3.0307 Evaluate side-chains 63 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 46 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 439 PHE Chi-restraints excluded: chain A residue 441 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 33 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 9 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.150427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.124329 restraints weight = 3625.229| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.84 r_work: 0.3306 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3191 Z= 0.159 Angle : 0.589 6.215 4362 Z= 0.314 Chirality : 0.043 0.189 505 Planarity : 0.004 0.033 523 Dihedral : 5.102 55.722 425 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 5.41 % Allowed : 18.32 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.52 (0.41), residues: 383 helix: 1.18 (0.27), residues: 326 sheet: None (None), residues: 0 loop : 0.53 (0.91), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 138 TYR 0.022 0.002 TYR A 280 PHE 0.021 0.002 PHE A 71 TRP 0.013 0.001 TRP A 284 HIS 0.003 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 3191) covalent geometry : angle 0.58893 ( 4362) hydrogen bonds : bond 0.05266 ( 251) hydrogen bonds : angle 4.49863 ( 753) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 49 time to evaluate : 0.076 Fit side-chains revert: symmetry clash REVERT: A 181 SER cc_start: 0.8398 (t) cc_final: 0.8062 (p) REVERT: A 270 LYS cc_start: 0.8078 (mtpt) cc_final: 0.7252 (tptp) REVERT: A 296 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8299 (mp) REVERT: A 315 TYR cc_start: 0.7475 (OUTLIER) cc_final: 0.6981 (t80) REVERT: A 322 ILE cc_start: 0.7709 (pt) cc_final: 0.7375 (mm) REVERT: A 365 TYR cc_start: 0.8069 (m-10) cc_final: 0.7767 (m-10) REVERT: A 427 ASP cc_start: 0.8105 (OUTLIER) cc_final: 0.7776 (m-30) REVERT: A 455 MET cc_start: 0.6587 (tmm) cc_final: 0.6319 (tmm) outliers start: 18 outliers final: 14 residues processed: 64 average time/residue: 0.0329 time to fit residues: 2.8347 Evaluate side-chains 63 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 46 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 439 PHE Chi-restraints excluded: chain A residue 441 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 12 optimal weight: 0.4980 chunk 24 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 6 optimal weight: 0.3980 chunk 26 optimal weight: 3.9990 chunk 3 optimal weight: 0.0670 chunk 4 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.152243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.126548 restraints weight = 3590.128| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.83 r_work: 0.3324 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3191 Z= 0.144 Angle : 0.588 6.432 4362 Z= 0.308 Chirality : 0.042 0.182 505 Planarity : 0.004 0.034 523 Dihedral : 5.067 55.693 425 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 5.11 % Allowed : 20.12 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.68 (0.42), residues: 383 helix: 1.27 (0.27), residues: 326 sheet: None (None), residues: 0 loop : 0.66 (0.93), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 29 TYR 0.019 0.001 TYR A 280 PHE 0.020 0.001 PHE A 71 TRP 0.013 0.001 TRP A 284 HIS 0.003 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 3191) covalent geometry : angle 0.58759 ( 4362) hydrogen bonds : bond 0.05041 ( 251) hydrogen bonds : angle 4.40906 ( 753) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 48 time to evaluate : 0.066 Fit side-chains revert: symmetry clash REVERT: A 181 SER cc_start: 0.8377 (t) cc_final: 0.8031 (p) REVERT: A 270 LYS cc_start: 0.8090 (OUTLIER) cc_final: 0.7190 (tptp) REVERT: A 296 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8408 (mp) REVERT: A 306 LYS cc_start: 0.7755 (ttmm) cc_final: 0.7545 (mttm) REVERT: A 315 TYR cc_start: 0.7415 (OUTLIER) cc_final: 0.6916 (t80) REVERT: A 322 ILE cc_start: 0.7688 (pt) cc_final: 0.7357 (mm) REVERT: A 365 TYR cc_start: 0.8089 (m-10) cc_final: 0.7807 (m-10) REVERT: A 427 ASP cc_start: 0.8056 (OUTLIER) cc_final: 0.7742 (m-30) REVERT: A 455 MET cc_start: 0.6569 (tmm) cc_final: 0.6301 (tmm) outliers start: 17 outliers final: 13 residues processed: 62 average time/residue: 0.0350 time to fit residues: 2.8491 Evaluate side-chains 61 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 44 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 439 PHE Chi-restraints excluded: chain A residue 