Starting phenix.real_space_refine on Wed Sep 17 04:58:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jj3_61516/09_2025/9jj3_61516.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jj3_61516/09_2025/9jj3_61516.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jj3_61516/09_2025/9jj3_61516.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jj3_61516/09_2025/9jj3_61516.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jj3_61516/09_2025/9jj3_61516.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jj3_61516/09_2025/9jj3_61516.map" } resolution = 3.03 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= 0.005 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 26 5.16 5 C 3004 2.51 5 N 752 2.21 5 O 804 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4586 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 2293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2293 Classifications: {'peptide': 291} Link IDs: {'PTRANS': 5, 'TRANS': 285} Chain breaks: 1 Chain: "A" Number of atoms: 2293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2293 Classifications: {'peptide': 291} Link IDs: {'PTRANS': 5, 'TRANS': 285} Chain breaks: 1 Time building chain proxies: 1.35, per 1000 atoms: 0.29 Number of scatterers: 4586 At special positions: 0 Unit cell: (53.95, 83.83, 100.43, 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 26 16.00 O 804 8.00 N 752 7.00 C 3004 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: 0.42 Conformation dependent library (CDL) restraints added in 172.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1108 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 3 sheets defined 70.3% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'B' and resid 101 through 135 removed outlier: 4.063A pdb=" N LEU B 105 " --> pdb=" O GLN B 101 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS B 106 " --> pdb=" O ARG B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 165 removed outlier: 3.705A pdb=" N MET B 141 " --> pdb=" O SER B 137 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASP B 143 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ALA B 144 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LEU B 145 " --> pdb=" O MET B 141 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N HIS B 146 " --> pdb=" O THR B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 206 removed outlier: 3.786A pdb=" N VAL B 181 " --> pdb=" O HIS B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 236 removed outlier: 3.778A pdb=" N LEU B 219 " --> pdb=" O GLY B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 297 Processing helix chain 'B' and resid 303 through 332 removed outlier: 4.337A pdb=" N ILE B 307 " --> pdb=" O ILE B 303 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ARG B 322 " --> pdb=" O PHE B 318 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ILE B 323 " --> pdb=" O THR B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 350 Processing helix chain 'B' and resid 386 through 402 Processing helix chain 'A' and resid 101 through 135 removed outlier: 3.873A pdb=" N LEU A 105 " --> pdb=" O GLN A 101 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS A 106 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 142 removed outlier: 3.721A pdb=" N MET A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 165 removed outlier: 4.265A pdb=" N HIS A 146 " --> pdb=" O THR A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 206 removed outlier: 3.804A pdb=" N VAL A 181 " --> pdb=" O HIS A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 236 removed outlier: 3.853A pdb=" N LEU A 219 " --> pdb=" O GLY A 215 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 297 Processing helix chain 'A' and resid 303 through 332 removed outlier: 4.556A pdb=" N ILE A 307 " --> pdb=" O ILE A 303 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ARG A 322 " --> pdb=" O PHE A 318 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ILE A 323 " --> pdb=" O THR A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 350 Processing helix chain 'A' and resid 386 through 402 Processing sheet with id=AA1, first strand: chain 'B' and resid 356 through 366 removed outlier: 6.121A pdb=" N VAL B 357 " --> pdb=" O GLN B 377 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N