Starting phenix.real_space_refine on Tue Feb 3 13:22:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kuy_62584/02_2026/9kuy_62584.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kuy_62584/02_2026/9kuy_62584.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kuy_62584/02_2026/9kuy_62584.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kuy_62584/02_2026/9kuy_62584.map" model { file = "/net/cci-nas-00/data/ceres_data/9kuy_62584/02_2026/9kuy_62584.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kuy_62584/02_2026/9kuy_62584.cif" } resolution = 3.6 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= 0.038 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 19 5.16 5 C 2019 2.51 5 N 486 2.21 5 O 543 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3067 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3067 Classifications: {'peptide': 409} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 16, 'TRANS': 392} Chain breaks: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 39 Time building chain proxies: 0.57, per 1000 atoms: 0.19 Number of scatterers: 3067 At special positions: 0 Unit cell: (77.35, 57.8, 69.7, 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 19 16.00 O 543 8.00 N 486 7.00 C 2019 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: 0.15 Conformation dependent library (CDL) restraints added in 71.8 milliseconds 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 738 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 0 sheets defined 85.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 6 through 42 removed outlier: 3.825A pdb=" N ARG A 10 " --> pdb=" O TYR A 6 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N PHE A 31 " --> pdb=" O ASN A 27 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N SER A 32 " --> pdb=" O ARG A 28 " (cutoff:3.500A) Proline residue: A 36 - end of helix Processing helix chain 'A' and resid 45 through 71 Processing helix chain 'A' and resid 77 through 95 removed outlier: 3.698A pdb=" N ALA A 95 " --> pdb=" O ASN A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 114 Processing helix chain 'A' and resid 117 through 129 removed outlier: 3.946A pdb=" N CYS A 121 " --> pdb=" O GLY A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 151 removed outlier: 4.183A pdb=" N SER A 144 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N MET A 145 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ASN A 146 " --> pdb=" O SER A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 163 removed outlier: 3.690A pdb=" N SER A 162 " --> pdb=" O ILE A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 187 Processing helix chain 'A' and resid 190 through 194 removed outlier: 3.696A pdb=" N VAL A 194 " --> pdb=" O PRO A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 221 Processing helix chain 'A' and resid 223 through 254 removed outlier: 3.860A pdb=" N TRP A 227 " --> pdb=" O SER A 223 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N GLN A 248 " --> pdb=" O THR A 244 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N PHE A 249 " --> pdb=" O ASP A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 291 Processing helix chain 'A' and resid 300 through 321 Processing helix chain 'A' and resid 327 through 357 removed outlier: 3.768A pdb=" N ILE A 331 " --> pdb=" O PRO A 327 " (cutoff:3.500A) Proline residue: A 345 - end of helix removed outlier: 3.720A pdb=" N GLY A 350 " --> pdb=" O ILE A 346 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA A 357 " --> pdb=" O ALA A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 380 removed outlier: 3.658A pdb=" N SER A 365 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA A 380 " --> pdb=" O GLY A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 391 Processing helix chain 'A' and resid 392 through 414 removed outlier: 3.702A pdb=" N ALA A 396 " --> pdb=" O SER A 392 " (cutoff:3.500A) 259 hydrogen bonds defined for protein. 774 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: 0.48 Time building geometry restraints manager: 0.