Starting phenix.real_space_refine on Fri Aug 22 18:37:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uc0_42111/08_2025/8uc0_42111.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uc0_42111/08_2025/8uc0_42111.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8uc0_42111/08_2025/8uc0_42111.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uc0_42111/08_2025/8uc0_42111.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8uc0_42111/08_2025/8uc0_42111.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uc0_42111/08_2025/8uc0_42111.map" } resolution = 2.42 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= 0.029 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 18 5.16 5 C 2274 2.51 5 N 508 2.21 5 O 686 1.98 5 H 3375 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 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: 6861 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 6654 Classifications: {'peptide': 422} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 403} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 207 Unusual residues: {'Y01': 3} Classifications: {'undetermined': 3, 'water': 102} Link IDs: {None: 104} Time building chain proxies: 1.44, per 1000 atoms: 0.21 Number of scatterers: 6861 At special positions: 0 Unit cell: (87, 57.275, 65.975, 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 18 16.00 O 686 8.00 N 508 7.00 C 2274 6.00 H 3375 1.00 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: 0.56 Conformation dependent library (CDL) restraints added in 199.1 milliseconds Enol-peptide restraints added in 1.2 microseconds 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 774 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 0 sheets defined 90.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 105 through 131 removed outlier: 3.762A pdb=" N VAL A 109 " --> pdb=" O PRO A 105 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N TYR A 128 " --> pdb=" O GLN A 124 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N SER A 129 " --> pdb=" O TRP A 125 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ILE A 131 " --> pdb=" O GLN A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 140 Processing helix chain 'A' and resid 142 through 172 removed outlier: 3.738A pdb=" N ILE A 146 " --> pdb=" O THR A 142 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N TYR A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N MET A 154 " --> pdb=" O SER A 150 " (cutoff:3.500A) Proline residue: A 159 - end of helix removed outlier: 5.157A pdb=" N PHE A 162 " --> pdb=" O VAL A 158 " (cutoff:3.500A) Proline residue: A 163 - end of helix Processing helix chain 'A' and resid 172 through 193 removed outlier: 3.829A pdb=" N THR A 176 " --> pdb=" O GLY A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 219 removed outlier: 3.618A pdb=" N THR A 203 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE A 216 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLY A 219 " --> pdb=" O VAL A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 229 removed outlier: 4.346A pdb=" N ARG A 223 " --> pdb=" O GLY A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 260 removed outlier: 3.623A pdb=" N ASN A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) Proline residue: A 256 - end of helix Processing helix chain 'A' and resid 266 through 296 Processing helix chain 'A' and resid 305 through 314 Processing helix chain 'A' and resid 320 through 331 removed outlier: 3.656A pdb=" N ASN A 331 " --> pdb=" O ASN A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 363 removed outlier: 5.008A pdb=" N ASN A 356 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N GLN A 357 " --> pdb=" O THR A 353 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR A 362 " --> pdb=" O MET A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 396 Processing helix chain 'A' and resid 397 through 420 removed outlier: 3.698A pdb=" N THR A 401 " --> pdb=" O THR A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 423 No H-bonds generated for 'chain 'A' and resid 421 through 423' Processing helix chain 'A' and resid 424 through 454 Proline residue: A 444 - end of helix Processing helix chain 'A' and resid 458 through 489 Processing helix chain 'A' and resid 489 through 511 removed outlier: 3.783A pdb=" N GLY A 493 " --> pdb=" O GLY A 489 " (cutoff:3.500A) 279 hydrogen bonds defined for protein. 