GLN B 377 " --> pdb=" O VAL B 357 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ASP B 359 " --> pdb=" O HIS B 375 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LYS B 369 " --> pdb=" O LEU B 365 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N SER B 370 " --> pdb=" O ARG B 405 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N THR B 407 " --> pdb=" O SER B 370 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ALA B 372 " --> pdb=" O THR B 407 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 356 through 357 removed outlier: 3.649A pdb=" N SER A 356 " --> pdb=" O GLN A 377 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 362 through 366 removed outlier: 7.013A pdb=" N LYS A 369 " --> pdb=" O LEU A 365 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N SER A 370 " --> pdb=" O ARG A 405 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N THR A 407 " --> pdb=" O SER A 370 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ALA A 372 " --> pdb=" O THR A 407 " (cutoff:3.500A) 329 hydrogen bonds defined for protein. 987 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: 0.56 Time building geometry restraints manager: 0.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1415 1.34 - 1.46: 668 1.46 - 1.57: 2539 1.57 - 1.69: 2 1.69 - 1.81: 46 Bond restraints: 4670 Sorted by residual: bond pdb=" CB PRO B 299 " pdb=" CG PRO B 299 " ideal model delta sigma weight residual 1.492 1.629 -0.137 5.00e-02 4.00e+02 7.51e+00 bond pdb=" CB PRO A 299 " pdb=" CG PRO A 299 " ideal model delta sigma weight residual 1.492 1.622 -0.130 5.00e-02 4.00e+02 6.77e+00 bond pdb=" CG PRO A 299 " pdb=" CD PRO A 299 " ideal model delta sigma weight residual 1.503 1.558 -0.055 3.40e-02 8.65e+02 2.62e+00 bond pdb=" CG PRO B 299 " pdb=" CD PRO B 299 " ideal model delta sigma weight residual 1.503 1.551 -0.048 3.40e-02 8.65e+02 1.97e+00 bond pdb=" CB ASN A 210 " pdb=" CG ASN A 210 " ideal model delta sigma weight residual 1.516 1.546 -0.030 2.50e-02 1.60e+03 1.46e+00 ... (remaining 4665 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 6239 2.41 - 4.83: 76 4.83 - 7.24: 13 7.24 - 9.66: 4 9.66 - 12.07: 4 Bond angle restraints: 6336 Sorted by residual: angle pdb=" CA PRO B 299 " pdb=" N PRO B 299 " pdb=" CD PRO B 299 " ideal model delta sigma weight residual 112.00 101.38 10.62 1.40e+00 5.10e-01 5.75e+01 angle pdb=" CA PRO A 299 " pdb=" N PRO A 299 " pdb=" CD PRO A 299 " ideal model delta sigma weight residual 112.00 101.79 10.21 1.40e+00 5.10e-01 5.32e+01 angle pdb=" CA LYS A 298 " pdb=" CB LYS A 298 " pdb=" CG LYS A 298 " ideal model delta sigma weight residual 114.10 121.59 -7.49 2.00e+00 2.50e-01 1.40e+01 angle pdb=" CA MET A 209 " pdb=" CB MET A 209 " pdb=" CG MET A 209 " ideal model delta sigma weight residual 114.10 121.51 -7.41 2.00e+00 2.50e-01 1.37e+01 angle pdb=" C MET A 209 " pdb=" N ASN A 210 " pdb=" CA ASN A 210 " ideal model delta sigma weight residual 121.54 128.50 -6.96 1.91e+00 2.74e-01 1.33e+01 ... (remaining 6331 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.12: 2247 13.12 - 26.23: 327 26.23 - 39.35: 144 39.35 - 52.46: 49 52.46 - 65.57: 13 Dihedral angle restraints: 2780 sinusoidal: 1070 harmonic: 1710 Sorted by residual: dihedral pdb=" CA ASN A 210 " pdb=" C ASN A 210 " pdb=" N TYR A 211 " pdb=" CA TYR A 211 " ideal model delta harmonic sigma weight residual 180.00 161.20 18.80 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA ASN B 210 " pdb=" C ASN B 210 " pdb=" N TYR B 211 " pdb=" CA TYR B 211 " ideal model delta harmonic sigma weight residual 180.00 162.42 17.58 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA ASN A 281 " pdb=" CB ASN A 281 " pdb=" CG ASN A 281 " pdb=" OD1 ASN A 281 " ideal model delta sinusoidal sigma weight residual 120.00 -176.08 -63.92 2 2.00e+01 2.50e-03 9.68e+00 ... (remaining 2777 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 562 0.039 - 0.078: 168 0.078 - 0.116: 33 0.116 - 0.155: 12 0.155 - 0.194: 5 Chirality restraints: 780 Sorted by residual: chirality pdb=" CB THR B 115 " pdb=" CA THR B 115 " pdb=" OG1 THR B 115 " pdb=" CG2 THR B 115 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.42e-01 chirality pdb=" CG LEU B 360 " pdb=" CB LEU B 360 " pdb=" CD1 LEU B 360 " pdb=" CD2 LEU B 360 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.85e-01 