Starting phenix.real_space_refine on Tue Mar 3 11:05:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7q67_13854/03_2026/7q67_13854.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q67_13854/03_2026/7q67_13854.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7q67_13854/03_2026/7q67_13854.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q67_13854/03_2026/7q67_13854.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7q67_13854/03_2026/7q67_13854.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q67_13854/03_2026/7q67_13854.map" } resolution = 3.37 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= 1.002 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: 3 Type Number sf(0) Gaussians C 1639 2.51 5 N 440 2.21 5 O 539 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2618 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 238 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 1, 'TRANS': 31} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K Time building chain proxies: 0.29, per 1000 atoms: 0.11 Number of scatterers: 2618 At special positions: 0 Unit cell: (88.2, 49.35, 44.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 539 8.00 N 440 7.00 C 1639 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.16 Conformation dependent library (CDL) restraints added in 83.4 milliseconds 682 Ramachandran restraints generated. 341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 616 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 2 sheets defined 0.0% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 103 through 109 removed outlier: 7.008A pdb=" N ALA A 107 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N GLN C 108 " --> pdb=" O ALA A 107 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASN A 109 " --> pdb=" O GLN C 108 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ALA C 107 " --> pdb=" O PHE E 106 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N GLN E 108 " --> pdb=" O ALA C 107 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASN C 109 " --> pdb=" O GLN E 108 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ALA E 107 " --> pdb=" O PHE G 106 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N GLN G 108 " --> pdb=" O ALA E 107 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ASN E 109 " --> pdb=" O GLN G 108 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ALA G 107 " --> pdb=" O PHE I 106 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N GLN I 108 " --> pdb=" O ALA G 107 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASN G 109 " --> pdb=" O GLN I 108 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ALA I 107 " --> pdb=" O PHE K 106 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N GLN K 108 " --> pdb=" O ALA I 107 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ASN I 109 " --> pdb=" O GLN K 108 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 103 through 109 removed outlier: 7.008A pdb=" N ALA B 107 " --> pdb=" O PHE D 106 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N GLN D 108 " --> pdb=" O ALA B 107 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASN B 109 " --> pdb=" O GLN D 108 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ALA D 107 " --> pdb=" O PHE F 106 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N GLN F 108 " --> pdb=" O ALA D 107 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASN D 109 " --> pdb=" O GLN F 108 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ALA F 107 " --> pdb=" O PHE H 106 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N GLN H 108 " --> pdb=" O ALA F 107 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ASN F 109 " --> pdb=" O GLN H 108 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ALA H 107 " --> pdb=" O PHE J 106 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N GLN J 108 " --> pdb=" O ALA H 107 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASN H 109 " --> pdb=" O GLN J 108 " (cutoff:3.500A) 27 hydrogen bonds defined for protein. 81 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: 0.30 Time building geometry restraints manager: 0.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.27: 429 1.27 - 1.33: 382 1.33 - 1.40: 379 1.40 - 1.47: 522 1.47 - 1.54: 961 Bond restraints: 2673 Sorted by residual: bond pdb=" CA PHE I 114 " pdb=" CB PHE I 114 " ideal model delta sigma weight residual 1.530 1.485 0.045 1.58e-02 4.01e+03 8.10e+00 bond pdb=" CA PHE E 114 " pdb=" CB PHE E 114 " ideal model delta sigma weight residual 1.530 1.486 0.045 1.58e-02 4.01e+03 7.99e+00 bond pdb=" CA PHE K 114 " pdb=" CB PHE K 114 " ideal model delta sigma weight residual 1.530 1.486 0.045 1.58e-02 4.01e+03 7.98e+00 bond pdb=" CA PHE C 114 " pdb=" CB PHE C 114 " ideal model delta sigma weight residual 1.530 1.486 0.045 1.58e-02 4.01e+03 7.98e+00 bond pdb=" CA PHE B 114 " pdb=" CB PHE B 114 " ideal model delta sigma weight residual 1.530 1.486 0.044 1.58e-02 4.01e+03 7.91e+00 ... (remaining 2668 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.19: 3241 3.19 - 6.38: 268 6.38 - 9.56: 88 9.56 - 12.75: 0 12.75 - 15.94: 11 Bond angle restraints: 3608 Sorted by residual: angle pdb=" N PHE F 114 " pdb=" CA PHE F 114 " pdb=" CB PHE F 114 " ideal model delta sigma weight residual 109.82 100.32 9.50 