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 922 1.34 - 1.46: 749 1.46 - 1.58: 1450 1.58 - 1.69: 0 1.69 - 1.81: 31 Bond restraints: 3152 Sorted by residual: bond pdb=" CB MET A 311 " pdb=" CG MET A 311 " ideal model delta sigma weight residual 1.520 1.491 0.029 3.00e-02 1.11e+03 9.21e-01 bond pdb=" CA GLY A 292 " pdb=" C GLY A 292 " ideal model delta sigma weight residual 1.517 1.528 -0.012 1.33e-02 5.65e+03 7.59e-01 bond pdb=" C LEU A 274 " pdb=" O LEU A 274 " ideal model delta sigma weight residual 1.236 1.245 -0.009 1.15e-02 7.56e+03 6.04e-01 bond pdb=" CA MET A 35 " pdb=" C MET A 35 " ideal model delta sigma weight residual 1.521 1.530 -0.009 1.17e-02 7.31e+03 5.63e-01 bond pdb=" C PHE A 340 " pdb=" O PHE A 340 " ideal model delta sigma weight residual 1.236 1.245 -0.009 1.16e-02 7.43e+03 5.61e-01 ... (remaining 3147 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 4204 1.61 - 3.22: 69 3.22 - 4.83: 19 4.83 - 6.44: 5 6.44 - 8.05: 3 Bond angle restraints: 4300 Sorted by residual: angle pdb=" CA LEU A 151 " pdb=" CB LEU A 151 " pdb=" CG LEU A 151 " ideal model delta sigma weight residual 116.30 124.35 -8.05 3.50e+00 8.16e-02 5.29e+00 angle pdb=" N PRO A 119 " pdb=" CA PRO A 119 " pdb=" C PRO A 119 " ideal model delta sigma weight residual 110.70 113.37 -2.67 1.22e+00 6.72e-01 4.80e+00 angle pdb=" CA LEU A 70 " pdb=" CB LEU A 70 " pdb=" CG LEU A 70 " ideal model delta sigma weight residual 116.30 123.69 -7.39 3.50e+00 8.16e-02 4.46e+00 angle pdb=" CB MET A 311 " pdb=" CG MET A 311 " pdb=" SD MET A 311 " ideal model delta sigma weight residual 112.70 106.43 6.27 3.00e+00 1.11e-01 4.37e+00 angle pdb=" CA TRP A 118 " pdb=" C TRP A 118 " pdb=" N PRO A 119 " ideal model delta sigma weight residual 118.44 121.49 -3.05 1.59e+00 3.96e-01 3.69e+00 ... (remaining 4295 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.71: 1588 14.71 - 29.42: 139 29.42 - 44.13: 47 44.13 - 58.84: 7 58.84 - 73.55: 2 Dihedral angle restraints: 1783 sinusoidal: 623 harmonic: 1160 Sorted by residual: dihedral pdb=" CA LEU A 151 " pdb=" C LEU A 151 " pdb=" N GLY A 152 " pdb=" CA GLY A 152 " ideal model delta harmonic sigma weight residual 180.00 163.58 16.42 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CA LEU A 371 " pdb=" C LEU A 371 " pdb=" N MET A 372 " pdb=" CA MET A 372 " ideal model delta harmonic sigma weight residual 180.00 164.23 15.77 0 5.00e+00 4.00e-02 9.94e+00 dihedral pdb=" CB MET A 288 " pdb=" CG MET A 288 " pdb=" SD MET A 288 " pdb=" CE MET A 288 " ideal model delta sinusoidal sigma weight residual -180.00 -133.80 -46.20 3 1.50e+01 4.44e-03 8.30e+00 ... (remaining 1780 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 312 0.028 - 0.056: 103 0.056 - 0.084: 54 0.084 - 0.112: 22 0.112 - 0.140: 3 Chirality restraints: 494 Sorted by residual: chirality pdb=" CB VAL A 34 " pdb=" CA VAL A 34 " pdb=" CG1 VAL A 34 " pdb=" CG2 VAL A 34 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.90e-01 chirality pdb=" CA TRP A 118 " pdb=" N TRP A 118 " pdb=" C TRP A 118 " pdb=" CB TRP A 118 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 3.97e-01 chirality pdb=" CA ILE A 42 " pdb=" N ILE A 42 " pdb=" C ILE A 42 " pdb=" CB ILE A 42 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.51e-01 ... (remaining 491 not shown) Planarity restraints: 528 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 165 " 0.012 2.00e-02 2.50e+03 9.42e-03 2.22e+00 pdb=" CG TRP A 165 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP A 165 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP A 165 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 165 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 165 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 165 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 165 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 165 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 165 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 344 " -0.021 5.00e-02 4.00e+02 3.20e-02 1.64e+00 pdb=" N PRO A 345 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 345 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 345 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 326 " 0.021 5.00e-02 4.00e+02 3.20e-02 1.64e+00 pdb=" N PRO A 327 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 327 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 327 " 0.018 5.00e-02 4.00e+02 ... (remaining 525 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 770 2.80 - 3.33: 3121 3.33 - 3.85: 5165 3.85 - 4.38: 5156 4.38 - 4.90: 9530 Nonbonded interactions: 23742 Sorted by model distance: nonbonded pdb=" O ILE A 140 " pdb=" OG1 THR A 143 " model vdw 2.277 3.040 nonbonded pdb=" OG SER A 63 " pdb=" O LEU A 112 " model vdw 2.277 3.040 nonbonded pdb=" NH1 ARG A 126 " pdb=" O GLU A 355 " model vdw 2.432 3.120 nonbonded pdb=" O PHE A 51 " pdb=" OG SER A 55 " model vdw 2.443 3.040 nonbonded pdb=" NE ARG A 28 " pdb=" OE1 GLN A 114 " model vdw 2.459 3.120 ... (remaining 23737 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.700 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: 0.000 Set scattering table: 0.010 Process input model: 3.390 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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: 0.010 Load rotamer database and sin/cos tables:0.