chirality pdb=" CB THR A 115 " pdb=" CA THR A 115 " pdb=" OG1 THR A 115 " pdb=" CG2 THR A 115 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.15e-01 ... (remaining 777 not shown) Planarity restraints: 762 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 298 " -0.078 5.00e-02 4.00e+02 1.11e-01 1.99e+01 pdb=" N PRO B 299 " 0.192 5.00e-02 4.00e+02 pdb=" CA PRO B 299 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO B 299 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 298 " 0.076 5.00e-02 4.00e+02 1.08e-01 1.86e+01 pdb=" N PRO A 299 " -0.186 5.00e-02 4.00e+02 pdb=" CA PRO A 299 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO A 299 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 360 " -0.009 2.00e-02 2.50e+03 1.84e-02 3.38e+00 pdb=" C LEU B 360 " 0.032 2.00e-02 2.50e+03 pdb=" O LEU B 360 " -0.012 2.00e-02 2.50e+03 pdb=" N ASN B 361 " -0.010 2.00e-02 2.50e+03 ... (remaining 759 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1005 2.78 - 3.31: 4809 3.31 - 3.84: 7671 3.84 - 4.37: 8288 4.37 - 4.90: 14298 Nonbonded interactions: 36071 Sorted by model distance: nonbonded pdb=" O TRP B 162 " pdb=" OG SER B 165 " model vdw 2.247 3.040 nonbonded pdb=" N GLU A 388 " pdb=" OE1 GLU A 388 " model vdw 2.249 3.120 nonbonded pdb=" N GLU B 388 " pdb=" OE1 GLU B 388 " model vdw 2.250 3.120 nonbonded pdb=" O TRP A 162 " pdb=" OG SER A 165 " model vdw 2.251 3.040 nonbonded pdb=" O MET B 209 " pdb=" ND2 ASN B 210 " model vdw 2.253 3.120 ... (remaining 36066 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 2.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.920 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 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 : 0.004 0.137 4670 Z= 0.154 Angle : 0.712 12.069 6336 Z= 0.377 Chirality : 0.042 0.194 780 Planarity : 0.006 0.111 762 Dihedral : 16.420 65.575 1672 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 0.20 % Allowed : 34.19 % Favored : 65.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.17 (0.38), residues: 574 helix: 2.64 (0.26), residues: 382 sheet: -0.89 (0.78), residues: 52 loop : -1.12 (0.63), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 205 TYR 0.010 0.001 TYR B 404 PHE 0.014 0.001 PHE A 312 TRP 0.004 0.001 TRP A 162 HIS 0.001 0.000 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 4670) covalent geometry : angle 0.71194 ( 6336) hydrogen bonds : bond 0.13583 ( 329) hydrogen bonds : angle 4.84417 ( 987) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 112 time to evaluate : 0.138 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 113 average time/residue: 0.0382 time to fit residues: 6.2211 Evaluate side-chains 110 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 54 optimal weight: 0.0010 chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 107 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 = 0.3500 r_free = 0.3500 target = 0.099965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.079284 restraints weight = 9129.736| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 3.08 r_work: 0.2958 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 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 0.062 4670 Z= 0.140 Angle : 0.585 8.694 6336 Z= 0.309 Chirality : 0.041 0.140 780 Planarity : 0.004 0.040 762 Dihedral : 4.090 17.880 624 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 5.53 % Allowed : 27.87 % Favored : 66.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.32 (0.37), residues: 574 helix: 2.72 (0.25), residues: 384 sheet: -0.93 (0.79), residues: 52 loop : -0.97 (0.62), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 205 TYR 0.011 0.001 TYR A 404 PHE 0.014 0.001 PHE A 312 TRP 0.005 0.001 TRP B 162 HIS 0.001 0.001 HIS B 146 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 4670) covalent geometry : angle 0.58513 ( 6336) hydrogen bonds : bond 0.04343 ( 329) hydrogen bonds : angle 3.73186 ( 987) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 113 time to evaluate : 0.249 Fit side-chains REVERT: B 210 ASN cc_start: 0.8545 (OUTLIER) cc_final: 0.8300 (p0) REVERT: B 285 SER cc_start: 0.8928 (m) cc_final: 0.8514 (t) REVERT: B 359 ASP cc_start: 0.7849 (t0) cc_final: 0.7420 (t0) REVERT: A 189 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8482 (tt) REVERT: A 285 SER cc_start: 0.8916 (m) cc_final: 0.8501 (t) REVERT: A 302 LYS cc_start: 0.8948 (tptm) cc_final: 0.8617 (tptp) REVERT: A 359 ASP cc_start: 0.7945 (t0) cc_final: 0.7595 (t0) outliers start: 28 outliers final: 13 residues processed: 131 average time/residue: 0.0418 time to fit residues: 7.9868 Evaluate side-chains 124 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain B residue 214 ASN Chi-restraints excluded: chain B residue 297 PHE Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 406 CYS Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 297 PHE Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 406 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 4 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 29 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 107 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 = 0.3441 r_free = 0.3441 target = 0.096444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.075673 restraints weight = 9145.560| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 3.06 r_work: 0.2895 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 4670 Z= 0.206 Angle : 0.600 7.507 6336 Z= 0.322 Chirality : 0.042 0.140 780 Planarity : 0.004 0.039 762 Dihedral : 4.174 16.757 624 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 5.53 % Allowed : 27.47 % Favored : 67.00 % 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 aren not related in a simple way. whole: 2.46 (0.37), residues: 574 helix: 2.71 (0.25), residues: 382 sheet: -0.86 (0.80), residues: 52 loop : -0.49 (0.63), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 178 TYR 0.013 0.001 TYR B 121 PHE 0.012 0.001 PHE A 312 TRP 0.005 0.001 TRP B 162 HIS 0.002 0.000 HIS B 177 Details of bonding type rmsd covalent geometry : bond 0.00482 ( 4670) covalent geometry : angle 0.59989 ( 6336) hydrogen bonds : bond 0.04741 ( 329) hydrogen bonds : angle 3.82568 ( 987) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 105 time to evaluate : 0.189 Fit side-chains REVERT: B 189 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8539 (tt) REVERT: B 208 HIS cc_start: 0.8114 (m90) cc_final: 0.7880 (m90) REVERT: B 210 ASN cc_start: 0.8529 (OUTLIER) cc_final: 0.8302 (p0) REVERT: B 285 SER cc_start: 0.8982 (m) cc_final: 0.8629 (t) REVERT: A 189 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8530 (tt) REVERT: A 285 SER cc_start: 0.8979 (m) cc_final: 0.8605 (t) REVERT: A 302 LYS cc_start: 0.9056 (tptm) cc_final: 0.8810 (tptp) REVERT: A 359 ASP cc_start: 0.8051 (t0) cc_final: 0.7518 (t0) outliers start: 28 outliers final: 18 residues processed: 129 average time/residue: 0.0457 time to fit residues: 8.4969 Evaluate side-chains 123 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain B residue 214 ASN Chi-restraints excluded: chain B residue 297 PHE Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 406 CYS Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 297 PHE Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 406 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 1.9990 chunk 10 optimal weight: 0.2980 chunk 55 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3497 r_free = 0.3497 target = 0.098597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.078316 restraints weight = 9077.589| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.98 r_work: 0.2966 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4670 Z= 0.140 Angle : 0.573 7.451 6336 Z= 0.304 Chirality : 0.040 0.141 780 Planarity : 0.004 0.044 762 Dihedral : 4.075 15.910 624 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 5.34 % Allowed : 28.85 % Favored : 65.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.40 (0.37), residues: 574 helix: 2.75 (0.25), residues: 384 sheet: -0.99 (0.78), residues: 52 loop : -0.78 (0.63), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 405 TYR 0.012 0.001 TYR A 404 PHE 0.014 0.001 PHE A 312 TRP 0.005 0.001 TRP B 162 HIS 0.009 0.001 HIS A 395 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 4670) covalent geometry : angle 0.57271 ( 6336) hydrogen bonds : bond 0.04251 ( 329) hydrogen bonds : angle 3.66371 ( 987) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 117 time to evaluate : 0.189 Fit side-chains REVERT: B 189 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8481 (tt) REVERT: B 210 ASN cc_start: 0.8580 (OUTLIER) cc_final: 0.8144 (p0) REVERT: B 285 SER cc_start: 0.8977 (m) cc_final: 0.8613 (t) REVERT: B 302 LYS cc_start: 0.9082 (tptm) cc_final: 0.8833 (tptp) REVERT: B 359 ASP cc_start: 0.7929 (t0) cc_final: 0.7681 (t0) REVERT: A 106 LYS cc_start: 0.9097 (mmtt) cc_final: 0.8751 (mttt) REVERT: A 189 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8477 (tt) REVERT: A 285 SER cc_start: 0.8944 (m) cc_final: 0.8555 (t) REVERT: A 359 ASP cc_start: 0.8013 (t0) cc_final: 0.7436 (t0) REVERT: A 360 LEU cc_start: 0.9104 (tt) cc_final: 0.8776 (tt) outliers start: 27 outliers final: 21 residues processed: 136 average time/residue: 0.0538 time to fit residues: 10.0589 Evaluate side-chains 129 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain B residue 214 ASN Chi-restraints excluded: chain B residue 297 PHE Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 406 CYS Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 297 PHE Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 406 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 32 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 chunk 57 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 3 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 = 0.3500 r_free = 0.3500 target = 0.098695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.078142 restraints weight = 9129.688| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 3.04 r_work: 0.2955 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4670 Z= 0.146 Angle : 0.575 7.333 6336 Z= 0.311 Chirality : 0.041 0.164 780 Planarity : 0.003 0.044 762 Dihedral : 4.078 16.694 624 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 6.52 % Allowed : 28.46 % Favored : 65.02 % 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 aren not related in a simple way. whole: 2.43 (0.37), residues: 574 helix: 2.76 (0.25), residues: 384 sheet: -1.10 (0.78), residues: 52 loop : -0.68 (0.64), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 205 TYR 0.012 0.001 TYR A 404 PHE 0.014 0.001 PHE A 312 TRP 0.005 0.001 TRP A 162 HIS 0.009 0.001 HIS B 395 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 4670) covalent geometry : angle 0.57514 ( 6336) hydrogen bonds : bond 0.04248 ( 329) hydrogen bonds : angle 3.65273 ( 987) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 112 time to evaluate : 0.240 Fit side-chains REVERT: B 189 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8477 (tt) REVERT: B 204 GLN cc_start: 0.7657 (tp40) cc_final: 0.7281 (mp10) REVERT: B 210 ASN cc_start: 0.8627 (OUTLIER) cc_final: 0.8312 (p0) REVERT: B 285 SER cc_start: 0.8980 (m) cc_final: 0.8599 (t) REVERT: A 189 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8477 (tt) REVERT: A 285 SER cc_start: 0.8945 (m) cc_final: 0.8577 (t) REVERT: A 359 ASP cc_start: 0.8062 (t0) cc_final: 0.7448 (t0) REVERT: A 360 LEU cc_start: 0.9156 (tt) cc_final: 0.8866 (tt) outliers start: 33 outliers final: 25 residues processed: 135 average time/residue: 0.0491 time to fit residues: 9.4354 Evaluate side-chains 139 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 111 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 297 PHE Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 406 CYS Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 297 PHE Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 406 CYS Chi-restraints excluded: chain A residue 407 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 15 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 29 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3475 r_free = 0.3475 target = 0.097598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.076859 restraints weight = 9305.045| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 3.08 r_work: 0.2933 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4670 Z= 0.166 Angle : 0.585 7.210 6336 Z= 0.315 Chirality : 0.041 0.156 780 Planarity : 0.004 0.045 762 Dihedral : 4.077 16.915 624 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 5.93 % Allowed : 30.04 % Favored : 64.