1.52e+00 4.33e-01 3.90e+01 angle pdb=" N PHE D 114 " pdb=" CA PHE D 114 " pdb=" CB PHE D 114 " ideal model delta sigma weight residual 109.82 100.34 9.48 1.52e+00 4.33e-01 3.89e+01 angle pdb=" N PHE A 114 " pdb=" CA PHE A 114 " pdb=" CB PHE A 114 " ideal model delta sigma weight residual 109.82 100.34 9.48 1.52e+00 4.33e-01 3.89e+01 angle pdb=" N PHE G 114 " pdb=" CA PHE G 114 " pdb=" CB PHE G 114 " ideal model delta sigma weight residual 109.82 100.35 9.47 1.52e+00 4.33e-01 3.88e+01 angle pdb=" N PHE B 114 " pdb=" CA PHE B 114 " pdb=" CB PHE B 114 " ideal model delta sigma weight residual 109.82 100.35 9.47 1.52e+00 4.33e-01 3.88e+01 ... (remaining 3603 not shown) Histogram of dihedral angle deviations from ideal: 0.05 - 8.42: 1024 8.42 - 16.80: 263 16.80 - 25.17: 99 25.17 - 33.54: 44 33.54 - 41.92: 33 Dihedral angle restraints: 1463 sinusoidal: 495 harmonic: 968 Sorted by residual: dihedral pdb=" CA GLY E 113 " pdb=" C GLY E 113 " pdb=" N PHE E 114 " pdb=" CA PHE E 114 " ideal model delta harmonic sigma weight residual -180.00 -138.08 -41.92 0 5.00e+00 4.00e-02 7.03e+01 dihedral pdb=" CA GLY J 113 " pdb=" C GLY J 113 " pdb=" N PHE J 114 " pdb=" CA PHE J 114 " ideal model delta harmonic sigma weight residual -180.00 -138.09 -41.91 0 5.00e+00 4.00e-02 7.03e+01 dihedral pdb=" CA GLY G 113 " pdb=" C GLY G 113 " pdb=" N PHE G 114 " pdb=" CA PHE G 114 " ideal model delta harmonic sigma weight residual 180.00 -138.09 -41.91 0 5.00e+00 4.00e-02 7.03e+01 ... (remaining 1460 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 186 0.068 - 0.135: 100 0.135 - 0.203: 46 0.203 - 0.270: 20 0.270 - 0.338: 44 Chirality restraints: 396 Sorted by residual: chirality pdb=" CA ASN H 103 " pdb=" N ASN H 103 " pdb=" C ASN H 103 " pdb=" CB ASN H 103 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.85e+00 chirality pdb=" CA ASN G 103 " pdb=" N ASN G 103 " pdb=" C ASN G 103 " pdb=" CB ASN G 103 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.85e+00 chirality pdb=" CA ASN A 103 " pdb=" N ASN A 103 " pdb=" C ASN A 103 " pdb=" CB ASN A 103 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.85e+00 ... (remaining 393 not shown) Planarity restraints: 484 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 99 " -0.020 2.00e-02 2.50e+03 1.76e-02 5.40e+00 pdb=" CG PHE E 99 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE E 99 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE E 99 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE E 99 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE E 99 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE E 99 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 99 " 0.020 2.00e-02 2.50e+03 1.75e-02 5.37e+00 pdb=" CG PHE D 99 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE D 99 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE D 99 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE D 99 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE D 99 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE D 99 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 99 " -0.020 2.00e-02 2.50e+03 1.75e-02 5.35e+00 pdb=" CG PHE C 99 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE C 99 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE C 99 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE C 99 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE C 99 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE C 99 " -0.003 2.00e-02 2.50e+03 ... (remaining 481 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 903 2.80 - 3.33: 2451 3.33 - 3.85: 4656 3.85 - 4.38: 5350 4.38 - 4.90: 9886 Nonbonded interactions: 23246 Sorted by model distance: nonbonded pdb=" O SER K 101 " pdb=" OG SER K 101 " model vdw 2.280 3.040 nonbonded pdb=" O SER D 101 " pdb=" OG SER D 101 " model vdw 2.280 3.040 nonbonded pdb=" O SER H 101 " pdb=" OG SER H 101 " model vdw 2.281 3.040 nonbonded pdb=" O SER F 101 " pdb=" OG SER F 101 " model vdw 2.281 3.040 nonbonded pdb=" O SER B 101 " pdb=" OG SER B 101 " model vdw 2.281 3.040 ... (remaining 23241 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' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.510 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: 0.030 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 3.710 Find NCS groups from input model: 0.020 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: 0.000 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 5.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 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 : 0.020 0.136 2673 Z= 0.952 Angle : 2.209 15.939 3608 Z= 1.304 Chirality : 0.136 0.338 396 Planarity : 0.009 0.019 484 Dihedral : 14.467 41.919 847 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.13 % Favored : 83.87 % Rotamer: Outliers : 8.00 % Allowed : 12.00 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.23 % 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: -4.98 (0.33), residues: 341 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.79 (0.25), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.041 0.009 PHE E 99 Details of bonding type rmsd covalent geometry : bond 0.02048 ( 2673) covalent geometry : angle 2.20877 ( 3608) hydrogen bonds : bond 0.30408 ( 27) hydrogen bonds : angle 11.32760 ( 81) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 682 Ramachandran restraints generated. 