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 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 : 0.003 0.029 3152 Z= 0.135 Angle : 0.598 8.048 4300 Z= 0.301 Chirality : 0.038 0.140 494 Planarity : 0.004 0.032 528 Dihedral : 13.266 73.551 1045 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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 are not related in a simple way. whole: 3.60 (0.42), residues: 405 helix: 2.95 (0.28), residues: 331 sheet: None (None), residues: 0 loop : -0.43 (0.66), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 319 TYR 0.011 0.001 TYR A 24 PHE 0.017 0.001 PHE A 349 TRP 0.025 0.002 TRP A 165 HIS 0.001 0.000 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 3152) covalent geometry : angle 0.59818 ( 4300) hydrogen bonds : bond 0.09658 ( 259) hydrogen bonds : angle 3.98449 ( 774) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.118 Fit side-chains REVERT: A 221 LEU cc_start: 0.8745 (mm) cc_final: 0.8489 (mt) REVERT: A 418 ARG cc_start: 0.7780 (tpp80) cc_final: 0.7431 (tpp80) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.0453 time to fit residues: 3.6271 Evaluate side-chains 53 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.4980 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 0.0270 chunk 30 optimal weight: 0.3980 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.4638 ------------------------------------------------------------------------------- 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 = 0.3652 r_free = 0.3652 target = 0.129273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.115411 restraints weight = 6274.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.118240 restraints weight = 3116.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.120380 restraints weight = 1921.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.121802 restraints weight = 1348.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.122887 restraints weight = 1037.469| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.0868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3152 Z= 0.128 Angle : 0.591 10.666 4300 Z= 0.289 Chirality : 0.039 0.124 494 Planarity : 0.004 0.034 528 Dihedral : 3.702 13.638 432 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.20 % Allowed : 10.06 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.53 (0.42), residues: 405 helix: 2.84 (0.28), residues: 334 sheet: None (None), residues: 0 loop : -0.30 (0.69), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 126 TYR 0.011 0.001 TYR A 24 PHE 0.027 0.002 PHE A 250 TRP 0.016 0.001 TRP A 165 HIS 0.001 0.000 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 3152) covalent geometry : angle 0.59067 ( 4300) hydrogen bonds : bond 0.05091 ( 259) hydrogen bonds : angle 3.62048 ( 774) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.070 Fit side-chains revert: symmetry clash REVERT: A 221 LEU cc_start: 0.8754 (mm) cc_final: 0.8552 (mt) REVERT: A 418 ARG cc_start: 0.7747 (tpp80) cc_final: 0.7531 (tpp80) outliers start: 7 outliers final: 5 residues processed: 54 average time/residue: 0.0334 time to fit residues: 2.3478 Evaluate side-chains 52 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 274 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 2 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3626 r_free = 0.3626 target = 0.126850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.113279 restraints weight = 6278.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.116027 restraints weight = 3133.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.118049 restraints weight = 1938.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.119393 restraints weight = 1363.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.120488 restraints weight = 1062.798| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3152 Z= 0.142 Angle : 0.593 9.504 4300 Z= 0.292 Chirality : 0.039 0.130 494 Planarity : 0.005 0.036 528 Dihedral : 3.707 13.967 432 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.52 % Allowed : 11.32 % Favored : 86.16 % 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 are not related in a simple way. whole: 3.43 (0.42), residues: 405 helix: 2.75 (0.28), residues: 334 sheet: None (None), residues: 0 loop : -0.21 (0.72), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 319 TYR 0.014 0.001 TYR A 24 PHE 0.025 0.002 PHE A 250 TRP 0.015 0.001 TRP A 165 HIS 0.002 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 3152) covalent geometry : angle 0.59264 ( 4300) hydrogen bonds : bond 0.05422 ( 259) hydrogen bonds : angle 3.59148 ( 774) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.067 Fit side-chains REVERT: A 221 LEU cc_start: 0.8815 (mm) cc_final: 0.8548 (mt) outliers start: 8 outliers final: 7 residues processed: 53 average time/residue: 0.0459 time to fit residues: 3.1306 Evaluate side-chains 55 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 403 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 6 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3623 r_free = 0.3623 target = 0.126435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.113058 restraints weight = 6235.