Starting phenix.real_space_refine on Mon Feb 10 21:09:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7q67_13854/02_2025/7q67_13854.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q67_13854/02_2025/7q67_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7q67_13854/02_2025/7q67_13854.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q67_13854/02_2025/7q67_13854.map" model { file = "/net/cci-nas-00/data/ceres_data/7q67_13854/02_2025/7q67_13854.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q67_13854/02_2025/7q67_13854.cif" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: C, B, E, D, G, F, I, H, K, J Time building chain proxies: 1.29, per 1000 atoms: 0.49 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: 0.66 Conformation dependent library (CDL) restraints added in 334.9 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: 0.23 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: 0.56 Time building geometry restraints manager: 0.75 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.640 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.330 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.830 ------------------------------------------------------------------------------- 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= 1.490 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 *********************** 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 : 0.227 Fit side-chains REVERT: A 104 ASN cc_start: 0.7201 (m110) cc_final: 0.6959 (m110) outliers start: 22 outliers final: 11 residues processed: 143 average time/residue: 0.1123 time to fit residues: 19.4216 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 : 0.300 ------------------------------------------------------------------------------- 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 27 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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** ** 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 = 0.4367 r_free = 0.4367 target = 0.181411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.163749 restraints weight = 4044.020| |-----------------------------------------------------------------------------| r_work (start): 0.4177 rms_B_bonded: 3.14 r_work: 0.4063 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.4063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.3203 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= 0.360 Angle : 1.113 10.344 3608 Z= 0.574 Chirality : 0.063 0.213 396 Planarity : 0.003 0.012 484 Dihedral : 9.148 27.489 374 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 21.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.84 % Favored : 84.16 % Rotamer: Outliers : 15.64 % Allowed : 17.82 % Favored : 66.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.88 (0.31), residues: 341 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.72 (0.24), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.017 0.003 PHE E 114 *********************** 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 159 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 116 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 LYS cc_start: 0.6656 (pttp) cc_final: 0.6285 (mmtt) REVERT: C 87 THR cc_start: 0.5104 (p) cc_final: 0.4897 (p) REVERT: C 91 THR cc_start: 0.8806 (p) cc_final: 0.8365 (t) REVERT: F 91 THR cc_start: 0.8631 (p) cc_final: 0.8061 (t) REVERT: G 94 THR cc_start: 0.8717 (p) cc_final: 0.8454 (m) REVERT: H 91 THR cc_start: 0.8688 (p) cc_final: 0.8194 (t) REVERT: J 91 THR cc_start: 0.8631 (p) cc_final: 0.8273 (t) REVERT: K 94 THR cc_start: 0.8736 (p) cc_final: 0.8487 (m) outliers start: 43 outliers final: 28 residues processed: 139 average time/residue: 0.0784 time to fit residues: 14.2645 Evaluate side-chains 113 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 85 time to evaluate : 0.313 ------------------------------------------------------------------------------- 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 101 SER 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 97 SER Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 97 SER 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 94 THR 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 14 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 chunk 18 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 4 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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** ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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** ** F 108 GLN ** 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** ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 104 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 = 0.4410 r_free = 0.4410 target = 0.185088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.167097 restraints weight = 3973.106| |-----------------------------------------------------------------------------| r_work (start): 0.4195 rms_B_bonded: 3.26 r_work: 0.4092 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 2673 Z= 0.345 Angle : 1.050 9.992 3608 Z= 0.527 Chirality : 0.061 0.208 396 Planarity : 0.003 0.015 484 Dihedral : 7.808 20.507 374 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 20.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.18 % Favored : 81.82 % Rotamer: Outliers : 15.64 % Allowed : 18.91 % Favored : 65.