341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 682 Ramachandran restraints generated. 341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 143 time to evaluate : 0.055 Fit side-chains REVERT: A 104 ASN cc_start: 0.7201 (m110) cc_final: 0.6958 (m110) outliers start: 22 outliers final: 11 residues processed: 143 average time/residue: 0.0395 time to fit residues: 6.9526 Evaluate side-chains 99 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain K residue 88 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 24 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 103 ASN ** 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 = 0.4411 r_free = 0.4411 target = 0.185245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.167199 restraints weight = 4024.421| |-----------------------------------------------------------------------------| r_work (start): 0.4200 rms_B_bonded: 3.32 r_work: 0.4093 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.4093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2673 Z= 0.205 Angle : 1.095 10.614 3608 Z= 0.558 Chirality : 0.060 0.204 396 Planarity : 0.003 0.017 484 Dihedral : 8.671 24.560 374 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 20.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.90 % Favored : 87.10 % Rotamer: Outliers : 15.64 % Allowed : 19.27 % Favored : 65.09 % 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: -4.69 (0.32), residues: 341 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.57 (0.25), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.018 0.002 PHE E 114 Details of bonding type rmsd covalent geometry : bond 0.00421 ( 2673) covalent geometry : angle 1.09510 ( 3608) hydrogen bonds : bond 0.11808 ( 27) hydrogen bonds : angle 10.29711 ( 81) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 682 Ramachandran restraints generated. 341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 682 Ramachandran restraints generated. 341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 117 time to evaluate : 0.092 Fit side-chains revert: symmetry clash REVERT: A 102 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.7770 (pp30) REVERT: A 110 LYS cc_start: 0.6480 (pttp) cc_final: 0.6198 (mmtp) REVERT: B 110 LYS cc_start: 0.6058 (pptt) cc_final: 0.5232 (mmmt) REVERT: C 87 THR cc_start: 0.5000 (p) cc_final: 0.4781 (p) REVERT: C 91 THR cc_start: 0.8743 (p) cc_final: 0.8298 (t) REVERT: F 91 THR cc_start: 0.8583 (p) cc_final: 0.8019 (t) REVERT: H 91 THR cc_start: 0.8655 (p) cc_final: 0.8165 (t) REVERT: J 91 THR cc_start: 0.8577 (p) cc_final: 0.8149 (t) outliers start: 43 outliers final: 23 residues processed: 141 average time/residue: 0.0314 time to fit residues: 5.9636 Evaluate side-chains 108 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 84 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 102 GLN Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 102 GLN Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 98 LEU Chi-restraints excluded: chain K residue 88 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 21 optimal weight: 20.0000 chunk 32 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 102 GLN ** K 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 104 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.178724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.161257 restraints weight = 4199.449| |-----------------------------------------------------------------------------| r_work (start): 0.4151 rms_B_bonded: 3.15 r_work: 0.4037 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.4037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.049 2673 Z= 0.340 Angle : 1.101 9.672 3608 Z= 0.578 Chirality : 0.066 0.217 396 Planarity : 0.004 0.017 484 Dihedral : 8.678 23.142 374 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 21.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.18 % Favored : 81.82 % Rotamer: Outliers : 17.09 % Allowed : 15.27 % Favored : 67.64 % 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: -5.09 (0.29), residues: 341 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.88 (0.22), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.022 0.004 PHE A 117 Details of bonding type rmsd covalent geometry : bond 0.00779 ( 2673) covalent geometry : angle 1.10125 ( 3608) hydrogen bonds : bond 0.11352 ( 27) hydrogen bonds : angle 9.81820 ( 81) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 682 Ramachandran restraints generated. 341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 682 Ramachandran restraints generated. 