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.115867 restraints weight = 3097.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.117886 restraints weight = 1904.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.119166 restraints weight = 1336.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.120216 restraints weight = 1044.338| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3152 Z= 0.140 Angle : 0.607 11.329 4300 Z= 0.295 Chirality : 0.039 0.131 494 Planarity : 0.005 0.038 528 Dihedral : 3.732 13.867 432 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.20 % Allowed : 13.84 % Favored : 83.96 % 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 are not related in a simple way. whole: 3.40 (0.42), residues: 405 helix: 2.73 (0.28), residues: 334 sheet: None (None), residues: 0 loop : -0.21 (0.73), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 126 TYR 0.014 0.001 TYR A 24 PHE 0.025 0.001 PHE A 250 TRP 0.016 0.001 TRP A 165 HIS 0.001 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 3152) covalent geometry : angle 0.60690 ( 4300) hydrogen bonds : bond 0.05392 ( 259) hydrogen bonds : angle 3.55642 ( 774) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.065 Fit side-chains REVERT: A 221 LEU cc_start: 0.8838 (mm) cc_final: 0.8521 (mt) outliers start: 7 outliers final: 5 residues processed: 54 average time/residue: 0.0340 time to fit residues: 2.3947 Evaluate side-chains 49 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 274 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 20 optimal weight: 0.0870 chunk 21 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 = 0.3620 r_free = 0.3620 target = 0.126350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.113085 restraints weight = 6253.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.115891 restraints weight = 3102.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.117769 restraints weight = 1894.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.119310 restraints weight = 1341.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.120242 restraints weight = 1021.457| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3152 Z= 0.139 Angle : 0.606 11.095 4300 Z= 0.299 Chirality : 0.039 0.136 494 Planarity : 0.005 0.039 528 Dihedral : 3.769 13.683 432 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.52 % Allowed : 14.47 % Favored : 83.02 % 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 are not related in a simple way. whole: 3.27 (0.42), residues: 405 helix: 2.60 (0.29), residues: 336 sheet: None (None), residues: 0 loop : -0.10 (0.75), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 126 TYR 0.014 0.001 TYR A 24 PHE 0.026 0.001 PHE A 250 TRP 0.020 0.001 TRP A 107 HIS 0.001 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 3152) covalent geometry : angle 0.60564 ( 4300) hydrogen bonds : bond 0.05318 ( 259) hydrogen bonds : angle 3.64610 ( 774) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.069 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 54 average time/residue: 0.0418 time to fit residues: 3.0364 Evaluate side-chains 52 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 274 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 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 = 0.3605 r_free = 0.3605 target = 0.125157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.111790 restraints weight = 6251.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.114604 restraints weight = 3138.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.116563 restraints weight = 1930.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.117662 restraints weight = 1356.