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.52 (0.37), residues: 574 helix: 2.78 (0.25), residues: 380 sheet: -1.14 (0.77), residues: 52 loop : -0.35 (0.63), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 205 TYR 0.012 0.001 TYR B 404 PHE 0.014 0.001 PHE A 312 TRP 0.005 0.001 TRP A 162 HIS 0.008 0.001 HIS B 395 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 4670) covalent geometry : angle 0.58544 ( 6336) hydrogen bonds : bond 0.04370 ( 329) hydrogen bonds : angle 3.66835 ( 987) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 107 time to evaluate : 0.222 Fit side-chains REVERT: B 189 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8457 (tt) REVERT: B 204 GLN cc_start: 0.7636 (tp40) cc_final: 0.7261 (mp10) REVERT: B 210 ASN cc_start: 0.8544 (OUTLIER) cc_final: 0.8050 (p0) REVERT: B 285 SER cc_start: 0.8972 (m) cc_final: 0.8605 (t) REVERT: B 359 ASP cc_start: 0.8241 (t0) cc_final: 0.7658 (t0) REVERT: A 189 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8473 (tt) REVERT: A 216 ASP cc_start: 0.8304 (t70) cc_final: 0.8004 (t0) REVERT: A 285 SER cc_start: 0.8959 (m) cc_final: 0.8603 (t) REVERT: A 359 ASP cc_start: 0.8123 (t0) cc_final: 0.7481 (t0) REVERT: A 360 LEU cc_start: 0.9186 (tt) cc_final: 0.8947 (tt) outliers start: 30 outliers final: 24 residues processed: 130 average time/residue: 0.0489 time to fit residues: 9.0391 Evaluate side-chains 129 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 102 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 297 PHE Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 406 CYS Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 297 PHE Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 406 CYS Chi-restraints excluded: chain A residue 407 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 30 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 56 optimal weight: 0.0570 chunk 14 optimal weight: 0.0670 chunk 0 optimal weight: 10.9990 chunk 47 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 overall best weight: 0.5436 ------------------------------------------------------------------------------- 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 = 0.3512 r_free = 0.3512 target = 0.100077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.079496 restraints weight = 9135.212| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 3.06 r_work: 0.2947 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4670 Z= 0.131 Angle : 0.590 7.861 6336 Z= 0.313 Chirality : 0.040 0.153 780 Planarity : 0.003 0.044 762 Dihedral : 3.966 17.475 624 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 5.34 % Allowed : 31.23 % Favored : 63.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.46 (0.37), residues: 574 helix: 2.76 (0.25), residues: 384 sheet: -1.07 (0.77), residues: 52 loop : -0.59 (0.64), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 205 TYR 0.012 0.001 TYR B 404 PHE 0.015 0.001 PHE A 312 TRP 0.004 0.001 TRP A 162 HIS 0.007 0.001 HIS B 395 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 4670) covalent geometry : angle 0.59025 ( 6336) hydrogen bonds : bond 0.03988 ( 329) hydrogen bonds : angle 3.56239 ( 987) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 116 time to evaluate : 0.208 Fit side-chains REVERT: B 189 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8456 (tt) REVERT: B 204 GLN cc_start: 0.7525 (tp40) cc_final: 0.7133 (mp10) REVERT: B 210 ASN cc_start: 0.8514 (OUTLIER) cc_final: 0.7892 (p0) REVERT: B 285 SER cc_start: 0.8956 (m) cc_final: 0.8572 (t) REVERT: B 359 ASP cc_start: 0.8251 (t0) cc_final: 0.7658 (t0) REVERT: A 189 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8438 (tt) REVERT: A 285 SER cc_start: 0.8963 (m) cc_final: 0.8582 (t) REVERT: A 302 LYS cc_start: 0.9089 (tptm) cc_final: 0.8747 (tptp) REVERT: A 359 ASP cc_start: 0.8021 (t0) cc_final: 0.7375 (t0) REVERT: A 360 LEU cc_start: 0.9169 (tt) cc_final: 0.8820 (tt) outliers start: 27 outliers final: 21 residues processed: 130 average time/residue: 0.0432 time to fit residues: 8.0297 Evaluate side-chains 134 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 297 PHE Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 406 CYS Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 297 PHE Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 406 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 39 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.3457 r_free = 0.3457 target = 0.096943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.076455 restraints weight = 9345.908| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 3.06 r_work: 0.2918 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4670 Z= 0.185 Angle : 0.615 7.204 6336 Z= 0.333 Chirality : 0.042 0.160 780 Planarity : 0.004 0.045 762 Dihedral : 4.147 19.495 624 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 4.35 % Allowed : 34.58 % Favored : 61.