341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 99 time to evaluate : 0.132 Fit side-chains REVERT: B 104 ASN cc_start: 0.7652 (m110) cc_final: 0.6456 (t0) REVERT: C 91 THR cc_start: 0.8788 (p) cc_final: 0.8349 (t) REVERT: D 102 GLN cc_start: 0.8299 (tt0) cc_final: 0.8055 (tt0) REVERT: E 97 SER cc_start: 0.8310 (OUTLIER) cc_final: 0.8101 (t) REVERT: F 91 THR cc_start: 0.8727 (p) cc_final: 0.8154 (t) REVERT: H 91 THR cc_start: 0.8716 (p) cc_final: 0.8193 (t) REVERT: J 91 THR cc_start: 0.8714 (p) cc_final: 0.8316 (t) outliers start: 47 outliers final: 35 residues processed: 129 average time/residue: 0.0277 time to fit residues: 4.8307 Evaluate side-chains 127 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 91 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 102 GLN Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 99 PHE Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 97 SER Chi-restraints excluded: chain E residue 99 PHE Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 99 PHE Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 101 SER Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 99 PHE Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain I residue 99 PHE Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 98 LEU Chi-restraints excluded: chain J residue 99 PHE Chi-restraints excluded: chain K residue 88 LEU Chi-restraints excluded: chain K residue 99 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 7 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 26 optimal weight: 0.2980 chunk 16 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 13 optimal weight: 0.3980 chunk 28 optimal weight: 8.9990 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 104 ASN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 ASN ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 102 GLN I 108 GLN ** J 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 102 GLN K 103 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.192209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.174531 restraints weight = 3893.573| |-----------------------------------------------------------------------------| r_work (start): 0.4304 rms_B_bonded: 3.24 r_work: 0.4186 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.4186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6940 moved from start: 0.4627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2673 Z= 0.175 Angle : 1.001 10.327 3608 Z= 0.484 Chirality : 0.056 0.190 396 Planarity : 0.003 0.018 484 Dihedral : 6.903 21.323 374 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 18.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.49 % Favored : 86.51 % Rotamer: Outliers : 13.09 % Allowed : 22.91 % Favored : 64.00 % 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: -4.87 (0.31), residues: 341 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.70 (0.24), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.019 0.002 PHE I 99 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 2673) covalent geometry : angle 1.00063 ( 3608) hydrogen bonds : bond 0.09343 ( 27) hydrogen bonds : angle 10.35953 ( 81) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 682 Ramachandran restraints generated. 341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 682 Ramachandran restraints generated. 341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 110 time to evaluate : 0.106 Fit side-chains REVERT: A 88 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7011 (mt) REVERT: A 110 LYS cc_start: 0.6503 (pttp) cc_final: 0.6172 (mmtt) REVERT: B 88 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7112 (mt) REVERT: B 91 THR cc_start: 0.8812 (p) cc_final: 0.8317 (t) REVERT: C 91 THR cc_start: 0.8836 (p) cc_final: 0.8284 (t) REVERT: D 91 THR cc_start: 0.8698 (p) cc_final: 0.8206 (t) REVERT: E 91 THR cc_start: 0.8862 (p) cc_final: 0.8286 (t) REVERT: F 91 THR cc_start: 0.8844 (p) cc_final: 0.8380 (t) REVERT: G 91 THR cc_start: 0.8775 (p) cc_final: 0.8485 (t) REVERT: H 91 THR cc_start: 0.8705 (p) cc_final: 0.8236 (t) REVERT: I 100 SER cc_start: 0.9010 (p) cc_final: 0.8759 (p) REVERT: J 91 THR cc_start: 0.8648 (p) cc_final: 0.8324 (t) REVERT: K 103 ASN cc_start: 0.7552 (OUTLIER) cc_final: 0.7304 (p0) outliers start: 36 outliers final: 29 residues processed: 130 average time/residue: 0.0308 time to fit residues: 5.4435 Evaluate side-chains 128 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 96 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 102 GLN Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 99 PHE Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 99 PHE Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 99 PHE Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 99 PHE Chi-restraints excluded: chain G residue 101 SER Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 99 PHE Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 99 PHE Chi-restraints excluded: chain I residue 102 GLN Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 98 LEU Chi-restraints excluded: chain J residue 99 PHE Chi-restraints excluded: chain K residue 88 LEU Chi-restraints excluded: chain K residue 99 PHE Chi-restraints excluded: chain K residue 103 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 8 optimal weight: 8.9990 chunk 24 optimal weight: 20.0000 chunk 23 optimal weight: 6.9990 chunk 12 optimal weight: 0.4980 chunk 13 optimal weight: 0.7980 chunk 22 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 3 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 108 GLN ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.189448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.172106 restraints weight = 3964.078| |-----------------------------------------------------------------------------| r_work (start): 0.4257 rms_B_bonded: 3.18 r_work: 0.4147 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.4147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 moved from start: 0.4707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2673 Z= 0.191 Angle : 0.956 9.800 3608 Z= 0.471 Chirality : 0.056 0.187 396 Planarity : 0.003 0.018 484 Dihedral : 6.962 22.552 374 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 18.