837 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: 1.64 Time building geometry restraints manager: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3367 1.03 - 1.23: 11 1.23 - 1.42: 1404 1.42 - 1.62: 2042 1.62 - 1.81: 28 Bond restraints: 6852 Sorted by residual: bond pdb=" N VAL A 195 " pdb=" CA VAL A 195 " ideal model delta sigma weight residual 1.474 1.458 0.016 1.57e-02 4.06e+03 1.07e+00 bond pdb=" N PRO A 221 " pdb=" CA PRO A 221 " ideal model delta sigma weight residual 1.469 1.479 -0.010 1.28e-02 6.10e+03 5.99e-01 bond pdb=" CB TRP A 391 " pdb=" CG TRP A 391 " ideal model delta sigma weight residual 1.498 1.519 -0.021 3.10e-02 1.04e+03 4.48e-01 bond pdb=" C PHE A 162 " pdb=" O PHE A 162 " ideal model delta sigma weight residual 1.244 1.237 0.007 1.00e-02 1.00e+04 4.36e-01 bond pdb=" CA ILE A 332 " pdb=" CB ILE A 332 " ideal model delta sigma weight residual 1.539 1.535 0.004 5.40e-03 3.43e+04 4.28e-01 ... (remaining 6847 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.07: 11676 1.07 - 2.15: 653 2.15 - 3.22: 36 3.22 - 4.29: 11 4.29 - 5.37: 4 Bond angle restraints: 12380 Sorted by residual: angle pdb=" N VAL A 195 " pdb=" CA VAL A 195 " pdb=" C VAL A 195 " ideal model delta sigma weight residual 106.21 109.31 -3.10 1.07e+00 8.73e-01 8.41e+00 angle pdb=" CA TYR A 117 " pdb=" CB TYR A 117 " pdb=" CG TYR A 117 " ideal model delta sigma weight residual 113.90 118.78 -4.88 1.80e+00 3.09e-01 7.35e+00 angle pdb=" N LEU A 220 " pdb=" CA LEU A 220 " pdb=" C LEU A 220 " ideal model delta sigma weight residual 109.81 115.18 -5.37 2.21e+00 2.05e-01 5.90e+00 angle pdb=" CA LEU A 220 " pdb=" C LEU A 220 " pdb=" N PRO A 221 " ideal model delta sigma weight residual 118.44 121.96 -3.52 1.59e+00 3.96e-01 4.90e+00 angle pdb=" C VAL A 195 " pdb=" CA VAL A 195 " pdb=" CB VAL A 195 " ideal model delta sigma weight residual 113.22 110.91 2.31 1.12e+00 7.97e-01 4.24e+00 ... (remaining 12375 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.00: 2902 13.00 - 26.00: 303 26.00 - 39.00: 87 39.00 - 52.00: 54 52.00 - 65.00: 49 Dihedral angle restraints: 3395 sinusoidal: 1906 harmonic: 1489 Sorted by residual: dihedral pdb=" CA LEU A 254 " pdb=" C LEU A 254 " pdb=" N LEU A 255 " pdb=" CA LEU A 255 " ideal model delta harmonic sigma weight residual 180.00 -162.25 -17.75 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" N THR A 203 " pdb=" CA THR A 203 " pdb=" CB THR A 203 " pdb=" OG1 THR A 203 " ideal model delta sinusoidal sigma weight residual -180.00 -120.53 -59.47 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA ARG A 326 " pdb=" CB ARG A 326 " pdb=" CG ARG A 326 " pdb=" CD ARG A 326 " ideal model delta sinusoidal sigma weight residual -180.00 -122.45 -57.55 3 1.50e+01 4.44e-03 9.44e+00 ... (remaining 3392 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.022: 377 0.022 - 0.043: 100 0.043 - 0.065: 42 0.065 - 0.087: 46 0.087 - 0.109: 8 Chirality restraints: 573 Sorted by residual: chirality pdb=" CA ILE A 131 " pdb=" N ILE A 131 " pdb=" C ILE A 131 " pdb=" CB ILE A 131 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.11 2.00e-01 2.50e+01 2.95e-01 chirality pdb=" CA PRO A 159 " pdb=" N PRO A 159 " pdb=" C PRO A 159 " pdb=" CB PRO A 159 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.66e-01 chirality pdb=" CA PRO A 221 " pdb=" N PRO A 221 " pdb=" C PRO A 221 " pdb=" CB PRO A 221 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.61e-01 ... (remaining 570 not shown) Planarity restraints: 965 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 332 " -0.026 5.00e-02 4.00e+02 4.01e-02 2.58e+00 pdb=" N PRO A 333 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 333 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 333 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 114 " 0.007 2.00e-02 2.50e+03 1.38e-02 1.89e+00 pdb=" C PHE A 114 " -0.024 2.00e-02 2.50e+03 pdb=" O PHE A 114 " 0.009 2.00e-02 2.50e+03 pdb=" N SER A 115 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 123 " -0.005 2.00e-02 2.50e+03 1.05e-02 1.10e+00 pdb=" C PHE A 123 " 0.018 2.00e-02 2.50e+03 pdb=" O PHE A 123 " -0.007 2.00e-02 2.50e+03 pdb=" N GLN A 124 " -0.006 2.00e-02 2.50e+03 ... (remaining 962 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 717 2.24 - 2.83: 15820 2.83 - 3.42: 19749 3.42 - 4.01: 26710 4.01 - 4.60: 40779 Nonbonded interactions: 103775 Sorted by model distance: nonbonded pdb=" O ILE A 415 " pdb=" HG1 THR A 419 " model vdw 1.653 2.450 nonbonded pdb=" OD1 ASP A 393 " pdb="HH11 ARG A 517 " model vdw 1.717 2.450 nonbonded pdb=" O ILE A 130 " pdb="HD22 ASN A 356 " model vdw 1.717 2.450 nonbonded pdb=" O SER A 104 " pdb="HH11 ARG A 107 " model vdw 1.733 2.450 nonbonded pdb=" OE1 GLU A 318 " pdb=" H GLU A 318 " model vdw 1.777 2.450 ... (remaining 103770 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: 4.