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.84 (0.31), residues: 341 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.68 (0.24), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.020 0.002 PHE I 99 *********************** 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 145 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 102 time to evaluate : 0.296 Fit side-chains revert: symmetry clash REVERT: A 110 LYS cc_start: 0.6461 (pttp) cc_final: 0.6038 (mmtp) REVERT: B 91 THR cc_start: 0.8696 (p) cc_final: 0.8293 (t) REVERT: C 91 THR cc_start: 0.8774 (p) cc_final: 0.8321 (t) REVERT: F 91 THR cc_start: 0.8625 (p) cc_final: 0.8121 (t) REVERT: G 106 PHE cc_start: 0.6955 (t80) cc_final: 0.6484 (t80) REVERT: H 91 THR cc_start: 0.8667 (p) cc_final: 0.8123 (t) REVERT: J 91 THR cc_start: 0.8617 (p) cc_final: 0.8240 (t) outliers start: 43 outliers final: 38 residues processed: 129 average time/residue: 0.0785 time to fit residues: 13.2834 Evaluate side-chains 128 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 90 time to evaluate : 0.261 ------------------------------------------------------------------------------- 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 101 SER 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 101 SER Chi-restraints excluded: chain C residue 102 GLN Chi-restraints excluded: chain C residue 116 ASN 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 97 SER Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 99 PHE Chi-restraints excluded: chain E residue 101 SER 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 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 94 THR Chi-restraints excluded: chain I residue 99 PHE Chi-restraints excluded: chain I residue 101 SER 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 17 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 27 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 2 optimal weight: 0.4980 chunk 25 optimal weight: 7.9990 chunk 26 optimal weight: 0.0970 chunk 7 optimal weight: 0.9990 chunk 14 optimal weight: 8.9990 chunk 28 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN B 102 GLN B 104 ASN C 104 ASN C 108 GLN ** F 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 108 GLN ** J 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 103 ASN ** K 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.195692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.178606 restraints weight = 3898.250| |-----------------------------------------------------------------------------| r_work (start): 0.4337 rms_B_bonded: 3.19 r_work: 0.4234 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.4234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 moved from start: 0.4601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2673 Z= 0.230 Angle : 0.980 10.157 3608 Z= 0.473 Chirality : 0.055 0.199 396 Planarity : 0.003 0.014 484 Dihedral : 6.525 20.329 374 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 18.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.78 % Favored : 86.22 % Rotamer: Outliers : 13.45 % Allowed : 24.36 % Favored : 62.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.73 (0.32), residues: 341 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.60 (0.24), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.020 0.002 PHE I 99 *********************** 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 147 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 110 time to evaluate : 0.278 Fit side-chains REVERT: A 88 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7227 (mt) REVERT: A 110 LYS cc_start: 0.6370 (pttp) cc_final: 0.6002 (mmtt) REVERT: B 88 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7237 (mt) REVERT: B 91 THR cc_start: 0.8779 (p) cc_final: 0.8299 (t) REVERT: C 91 THR cc_start: 0.8797 (p) cc_final: 0.8225 (t) REVERT: D 91 THR cc_start: 0.8657 (p) cc_final: 0.8169 (t) REVERT: E 91 THR cc_start: 0.8790 (p) cc_final: 0.8306 (t) REVERT: F 91 THR cc_start: 0.8824 (p) cc_final: 0.8385 (t) REVERT: F 106 PHE cc_start: 0.6829 (t80) cc_final: 0.6214 (t80) REVERT: G 106 PHE cc_start: 0.6572 (t80) cc_final: 0.6322 (t80) REVERT: H 91 THR cc_start: 0.8759 (p) cc_final: 0.8267 (t) REVERT: J 91 THR cc_start: 0.8652 (p) cc_final: 0.8317 (t) REVERT: K 103 ASN cc_start: 0.7426 (OUTLIER) cc_final: 0.7123 (p0) outliers start: 37 outliers final: 28 residues processed: 129 average time/residue: 0.0820 time to fit residues: 13.8912 Evaluate side-chains 127 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 96 time to evaluate : 0.272 ------------------------------------------------------------------------------- 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 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 99 PHE 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 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 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 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 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 12 optimal weight: 20.0000 chunk 29 optimal weight: 0.0980 chunk 3 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 25 optimal weight: 8.9990 chunk 9 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 23 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 24 optimal weight: 20.0000 chunk 32 optimal weight: 0.0170 overall best weight: 1.8224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 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 = 0.4499 r_free = 0.4499 target = 0.192831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.175586 restraints weight = 3914.267| |-----------------------------------------------------------------------------| r_work (start): 0.4309 rms_B_bonded: 3.15 r_work: 0.4206 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.4206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 moved from start: 0.4703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 2673 Z= 0.264 Angle : 0.935 9.926 3608 Z= 0.455 Chirality : 0.055 0.189 396 Planarity : 0.003 0.018 484 Dihedral : 6.539 21.706 374 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 19.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.30 % Favored : 82.70 % Rotamer: Outliers : 11.64 % Allowed : 24.