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.01 % Favored : 82.99 % Rotamer: Outliers : 13.82 % Allowed : 21.82 % Favored : 64.36 % 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: -4.94 (0.31), residues: 341 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.76 (0.23), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.002 PHE I 99 Details of bonding type rmsd covalent geometry : bond 0.00421 ( 2673) covalent geometry : angle 0.95564 ( 3608) hydrogen bonds : bond 0.09185 ( 27) hydrogen bonds : angle 10.08357 ( 81) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 682 Ramachandran restraints generated. 341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 682 Ramachandran restraints generated. 341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 103 time to evaluate : 0.088 Fit side-chains REVERT: A 88 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.6920 (mt) REVERT: A 110 LYS cc_start: 0.6321 (pttp) cc_final: 0.5984 (mmtt) REVERT: B 88 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7262 (mt) REVERT: B 91 THR cc_start: 0.8773 (p) cc_final: 0.8251 (t) REVERT: B 104 ASN cc_start: 0.7141 (m110) cc_final: 0.6740 (t0) REVERT: C 91 THR cc_start: 0.8826 (p) cc_final: 0.8400 (t) REVERT: D 91 THR cc_start: 0.8689 (p) cc_final: 0.8207 (t) REVERT: F 91 THR cc_start: 0.8878 (p) cc_final: 0.8425 (t) REVERT: H 91 THR cc_start: 0.8748 (p) cc_final: 0.8254 (t) REVERT: I 100 SER cc_start: 0.9114 (p) cc_final: 0.8788 (p) REVERT: J 91 THR cc_start: 0.8662 (p) cc_final: 0.8270 (t) outliers start: 38 outliers final: 35 residues processed: 124 average time/residue: 0.0282 time to fit residues: 4.8055 Evaluate side-chains 131 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 94 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 99 PHE Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 102 GLN Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 99 PHE Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 97 SER Chi-restraints excluded: chain E residue 99 PHE Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 99 PHE Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 99 PHE Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain G residue 101 SER Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 99 PHE Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 99 PHE Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 98 LEU Chi-restraints excluded: chain J residue 99 PHE Chi-restraints excluded: chain K residue 88 LEU Chi-restraints excluded: chain K residue 99 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 30 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 1 optimal weight: 9.9990 chunk 23 optimal weight: 0.0980 chunk 14 optimal weight: 6.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 103 ASN ** 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 = 0.4463 r_free = 0.4463 target = 0.189782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.171821 restraints weight = 3950.086| |-----------------------------------------------------------------------------| r_work (start): 0.4279 rms_B_bonded: 3.20 r_work: 0.4159 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.4159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.4913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2673 Z= 0.188 Angle : 0.942 9.947 3608 Z= 0.459 Chirality : 0.055 0.188 396 Planarity : 0.003 0.015 484 Dihedral : 6.785 22.890 374 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 17.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.25 % Favored : 84.75 % Rotamer: Outliers : 15.27 % Allowed : 23.27 % Favored : 61.45 % 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: -4.98 (0.29), residues: 341 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.79 (0.22), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.002 PHE I 99 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 2673) covalent geometry : angle 0.94165 ( 3608) hydrogen bonds : bond 0.08354 ( 27) hydrogen bonds : angle 10.04497 ( 81) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 682 Ramachandran restraints generated. 341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 682 Ramachandran restraints generated. 