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.600 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 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 : 0.002 0.021 3477 Z= 0.110 Angle : 0.474 5.369 4760 Z= 0.266 Chirality : 0.032 0.109 573 Planarity : 0.003 0.040 563 Dihedral : 13.633 65.004 1381 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.84 % Allowed : 11.20 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 3.55 (0.41), residues: 420 helix: 3.04 (0.27), residues: 345 sheet: None (None), residues: 0 loop : -1.31 (0.65), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 106 TYR 0.016 0.001 TYR A 117 PHE 0.011 0.001 PHE A 496 TRP 0.005 0.001 TRP A 201 HIS 0.000 0.000 HIS A 145 Details of bonding type rmsd covalent geometry : bond 0.00205 ( 3477) covalent geometry : angle 0.47353 ( 4760) hydrogen bonds : bond 0.12218 ( 279) hydrogen bonds : angle 5.92053 ( 837) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.206 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 46 average time/residue: 0.9898 time to fit residues: 47.0628 Evaluate side-chains 38 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain A residue 282 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.3980 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 0.4980 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 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 184 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.098763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.081228 restraints weight = 15640.482| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.74 r_work: 0.3080 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3477 Z= 0.149 Angle : 0.515 5.937 4760 Z= 0.275 Chirality : 0.034 0.124 573 Planarity : 0.004 0.038 563 Dihedral : 5.862 56.447 668 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.40 % Allowed : 12.32 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 3.82 (0.40), residues: 420 helix: 3.08 (0.26), residues: 354 sheet: None (None), residues: 0 loop : -0.88 (0.79), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 326 TYR 0.023 0.001 TYR A 117 PHE 0.011 0.001 PHE A 496 TRP 0.007 0.001 TRP A 201 HIS 0.001 0.001 HIS A 198 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 3477) covalent geometry : angle 0.51469 ( 4760) hydrogen bonds : bond 0.05260 ( 279) hydrogen bonds : angle 4.61253 ( 837) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.159 Fit side-chains REVERT: A 171 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.7470 (mpt90) REVERT: A 312 GLN cc_start: 0.6955 (mt0) cc_final: 0.6698 (mt0) REVERT: A 421 ASP cc_start: 0.8479 (p0) cc_final: 0.8210 (p0) REVERT: A 448 GLU cc_start: 0.8453 (tt0) cc_final: 0.8165 (tt0) outliers start: 5 outliers final: 3 residues processed: 39 average time/residue: 0.9170 time to fit residues: 37.1909 Evaluate side-chains 39 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 514 ASP Chi-restraints excluded: chain A residue 516 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 15 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 7 optimal weight: 0.4980 chunk 17 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.094394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.076558 restraints weight = 16102.358| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.77 r_work: 0.3043 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3477 Z= 0.149 Angle : 0.504 6.082 4760 Z= 0.270 Chirality : 0.035 0.131 573 Planarity : 0.004 0.036 563 Dihedral : 5.808 53.055 666 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 1.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.40 % Allowed : 12.04 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 3.67 (0.41), residues: 420 helix: 2.94 (0.26), residues: 356 sheet: None (None), residues: 0 loop : -0.81 (0.84), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 372 TYR 0.023 0.001 TYR A 117 PHE 0.014 0.001 PHE A 114 TRP 0.008 0.001 TRP A 201 HIS 0.001 0.000 HIS A 145 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 3477) covalent geometry : angle 0.50359 ( 4760) hydrogen bonds : bond 0.05270 ( 279) hydrogen bonds : angle 4.45357 ( 837) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.184 Fit side-chains REVERT: A 171 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.7283 (mpt90) REVERT: A 312 GLN cc_start: 0.6948 (mt0) cc_final: 0.6693 (mt0) REVERT: A 421 ASP cc_start: 0.8539 (p0) cc_final: 0.8265 (p0) REVERT: A 448 GLU cc_start: 0.8570 (tt0) cc_final: 0.8296 (tt0) outliers start: 5 outliers final: 2 residues processed: 38 average time/residue: 1.0579 time to fit residues: 41.5709 Evaluate side-chains 37 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 514 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 39 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.092969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.075354 restraints weight = 16164.802| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.76 r_work: 0.3012 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3477 Z= 0.155 Angle : 0.508 6.199 4760 Z= 0.272 Chirality : 0.035 0.131 573 Planarity : 0.004 0.038 563 Dihedral : 5.947 55.268 666 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.84 % Allowed : 12.89 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 3.55 (0.41), residues: 420 helix: 2.93 (0.27), residues: 351 sheet: None (None), residues: 0 loop : -1.02 (0.76), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 223 TYR 0.024 0.001 TYR A 117 PHE 0.015 0.001 PHE A 114 TRP 0.007 0.001 TRP A 500 HIS 0.001 0.000 HIS A 145 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 3477) covalent geometry : angle 0.50786 ( 4760) hydrogen bonds : bond 0.05121 ( 279) hydrogen bonds : angle 4.37306 ( 837) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.138 Fit side-chains REVERT: A 171 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.7406 (mpt90) REVERT: A 312 GLN cc_start: 0.6944 (mt0) cc_final: 0.6695 (mt0) REVERT: A 448 GLU cc_start: 0.8555 (tt0) cc_final: 0.8282 (tt0) outliers start: 3 outliers final: 2 residues processed: 35 average time/residue: 1.1144 time to fit residues: 40.3945 Evaluate side-chains 35 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 514 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 16 optimal weight: 0.1980 chunk 11 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.092790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.075042 restraints weight = 16110.386| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 1.78 r_work: 0.3013 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3477 Z= 0.150 Angle : 0.499 6.139 4760 Z= 0.268 Chirality : 0.035 0.131 573 Planarity : 0.004 0.038 563 Dihedral : 6.061 59.763 666 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.12 % Allowed : 12.89 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 3.47 (0.41), residues: 420 helix: 2.90 (0.27), residues: 351 sheet: None (None), residues: 0 loop : -1.18 (0.72), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 223 TYR 0.024 0.001 TYR A 117 PHE 0.016 0.001 PHE A 114 TRP 0.007 0.001 TRP A 500 HIS 0.001 0.000 HIS A 145 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 3477) covalent geometry : angle 0.49874 ( 4760) hydrogen bonds : bond 0.05087 ( 279) hydrogen bonds : angle 4.35576 ( 837) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.177 Fit side-chains REVERT: A 171 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.7232 (mpt90) REVERT: A 312 GLN cc_start: 0.6921 (mt0) cc_final: 0.6658 (mt0) REVERT: A 421 ASP cc_start: 0.8523 (p0) cc_final: 0.8193 (p0) REVERT: A 448 GLU cc_start: 0.8572 (tt0) cc_final: 0.8297 (tt0) outliers start: 4 outliers final: 3 residues processed: 35 average time/residue: 1.0347 time to fit residues: 37.5402 Evaluate side-chains 35 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 514 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 34 optimal weight: 0.4980 chunk 23 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.091642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.073999 restraints weight = 16316.517| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 1.77 r_work: 0.3001 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3477 Z= 0.165 Angle : 0.512 6.233 4760 Z= 0.276 Chirality : 0.035 0.133 573 Planarity : 0.004 0.038 563 Dihedral : 6.166 56.684 666 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 1.