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.118755 restraints weight = 1082.759| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3152 Z= 0.150 Angle : 0.628 12.173 4300 Z= 0.311 Chirality : 0.041 0.141 494 Planarity : 0.005 0.038 528 Dihedral : 3.865 13.661 432 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.83 % Allowed : 16.04 % Favored : 81.13 % 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 are not related in a simple way. whole: 3.18 (0.43), residues: 405 helix: 2.54 (0.29), residues: 336 sheet: None (None), residues: 0 loop : -0.17 (0.75), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 319 TYR 0.016 0.001 TYR A 24 PHE 0.028 0.002 PHE A 250 TRP 0.017 0.001 TRP A 165 HIS 0.002 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 3152) covalent geometry : angle 0.62839 ( 4300) hydrogen bonds : bond 0.05561 ( 259) hydrogen bonds : angle 3.72530 ( 774) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.113 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 53 average time/residue: 0.0425 time to fit residues: 3.0772 Evaluate side-chains 49 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 274 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 0 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 29 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 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 = 0.3642 r_free = 0.3642 target = 0.127297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.114017 restraints weight = 6166.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.116767 restraints weight = 3096.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.118612 restraints weight = 1910.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.120038 restraints weight = 1368.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.121085 restraints weight = 1058.041| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 3152 Z= 0.160 Angle : 0.638 12.344 4300 Z= 0.315 Chirality : 0.040 0.142 494 Planarity : 0.005 0.038 528 Dihedral : 3.895 13.772 432 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.20 % Allowed : 16.04 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.12 (0.43), residues: 405 helix: 2.50 (0.29), residues: 336 sheet: None (None), residues: 0 loop : -0.17 (0.76), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 10 TYR 0.016 0.001 TYR A 24 PHE 0.027 0.002 PHE A 250 TRP 0.018 0.001 TRP A 165 HIS 0.002 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 3152) covalent geometry : angle 0.63831 ( 4300) hydrogen bonds : bond 0.05708 ( 259) hydrogen bonds : angle 3.73825 ( 774) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.068 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 51 average time/residue: 0.0327 time to fit residues: 2.1744 Evaluate side-chains 51 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 274 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 35 optimal weight: 0.0870 chunk 17 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 19 optimal weight: 0.0770 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 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 = 0.3686 r_free = 0.3686 target = 0.130827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.117423 restraints weight = 6197.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.120175 restraints weight = 3081.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.122165 restraints weight = 1895.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.123510 restraints weight = 1338.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.124566 restraints weight = 1045.734| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 3152 Z= 0.133 Angle : 0.640 14.899 4300 Z= 0.309 Chirality : 0.039 0.149 494 Planarity : 0.005 0.040 528 Dihedral : 3.831 13.818 432 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.89 % Allowed : 17.30 % Favored : 80.82 % 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 are not related in a simple way. whole: 3.19 (0.43), residues: 405 helix: 2.55 (0.29), residues: 336 sheet: None (None), residues: 0 loop : -0.18 (0.76), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 418 TYR 0.013 0.001 TYR A 24 PHE 0.027 0.001 PHE A 250 TRP 0.020 0.001 TRP A 165 HIS 0.001 0.000 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 3152) covalent geometry : angle 0.63961 ( 4300) hydrogen bonds : bond 0.05062 ( 259) hydrogen bonds : angle 3.64615 ( 774) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.067 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 51 average time/residue: 0.0279 time to fit residues: 1.9437 Evaluate side-chains 50 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 274 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 11 optimal weight: 0.3980 chunk 28 optimal weight: 0.0030 chunk 13 optimal weight: 0.7980 chunk 10 optimal weight: 50.0000 chunk 37 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 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 = 0.3671 r_free = 0.3671 target = 0.129656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.116493 restraints weight = 6159.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.119352 restraints weight = 2985.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.121378 restraints weight = 1795.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.122733 restraints weight = 1239.