341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 100 time to evaluate : 0.098 Fit side-chains REVERT: A 88 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.6965 (mt) REVERT: A 110 LYS cc_start: 0.6204 (pttp) cc_final: 0.5907 (mmmt) REVERT: B 88 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7186 (mt) REVERT: B 91 THR cc_start: 0.8827 (p) cc_final: 0.8423 (t) REVERT: B 104 ASN cc_start: 0.7159 (m110) cc_final: 0.6637 (t0) REVERT: C 91 THR cc_start: 0.8855 (p) cc_final: 0.8462 (t) REVERT: F 91 THR cc_start: 0.8882 (p) cc_final: 0.8417 (t) REVERT: F 106 PHE cc_start: 0.6766 (t80) cc_final: 0.6272 (t80) REVERT: H 91 THR cc_start: 0.8803 (p) cc_final: 0.8412 (t) REVERT: I 100 SER cc_start: 0.9001 (p) cc_final: 0.8729 (p) outliers start: 42 outliers final: 36 residues processed: 122 average time/residue: 0.0298 time to fit residues: 4.9801 Evaluate side-chains 135 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 97 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 102 GLN Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 97 SER Chi-restraints excluded: chain E residue 99 PHE Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 99 PHE Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 99 PHE Chi-restraints excluded: chain G residue 101 SER Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 99 PHE Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 99 PHE Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 98 LEU Chi-restraints excluded: chain J residue 99 PHE Chi-restraints excluded: chain K residue 88 LEU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 99 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 9 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 22 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 5 optimal weight: 0.0570 chunk 17 optimal weight: 0.0770 chunk 27 optimal weight: 9.9990 chunk 30 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 overall best weight: 3.2262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 104 ASN ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 102 GLN ** J 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.183613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.165923 restraints weight = 4116.297| |-----------------------------------------------------------------------------| r_work (start): 0.4218 rms_B_bonded: 3.18 r_work: 0.4101 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.4101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.4900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 2673 Z= 0.251 Angle : 0.962 9.702 3608 Z= 0.485 Chirality : 0.058 0.190 396 Planarity : 0.003 0.015 484 Dihedral : 7.372 24.531 374 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 19.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.77 % Favored : 81.23 % Rotamer: Outliers : 16.00 % Allowed : 26.18 % Favored : 57.82 % 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: -4.95 (0.30), residues: 341 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.77 (0.23), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.019 0.003 PHE K 114 Details of bonding type rmsd covalent geometry : bond 0.00571 ( 2673) covalent geometry : angle 0.96192 ( 3608) hydrogen bonds : bond 0.08644 ( 27) hydrogen bonds : angle 9.87184 ( 81) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 682 Ramachandran restraints generated. 341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 682 Ramachandran restraints generated. 341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 100 time to evaluate : 0.088 Fit side-chains REVERT: A 88 LEU cc_start: 0.7652 (OUTLIER) cc_final: 0.6727 (mt) REVERT: A 99 PHE cc_start: 0.7566 (OUTLIER) cc_final: 0.7140 (t80) REVERT: B 88 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7195 (mt) REVERT: B 104 ASN cc_start: 0.7031 (OUTLIER) cc_final: 0.6644 (t0) REVERT: F 106 PHE cc_start: 0.6838 (t80) cc_final: 0.6297 (t80) REVERT: K 114 PHE cc_start: 0.7581 (m-80) cc_final: 0.7147 (m-10) outliers start: 44 outliers final: 36 residues processed: 124 average time/residue: 0.0289 time to fit residues: 4.9843 Evaluate side-chains 137 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 97 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 99 PHE Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 102 GLN Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 99 PHE Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 99 PHE Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 99 PHE Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 99 PHE Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain G residue 101 SER Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 99 PHE Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 99 PHE Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 98 LEU Chi-restraints excluded: chain J residue 99 PHE Chi-restraints excluded: chain K residue 88 LEU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 99 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 14 optimal weight: 0.8980 chunk 24 optimal weight: 20.0000 chunk 3 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 23 optimal weight: 0.0470 chunk 6 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 overall best weight: 0.9480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 102 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 = 0.4470 r_free = 0.4470 target = 0.190474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.172691 restraints weight = 3981.489| |-----------------------------------------------------------------------------| r_work (start): 0.4302 rms_B_bonded: 3.22 r_work: 0.4183 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.4183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.5194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2673 Z= 0.156 Angle : 0.925 9.879 3608 Z= 0.449 Chirality : 0.054 0.179 396 Planarity : 0.003 0.016 484 Dihedral : 6.743 24.695 374 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 18.