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.12 % Allowed : 13.45 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 3.39 (0.41), residues: 420 helix: 2.85 (0.27), residues: 351 sheet: None (None), residues: 0 loop : -1.19 (0.71), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 223 TYR 0.024 0.001 TYR A 117 PHE 0.017 0.001 PHE A 114 TRP 0.007 0.001 TRP A 500 HIS 0.001 0.000 HIS A 145 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 3477) covalent geometry : angle 0.51163 ( 4760) hydrogen bonds : bond 0.05246 ( 279) hydrogen bonds : angle 4.38082 ( 837) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.138 Fit side-chains REVERT: A 171 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.7390 (mpt90) REVERT: A 312 GLN cc_start: 0.6913 (mt0) cc_final: 0.6662 (mt0) REVERT: A 448 GLU cc_start: 0.8562 (tt0) cc_final: 0.8291 (tt0) outliers start: 4 outliers final: 3 residues processed: 33 average time/residue: 1.0961 time to fit residues: 37.5473 Evaluate side-chains 34 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 514 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 33 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 7 optimal weight: 0.4980 chunk 38 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.091501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.073799 restraints weight = 16060.842| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.77 r_work: 0.2993 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3477 Z= 0.163 Angle : 0.510 6.275 4760 Z= 0.274 Chirality : 0.035 0.131 573 Planarity : 0.004 0.038 563 Dihedral : 6.209 56.640 666 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.40 % Allowed : 12.61 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 3.34 (0.40), residues: 420 helix: 2.81 (0.27), residues: 351 sheet: None (None), residues: 0 loop : -1.24 (0.70), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 223 TYR 0.023 0.001 TYR A 117 PHE 0.017 0.001 PHE A 114 TRP 0.007 0.001 TRP A 500 HIS 0.001 0.000 HIS A 145 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 3477) covalent geometry : angle 0.51010 ( 4760) hydrogen bonds : bond 0.05236 ( 279) hydrogen bonds : angle 4.37878 ( 837) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.210 Fit side-chains REVERT: A 171 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.7331 (mpt90) REVERT: A 312 GLN cc_start: 0.6933 (mt0) cc_final: 0.6694 (mt0) REVERT: A 421 ASP cc_start: 0.8517 (p0) cc_final: 0.8225 (p0) REVERT: A 448 GLU cc_start: 0.8556 (tt0) cc_final: 0.8292 (tt0) outliers start: 5 outliers final: 3 residues processed: 33 average time/residue: 1.0921 time to fit residues: 37.3266 Evaluate side-chains 34 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 514 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 25 optimal weight: 0.9990 chunk 3 optimal weight: 0.4980 chunk 20 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 13 optimal weight: 0.2980 chunk 39 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.092085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.074505 restraints weight = 16353.456| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 1.78 r_work: 0.3013 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3477 Z= 0.143 Angle : 0.498 6.234 4760 Z= 0.266 Chirality : 0.035 0.130 573 Planarity : 0.004 0.038 563 Dihedral : 6.145 56.383 666 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.40 % Allowed : 12.89 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 3.38 (0.40), residues: 420 helix: 2.84 (0.27), residues: 351 sheet: None (None), residues: 0 loop : -1.25 (0.70), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 326 TYR 0.024 0.001 TYR A 117 PHE 0.015 0.001 PHE A 114 TRP 0.008 0.001 TRP A 500 HIS 0.001 0.000 HIS A 145 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 3477) covalent geometry : angle 0.49755 ( 4760) hydrogen bonds : bond 0.05002 ( 279) hydrogen bonds : angle 4.32637 ( 837) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.123 Fit side-chains REVERT: A 171 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.7326 (mpt90) REVERT: A 312 GLN cc_start: 0.6913 (mt0) cc_final: 0.6671 (mt0) REVERT: A 421 ASP cc_start: 0.8515 (p0) cc_final: 0.8284 (p0) REVERT: A 448 GLU cc_start: 0.8527 (tt0) cc_final: 0.8264 (tt0) outliers start: 5 outliers final: 3 residues processed: 34 average time/residue: 0.8727 time to fit residues: 30.9980 Evaluate side-chains 34 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 514 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 1.9990 chunk 3 optimal weight: 0.0980 chunk 32 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 1 optimal weight: 0.0980 chunk 30 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.093054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.075401 restraints weight = 16087.162| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 1.77 r_work: 0.3021 