441 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 31 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 7 optimal weight: 0.2980 chunk 14 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.151682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.124639 restraints weight = 3573.667| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.87 r_work: 0.3259 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3191 Z= 0.162 Angle : 0.599 6.874 4362 Z= 0.315 Chirality : 0.042 0.186 505 Planarity : 0.004 0.033 523 Dihedral : 5.110 56.826 425 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 5.71 % Allowed : 19.52 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.71 (0.42), residues: 383 helix: 1.29 (0.27), residues: 326 sheet: None (None), residues: 0 loop : 0.64 (0.93), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 144 TYR 0.027 0.002 TYR A 373 PHE 0.021 0.002 PHE A 71 TRP 0.014 0.001 TRP A 284 HIS 0.003 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 3191) covalent geometry : angle 0.59932 ( 4362) hydrogen bonds : bond 0.05164 ( 251) hydrogen bonds : angle 4.44198 ( 753) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 46 time to evaluate : 0.067 Fit side-chains revert: symmetry clash REVERT: A 181 SER cc_start: 0.8372 (t) cc_final: 0.8046 (p) REVERT: A 270 LYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7185 (tptt) REVERT: A 315 TYR cc_start: 0.7385 (OUTLIER) cc_final: 0.6864 (t80) REVERT: A 322 ILE cc_start: 0.7730 (pt) cc_final: 0.7419 (mm) REVERT: A 365 TYR cc_start: 0.8102 (m-10) cc_final: 0.7838 (m-10) REVERT: A 382 SER cc_start: 0.8494 (t) cc_final: 0.8284 (m) REVERT: A 427 ASP cc_start: 0.8109 (OUTLIER) cc_final: 0.7809 (m-30) REVERT: A 455 MET cc_start: 0.6506 (tmm) cc_final: 0.6229 (tmm) outliers start: 19 outliers final: 14 residues processed: 61 average time/residue: 0.0413 time to fit residues: 3.3374 Evaluate side-chains 61 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 44 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 439 PHE Chi-restraints excluded: chain A residue 441 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 21 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.149674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.123515 restraints weight = 3705.273| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 1.86 r_work: 0.3293 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3191 Z= 0.167 Angle : 0.623 8.323 4362 Z= 0.322 Chirality : 0.043 0.190 505 Planarity : 0.004 0.034 523 Dihedral : 5.137 57.218 425 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 5.11 % Allowed : 21.62 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.71 (0.42), residues: 383 helix: 1.28 (0.27), residues: 327 sheet: None (None), residues: 0 loop : 0.70 (0.94), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 144 TYR 0.022 0.002 TYR A 280 PHE 0.022 0.002 PHE A 71 TRP 0.013 0.001 TRP A 284 HIS 0.003 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 3191) covalent geometry : angle 0.62299 ( 4362) hydrogen bonds : bond 0.05215 ( 251) hydrogen bonds : angle 4.45964 ( 753) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 46 time to evaluate : 0.082 Fit side-chains revert: symmetry clash REVERT: A 181 SER cc_start: 0.8428 (t) cc_final: 0.8089 (p) REVERT: A 270 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7261 (tptt) REVERT: A 315 TYR cc_start: 0.7451 (OUTLIER) cc_final: 0.6917 (t80) REVERT: A 322 ILE cc_start: 0.7724 (pt) cc_final: 0.7414 (mm) REVERT: A 427 ASP cc_start: 0.8180 (OUTLIER) cc_final: 0.7893 (m-30) REVERT: A 455 MET cc_start: 0.6565 (tmm) cc_final: 0.6327 (tmm) outliers start: 17 outliers final: 14 residues processed: 60 average time/residue: 0.0364 time to fit residues: 2.9698 Evaluate side-chains 61 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 44 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 439 PHE Chi-restraints excluded: chain A residue 441 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 10 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 32 optimal weight: 0.0570 chunk 4 optimal weight: 0.0370 chunk 31 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.153282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.126283 restraints weight = 3583.315| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.86 r_work: 0.3283 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3191 Z= 0.145 Angle : 0.605 8.173 4362 Z= 0.314 Chirality : 0.042 0.182 505 Planarity : 0.004 0.035 523 Dihedral : 5.092 56.848 425 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.80 % Allowed : 20.72 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.82 (0.42), residues: 383 helix: 1.36 (0.27), residues: 326 sheet: None (None), residues: 0 loop : 0.74 (0.96), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 29 TYR 0.022 0.002 TYR A 280 PHE 0.020 0.001 PHE A 71 TRP 0.012 0.001 TRP A 94 HIS 0.000 0.000 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 3191) covalent geometry : angle 0.60482 ( 4362) hydrogen bonds : bond 0.05013 ( 251) hydrogen bonds : angle 4.36533 ( 753) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 47 time to evaluate : 0.078 Fit side-chains revert: symmetry clash REVERT: A 181 SER cc_start: 0.8374 (t) cc_final: 0.8055 (p) REVERT: A 270 LYS cc_start: 0.8074 (OUTLIER) cc_final: 0.7140 (tptt) REVERT: A 315 TYR cc_start: 0.7318 (OUTLIER) cc_final: 0.6811 (t80) REVERT: A 322 ILE cc_start: 0.7680 (pt) cc_final: 0.7359 (mm) REVERT: A 455 MET cc_start: 0.6406 (tmm) cc_final: 0.6183 (tmm) outliers start: 16 outliers final: 12 residues processed: 60 average time/residue: 0.0356 time to fit residues: 2.9230 Evaluate side-chains 58 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 44 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 439 PHE Chi-restraints excluded: chain A residue 441 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 0 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 4 optimal weight: 0.0980 chunk 37 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 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 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.151487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.124261 restraints weight = 3522.220| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.86 r_work: 0.3250 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3191 Z= 0.172 Angle : 0.635 8.217 4362 Z= 0.329 Chirality : 0.043 0.192 505 Planarity : 0.004 0.034 523 Dihedral : 5.151 57.217 425 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.50 % Allowed : 21.62 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.71 (0.42), residues: 383 helix: 1.28 (0.27), residues: 327 sheet: None (None), residues: 0 loop : 0.78 (0.97), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 144 TYR 0.027 0.002 TYR A 373 PHE 0.022 0.002 PHE A 71 TRP 0.014 0.001 TRP A 284 HIS 0.002 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 3191) covalent geometry : angle 0.63532 ( 4362) hydrogen bonds : bond 0.05217 ( 251) hydrogen bonds : angle 4.42749 ( 753) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 0.164 Fit side-chains revert: symmetry clash REVERT: A 181 SER cc_start: 0.8401 (t) cc_final: 0.8072 (p) REVERT: A 270 LYS cc_start: 0.8138 (OUTLIER) cc_final: 0.7220 (tptt) REVERT: A 315 TYR cc_start: 0.7359 (OUTLIER) cc_final: 0.6834 (t80) REVERT: A 322 ILE cc_start: 0.7752 (pt) cc_final: 0.7408 (mm) REVERT: A 455 MET cc_start: 0.6412 (tmm) cc_final: 0.6192 (tmm) outliers start: 15 outliers final: 12 residues processed: 60 average time/residue: 0.0415 time to fit residues: 3.3810 Evaluate side-chains 60 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 46 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 439 PHE Chi-restraints excluded: chain A residue 441 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 36 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.150851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.123306 restraints weight = 3592.879| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.88 r_work: 0.3235 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3191 Z= 0.179 Angle : 0.645 8.383 4362 Z= 0.333 Chirality : 0.044 0.199 505 Planarity : 0.004 0.034 523 Dihedral : 5.224 57.761 425 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.50 % Allowed : 21.92 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.64 (0.42), residues: 383 helix: 1.24 (0.27), residues: 327 sheet: None (None), residues: 0 loop : 0.67 (0.97), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 144 TYR 0.023 0.002 TYR A 280 PHE 0.023 0.002 PHE A 71 TRP 0.014 0.001 TRP A 284 HIS 0.002 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 3191) covalent geometry : angle 0.64474 ( 4362) hydrogen bonds : bond 0.05287 ( 251) hydrogen bonds : angle 4.48885 ( 753) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 811.67 seconds wall clock time: 14 minutes 34.71 seconds (874.71 seconds total)