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.42 % Favored : 83.58 % Rotamer: Outliers : 10.91 % Allowed : 34.55 % Favored : 54.55 % 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: -4.93 (0.29), residues: 341 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.75 (0.22), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.002 PHE I 99 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 2673) covalent geometry : angle 0.92518 ( 3608) hydrogen bonds : bond 0.07831 ( 27) hydrogen bonds : angle 10.09791 ( 81) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 682 Ramachandran restraints generated. 341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 682 Ramachandran restraints generated. 341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 106 time to evaluate : 0.071 Fit side-chains REVERT: A 88 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.6749 (mt) REVERT: A 110 LYS cc_start: 0.6080 (pttp) cc_final: 0.5827 (mmmt) REVERT: B 88 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7180 (mt) REVERT: B 91 THR cc_start: 0.8836 (p) cc_final: 0.8448 (t) REVERT: B 102 GLN cc_start: 0.7694 (tt0) cc_final: 0.7149 (tt0) REVERT: B 104 ASN cc_start: 0.6896 (m110) cc_final: 0.6487 (t0) REVERT: C 91 THR cc_start: 0.8889 (p) cc_final: 0.8467 (t) REVERT: D 104 ASN cc_start: 0.8187 (m110) cc_final: 0.7982 (m-40) REVERT: F 91 THR cc_start: 0.8821 (p) cc_final: 0.8362 (t) REVERT: F 106 PHE cc_start: 0.6438 (t80) cc_final: 0.6077 (t80) REVERT: G 106 PHE cc_start: 0.6887 (t80) cc_final: 0.6592 (t80) REVERT: H 91 THR cc_start: 0.8706 (p) cc_final: 0.8294 (t) outliers start: 30 outliers final: 26 residues processed: 121 average time/residue: 0.0288 time to fit residues: 4.7670 Evaluate side-chains 129 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 101 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 102 GLN Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 99 PHE Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 99 PHE Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 99 PHE Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 99 PHE Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain I residue 99 PHE Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 98 LEU Chi-restraints excluded: chain J residue 99 PHE Chi-restraints excluded: chain K residue 88 LEU Chi-restraints excluded: chain K residue 99 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 19 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 12 optimal weight: 9.9990 chunk 16 optimal weight: 8.9990 chunk 15 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 30 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 108 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 = 0.4373 r_free = 0.4373 target = 0.178310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.160787 restraints weight = 4357.352| |-----------------------------------------------------------------------------| r_work (start): 0.4185 rms_B_bonded: 3.19 r_work: 0.4067 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.4067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.4939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.052 2673 Z= 0.341 Angle : 1.017 9.378 3608 Z= 0.533 Chirality : 0.061 0.192 396 Planarity : 0.004 0.015 484 Dihedral : 8.171 25.966 374 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 21.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.94 % Favored : 80.06 % Rotamer: Outliers : 14.91 % Allowed : 29.82 % Favored : 55.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.16 (0.28), residues: 341 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.93 (0.22), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.034 0.004 PHE K 114 Details of bonding type rmsd covalent geometry : bond 0.00778 ( 2673) covalent geometry : angle 1.01694 ( 3608) hydrogen bonds : bond 0.09412 ( 27) hydrogen bonds : angle 9.83905 ( 81) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 682 Ramachandran restraints generated. 341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 682 Ramachandran restraints generated. 341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 98 time to evaluate : 0.069 Fit side-chains REVERT: A 88 LEU cc_start: 0.7638 (OUTLIER) cc_final: 0.6555 (mt) REVERT: A 99 PHE cc_start: 0.7668 (OUTLIER) cc_final: 0.7126 (t80) REVERT: B 88 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7078 (mt) REVERT: B 104 ASN cc_start: 0.7139 (m110) cc_final: 0.6705 (t0) REVERT: B 110 LYS cc_start: 0.5350 (OUTLIER) cc_final: 0.2565 (pptt) REVERT: D 104 ASN cc_start: 0.8403 (m110) cc_final: 0.8133 (m-40) REVERT: F 106 PHE cc_start: 0.6831 (t80) cc_final: 0.6319 (t80) outliers start: 41 outliers final: 34 residues processed: 122 average time/residue: 0.0276 time to fit residues: 4.6754 Evaluate side-chains 134 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 96 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 99 PHE Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 110 LYS Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 99 PHE Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 102 GLN Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 99 PHE Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 99 PHE Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 99 PHE Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain G residue 101 