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.48 (0.37), residues: 574 helix: 2.75 (0.25), residues: 384 sheet: -1.13 (0.77), residues: 52 loop : -0.48 (0.65), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 205 TYR 0.012 0.001 TYR B 404 PHE 0.012 0.001 PHE A 312 TRP 0.004 0.001 TRP A 162 HIS 0.008 0.001 HIS B 395 Details of bonding type rmsd covalent geometry : bond 0.00431 ( 4670) covalent geometry : angle 0.61515 ( 6336) hydrogen bonds : bond 0.04471 ( 329) hydrogen bonds : angle 3.67099 ( 987) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.187 Fit side-chains REVERT: B 189 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8484 (tt) REVERT: B 204 GLN cc_start: 0.7651 (tp40) cc_final: 0.7266 (mp10) REVERT: B 210 ASN cc_start: 0.8377 (OUTLIER) cc_final: 0.7847 (p0) REVERT: B 285 SER cc_start: 0.8972 (m) cc_final: 0.8614 (t) REVERT: B 359 ASP cc_start: 0.8256 (t0) cc_final: 0.7674 (t0) REVERT: A 189 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8474 (tt) REVERT: A 285 SER cc_start: 0.8956 (m) cc_final: 0.8600 (t) REVERT: A 302 LYS cc_start: 0.9151 (tptm) cc_final: 0.8820 (tptp) REVERT: A 359 ASP cc_start: 0.8130 (t0) cc_final: 0.7598 (t0) REVERT: A 360 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8955 (tt) outliers start: 22 outliers final: 18 residues processed: 120 average time/residue: 0.0455 time to fit residues: 7.8835 Evaluate side-chains 125 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 297 PHE Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 406 CYS Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 297 PHE Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 406 CYS Chi-restraints excluded: chain A residue 407 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 37 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 21 optimal weight: 0.0000 chunk 29 optimal weight: 10.0000 chunk 4 optimal weight: 7.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.5584 ------------------------------------------------------------------------------- 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 = 0.3509 r_free = 0.3509 target = 0.100372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.079716 restraints weight = 9161.487| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 3.10 r_work: 0.2957 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4670 Z= 0.135 Angle : 0.602 7.583 6336 Z= 0.322 Chirality : 0.040 0.162 780 Planarity : 0.003 0.043 762 Dihedral : 4.026 17.890 624 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 4.74 % Allowed : 33.99 % Favored : 61.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.45 (0.37), residues: 574 helix: 2.70 (0.25), residues: 386 sheet: -1.08 (0.77), residues: 52 loop : -0.49 (0.65), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 205 TYR 0.012 0.001 TYR B 404 PHE 0.015 0.001 PHE A 312 TRP 0.004 0.001 TRP A 162 HIS 0.007 0.001 HIS B 395 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 4670) covalent geometry : angle 0.60229 ( 6336) hydrogen bonds : bond 0.03974 ( 329) hydrogen bonds : angle 3.55062 ( 987) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 0.195 Fit side-chains REVERT: B 189 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8452 (tt) REVERT: B 204 GLN cc_start: 0.7548 (tp40) cc_final: 0.7158 (mp10) REVERT: B 210 ASN cc_start: 0.8361 (OUTLIER) cc_final: 0.7808 (p0) REVERT: B 285 SER cc_start: 0.8955 (m) cc_final: 0.8571 (t) REVERT: B 359 ASP cc_start: 0.8133 (t0) cc_final: 0.7521 (t0) REVERT: A 106 LYS cc_start: 0.9134 (mmtt) cc_final: 0.8791 (mttt) REVERT: A 189 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8423 (tt) REVERT: A 285 SER cc_start: 0.8961 (m) cc_final: 0.8586 (t) REVERT: A 302 LYS cc_start: 0.9092 (tptm) cc_final: 0.8887 (tptm) REVERT: A 359 ASP cc_start: 0.7939 (t0) cc_final: 0.7417 (t0) REVERT: A 360 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8889 (tt) outliers