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.123860 restraints weight = 955.243| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 3152 Z= 0.140 Angle : 0.638 14.615 4300 Z= 0.312 Chirality : 0.040 0.156 494 Planarity : 0.005 0.039 528 Dihedral : 3.811 13.913 432 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.20 % Allowed : 17.30 % Favored : 80.50 % 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 are not related in a simple way. whole: 3.18 (0.43), residues: 405 helix: 2.54 (0.29), residues: 336 sheet: None (None), residues: 0 loop : -0.16 (0.76), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 418 TYR 0.015 0.001 TYR A 24 PHE 0.028 0.002 PHE A 250 TRP 0.022 0.002 TRP A 107 HIS 0.001 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 3152) covalent geometry : angle 0.63780 ( 4300) hydrogen bonds : bond 0.05151 ( 259) hydrogen bonds : angle 3.65339 ( 774) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.066 Fit side-chains outliers start: 7 outliers final: 7 residues processed: 49 average time/residue: 0.0369 time to fit residues: 2.4786 Evaluate side-chains 53 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 274 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 10 optimal weight: 0.7980 chunk 11 optimal weight: 0.0270 chunk 18 optimal weight: 0.0010 chunk 8 optimal weight: 3.9990 chunk 20 optimal weight: 0.0370 chunk 2 optimal weight: 0.5980 chunk 30 optimal weight: 0.0000 chunk 4 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.1326 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 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 = 0.3739 r_free = 0.3739 target = 0.134908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.122402 restraints weight = 6140.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.125207 restraints weight = 2995.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.127031 restraints weight = 1799.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.128601 restraints weight = 1265.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.129504 restraints weight = 941.676| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 3152 Z= 0.123 Angle : 0.640 17.192 4300 Z= 0.305 Chirality : 0.038 0.157 494 Planarity : 0.005 0.040 528 Dihedral : 3.736 14.088 432 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.57 % Allowed : 17.92 % Favored : 80.50 % 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 are not related in a simple way. whole: 3.27 (0.43), residues: 405 helix: 2.61 (0.29), residues: 336 sheet: None (None), residues: 0 loop : -0.17 (0.75), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 126 TYR 0.011 0.001 TYR A 24 PHE 0.029 0.001 PHE A 250 TRP 0.021 0.002 TRP A 165 HIS 0.000 0.000 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 3152) covalent geometry : angle 0.64035 ( 4300) hydrogen bonds : bond 0.04142 ( 259) hydrogen bonds : angle 3.64747 ( 774) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.065 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 49 average time/residue: 0.0255 time to fit residues: 1.7374 Evaluate side-chains 46 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 221 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 38 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 22 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 114 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 = 0.3669 r_free = 0.3669 target = 0.129677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.117009 restraints weight = 6270.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.119717 restraints weight = 3097.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.121710 restraints weight = 1879.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.122740 restraints weight = 1294.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.123915 restraints weight = 1028.749| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 3152 Z= 0.143 Angle : 0.671 15.017 4300 Z= 0.319 Chirality : 0.040 0.163 494 Planarity : 0.005 0.039 528 Dihedral : 3.746 13.520 432 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.57 % Allowed : 18.24 % Favored : 80.19 % 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 are not related in a simple way. whole: 3.26 (0.43), residues: 405 helix: 2.59 (0.29), residues: 336 sheet: None (None), residues: 0 loop : -0.12 (0.75), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 300 TYR 0.015 0.001 TYR A 24 PHE 0.028 0.002 PHE A 250 TRP 0.017 0.001 TRP A 165 HIS 0.002 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 3152) covalent geometry : angle 0.67077 ( 4300) hydrogen bonds : bond 0.05007 ( 259) hydrogen bonds : angle 3.66952 ( 774) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 516.40 seconds wall clock time: 9 minutes 33.76 seconds (573.76 seconds total)