SER Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 99 PHE Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 99 PHE Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 98 LEU Chi-restraints excluded: chain J residue 99 PHE Chi-restraints excluded: chain K residue 88 LEU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 99 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 3 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 21 optimal weight: 20.0000 chunk 23 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 chunk 26 optimal weight: 0.4980 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 104 ASN ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 ASN ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 102 GLN ** J 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.183758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.166053 restraints weight = 4151.063| |-----------------------------------------------------------------------------| r_work (start): 0.4246 rms_B_bonded: 3.19 r_work: 0.4125 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.4125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7039 moved from start: 0.5180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 2673 Z= 0.215 Angle : 0.958 9.827 3608 Z= 0.478 Chirality : 0.056 0.190 396 Planarity : 0.003 0.016 484 Dihedral : 7.525 26.295 374 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 19.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.89 % Favored : 82.11 % Rotamer: Outliers : 13.45 % Allowed : 30.55 % Favored : 56.00 % 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: -5.26 (0.26), residues: 341 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.00 (0.20), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.026 0.002 PHE G 99 Details of bonding type rmsd covalent geometry : bond 0.00484 ( 2673) covalent geometry : angle 0.95849 ( 3608) hydrogen bonds : bond 0.08470 ( 27) hydrogen bonds : angle 9.95607 ( 81) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 682 Ramachandran restraints generated. 341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 682 Ramachandran restraints generated. 341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 106 time to evaluate : 0.097 Fit side-chains REVERT: A 88 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.6698 (mt) REVERT: B 88 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7021 (mt) REVERT: B 104 ASN cc_start: 0.7068 (OUTLIER) cc_final: 0.6635 (t0) REVERT: B 110 LYS cc_start: 0.5078 (OUTLIER) cc_final: 0.2485 (pptt) REVERT: D 104 ASN cc_start: 0.8483 (m-40) cc_final: 0.8225 (m-40) REVERT: F 106 PHE cc_start: 0.6930 (t80) cc_final: 0.6309 (t80) outliers start: 37 outliers final: 31 residues processed: 124 average time/residue: 0.0297 time to fit residues: 5.0239 Evaluate side-chains 139 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 104 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain B residue 110 LYS Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 102 GLN Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 99 PHE Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 99 PHE Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 99 PHE Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 99 PHE Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 99 PHE Chi-restraints excluded: chain I residue 102 GLN Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 98 LEU Chi-restraints excluded: chain J residue 99 PHE Chi-restraints excluded: chain K residue 88 LEU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 99 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 5 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 21 optimal weight: 0.0050 chunk 12 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 29 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 overall best weight: 1.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 102 GLN ** J 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.184499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.166747 restraints weight = 4113.938| |-----------------------------------------------------------------------------| r_work (start): 0.4257 rms_B_bonded: 3.19 r_work: 0.4140 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.4140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.5218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.169 2673 Z= 0.321 Angle : 1.744 59.199 3608 Z= 1.036 Chirality : 0.059 0.415 396 Planarity : 0.009 0.179 484 Dihedral : 7.503 26.446 374 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 20.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.77 % Favored : 81.23 % Rotamer: Outliers : 12.73 % Allowed : 31.64 % Favored : 55.64 % Cbeta Deviations : 0.32 % 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: -5.24 (0.27), residues: 341 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.99 (0.20), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.026 0.002 PHE G 99 Details of bonding type rmsd covalent geometry : bond 0.00654 ( 2673) covalent geometry : angle 1.74438 ( 3608) hydrogen bonds : bond 0.09510 ( 27) hydrogen bonds : angle 10.01794 ( 81) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 723.22 seconds wall clock time: 13 minutes 5.69 seconds (785.69 seconds total)