start: 24 outliers final: 20 residues processed: 131 average time/residue: 0.0480 time to fit residues: 9.0479 Evaluate side-chains 138 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 297 PHE Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 406 CYS Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 297 PHE Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 406 CYS Chi-restraints excluded: chain A residue 407 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 1.9990 chunk 6 optimal weight: 0.0870 chunk 1 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.8760 ------------------------------------------------------------------------------- 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 = 0.3492 r_free = 0.3492 target = 0.099274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.078762 restraints weight = 9239.609| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 3.09 r_work: 0.2936 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 4670 Z= 0.160 Angle : 0.624 7.347 6336 Z= 0.336 Chirality : 0.042 0.187 780 Planarity : 0.004 0.044 762 Dihedral : 4.217 19.675 624 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 4.94 % Allowed : 33.99 % Favored : 61.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.52 (0.37), residues: 574 helix: 2.76 (0.25), residues: 384 sheet: -1.01 (0.77), residues: 52 loop : -0.45 (0.65), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 205 TYR 0.011 0.001 TYR B 404 PHE 0.014 0.001 PHE A 312 TRP 0.004 0.001 TRP A 162 HIS 0.007 0.001 HIS B 395 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 4670) covalent geometry : angle 0.62431 ( 6336) hydrogen bonds : bond 0.04144 ( 329) hydrogen bonds : angle 3.57990 ( 987) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 0.192 Fit side-chains REVERT: B 189 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8460 (tt) REVERT: B 204 GLN cc_start: 0.7610 (tp40) cc_final: 0.7214 (mp10) REVERT: B 210 ASN cc_start: 0.8211 (OUTLIER) cc_final: 0.7663 (p0) REVERT: B 285 SER cc_start: 0.8956 (m) cc_final: 0.8583 (t) REVERT: B 359 ASP cc_start: 0.8202 (t0) cc_final: 0.7561 (t0) REVERT: A 189 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8443 (tt) REVERT: A 285 SER cc_start: 0.8959 (m) cc_final: 0.8591 (t) REVERT: A 302 LYS cc_start: 0.9116 (tptm) cc_final: 0.8913 (tptm) REVERT: A 359 ASP cc_start: 0.8096 (t0) cc_final: 0.7551 (t0) REVERT: A 360 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8859 (tt) outliers start: 25 outliers final: 19 residues processed: 127 average time/residue: 0.0471 time to fit residues: 8.6101 Evaluate side-chains 136 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 297 PHE Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 406 CYS Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 297 PHE Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 406 CYS Chi-restraints excluded: chain A residue 407 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 55 optimal weight: 0.0770 chunk 53 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 40 optimal weight: 8.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- 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 = 0.3519 r_free = 0.3519 target = 0.100672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.080088 restraints weight = 9158.742| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 3.09 r_work: 0.2983 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 4670 Z= 0.146 Angle : 0.616 7.451 6336 Z= 0.331 Chirality : 0.041 0.180 780 Planarity : 0.003 0.044 762 Dihedral : 4.126 19.184 624 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 4.94 % Allowed : 33.40 % Favored : 61.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.52 (0.37), residues: 574 helix: 2.74 (0.25), residues: 384 sheet: -0.83 (0.79), residues: 52 loop : -0.44 (0.64), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 205 TYR 0.011 0.001 TYR B 404 PHE 0.014 0.001 PHE A 312 TRP 0.004 0.001 TRP A 162 HIS 0.007 0.001 HIS B 395 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 4670) covalent geometry : angle 0.61599 ( 6336) hydrogen bonds : bond 0.04021 ( 329) hydrogen bonds : angle 3.56260 ( 987) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1147.78 seconds wall clock time: 20 minutes 27.05 seconds (1227.05 seconds total)