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3477 Z= 0.127 Angle : 0.492 6.160 4760 Z= 0.261 Chirality : 0.035 0.127 573 Planarity : 0.004 0.038 563 Dihedral : 6.042 56.112 666 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.12 % Allowed : 13.73 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 3.44 (0.41), residues: 420 helix: 2.85 (0.27), residues: 353 sheet: None (None), residues: 0 loop : -1.17 (0.72), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 107 TYR 0.024 0.001 TYR A 117 PHE 0.013 0.001 PHE A 114 TRP 0.007 0.001 TRP A 500 HIS 0.001 0.000 HIS A 145 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 3477) covalent geometry : angle 0.49204 ( 4760) hydrogen bonds : bond 0.04751 ( 279) hydrogen bonds : angle 4.26750 ( 837) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.199 Fit side-chains REVERT: A 171 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.7212 (mpt90) REVERT: A 312 GLN cc_start: 0.6938 (mt0) cc_final: 0.6700 (mt0) REVERT: A 421 ASP cc_start: 0.8506 (p0) cc_final: 0.8274 (p0) REVERT: A 448 GLU cc_start: 0.8528 (tt0) cc_final: 0.8258 (tt0) outliers start: 4 outliers final: 3 residues processed: 32 average time/residue: 0.9042 time to fit residues: 30.1944 Evaluate side-chains 34 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 514 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 8 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 13 optimal weight: 0.1980 chunk 41 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 26 optimal weight: 0.4980 chunk 10 optimal weight: 0.2980 chunk 28 optimal weight: 0.9980 chunk 39 optimal weight: 0.0980 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.093873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.076367 restraints weight = 16016.240| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.77 r_work: 0.3039 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3477 Z= 0.114 Angle : 0.479 6.085 4760 Z= 0.253 Chirality : 0.034 0.125 573 Planarity : 0.004 0.038 563 Dihedral : 5.898 55.711 666 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.40 % Allowed : 13.73 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 3.51 (0.41), residues: 420 helix: 2.90 (0.27), residues: 353 sheet: None (None), residues: 0 loop : -1.12 (0.73), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 326 TYR 0.025 0.001 TYR A 117 PHE 0.012 0.001 PHE A 496 TRP 0.007 0.001 TRP A 500 HIS 0.000 0.000 HIS A 145 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 3477) covalent geometry : angle 0.47885 ( 4760) hydrogen bonds : bond 0.04471 ( 279) hydrogen bonds : angle 4.19194 ( 837) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 0.170 Fit side-chains REVERT: A 171 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7194 (mpt90) REVERT: A 312 GLN cc_start: 0.6916 (mt0) cc_final: 0.6697 (mt0) REVERT: A 421 ASP cc_start: 0.8448 (p0) cc_final: 0.8175 (p0) REVERT: A 448 GLU cc_start: 0.8533 (tt0) cc_final: 0.8269 (tt0) outliers start: 5 outliers final: 3 residues processed: 33 average time/residue: 0.9444 time to fit residues: 32.5119 Evaluate side-chains 34 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 514 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 26 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 20 optimal weight: 0.4980 chunk 14 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 32 optimal weight: 0.4980 chunk 23 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.092526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.074940 restraints weight = 16039.171| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 1.77 r_work: 0.2977 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3477 Z= 0.143 Angle : 0.498 6.132 4760 Z= 0.264 Chirality : 0.035 0.127 573 Planarity : 0.004 0.038 563 Dihedral : 6.004 56.845 666 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.12 % Allowed : 13.45 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 3.46 (0.41), residues: 420 helix: 2.88 (0.27), residues: 353 sheet: None (None), residues: 0 loop : -1.19 (0.72), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 326 TYR 0.024 0.001 TYR A 117 PHE 0.016 0.001 PHE A 114 TRP 0.006 0.001 TRP A 500 HIS 0.001 0.000 HIS A 145 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 3477) covalent geometry : angle 0.49839 ( 4760) hydrogen bonds : bond 0.04839 ( 279) hydrogen bonds : angle 4.26463 ( 837) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2629.56 seconds wall clock time: 45 minutes 20.67 seconds (2720.67 seconds total)