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.85 (0.31), residues: 341 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.69 (0.24), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.018 0.002 PHE I 99 *********************** 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 137 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 105 time to evaluate : 0.297 Fit side-chains REVERT: A 88 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7046 (mt) REVERT: A 110 LYS cc_start: 0.6270 (pttp) cc_final: 0.5896 (mmtt) REVERT: B 88 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7332 (mt) REVERT: B 91 THR cc_start: 0.8737 (p) cc_final: 0.8291 (t) REVERT: B 104 ASN cc_start: 0.6980 (m-40) cc_final: 0.6648 (t0) REVERT: C 91 THR cc_start: 0.8799 (p) cc_final: 0.8245 (t) REVERT: E 91 THR cc_start: 0.8827 (p) cc_final: 0.8340 (t) REVERT: F 91 THR cc_start: 0.8849 (p) cc_final: 0.8392 (t) REVERT: F 106 PHE cc_start: 0.6852 (t80) cc_final: 0.6288 (t80) REVERT: H 91 THR cc_start: 0.8777 (p) cc_final: 0.8243 (t) REVERT: I 100 SER cc_start: 0.9033 (p) cc_final: 0.8777 (p) REVERT: J 91 THR cc_start: 0.8654 (p) cc_final: 0.8304 (t) outliers start: 32 outliers final: 28 residues processed: 122 average time/residue: 0.0759 time to fit residues: 12.2435 Evaluate side-chains 127 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 97 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 98 LEU 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 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 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 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 27 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 32 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 30 optimal weight: 10.0000 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 GLN ** 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** ** J 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 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 = 0.4434 r_free = 0.4434 target = 0.185988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.167619 restraints weight = 4019.705| |-----------------------------------------------------------------------------| r_work (start): 0.4222 rms_B_bonded: 3.21 r_work: 0.4111 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.4111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.4655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 2673 Z= 0.406 Angle : 0.969 9.860 3608 Z= 0.483 Chirality : 0.059 0.195 396 Planarity : 0.003 0.012 484 Dihedral : 7.129 24.101 374 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 21.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.06 % Favored : 80.94 % Rotamer: Outliers : 12.36 % Allowed : 26.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.99 (0.29), residues: 341 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.80 (0.22), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.018 0.003 PHE G 99 *********************** 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 135 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 101 time to evaluate : 0.332 Fit side-chains REVERT: A 88 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.6950 (mt) REVERT: A 104 ASN cc_start: 0.7234 (m-40) cc_final: 0.7006 (t0) REVERT: B 88 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7247 (mt) REVERT: C 91 THR cc_start: 0.8816 (p) cc_final: 0.8366 (t) REVERT: F 106 PHE cc_start: 0.6720 (t80) cc_final: 0.6373 (t80) REVERT: H 91 THR cc_start: 0.8789 (p) cc_final: 0.8336 (t) REVERT: I 100 SER cc_start: 0.9078 (p) cc_final: 0.8826 (p) REVERT: K 114 PHE cc_start: 0.7630 (m-80) cc_final: 0.7019 (m-10) outliers start: 34 outliers final: 30 residues processed: 121 average time/residue: 0.0803 time to fit residues: 12.8524 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 : 0.293 ------------------------------------------------------------------------------- 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 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 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 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 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 94 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 17 optimal weight: 0.8980 chunk 15 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 19 optimal weight: 0.9980 chunk 18 optimal weight: 8.9990 chunk 12 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 30 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 102 GLN ** 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 108 GLN ** 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 = 0.4479 r_free = 0.4479 target = 0.191089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.173358 restraints weight = 4063.577| |-----------------------------------------------------------------------------| r_work (start): 0.4284 rms_B_bonded: 3.23 r_work: 0.4176 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.4176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 moved from start: 0.5058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2673 Z= 0.242 Angle : 0.921 10.027 3608 Z= 0.442 Chirality : 0.055 0.186 396 Planarity : 0.003 0.013 484 Dihedral : 6.511 22.800 374 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 19.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.89 % Favored : 82.11 % Rotamer: Outliers : 13.09 % Allowed : 27.64 % Favored : 59.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.88 (0.29), residues: 341 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.71 (0.23), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.017 0.002 PHE G 99 *********************** 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: 36 poor density : 108 time to evaluate : 0.283 Fit side-chains REVERT: A 88 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7077 (mt) REVERT: A 110 LYS cc_start: 0.6234 (pttp) cc_final: 0.5871 (mmtt) REVERT: B 88 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7276 (mt) REVERT: B 91 THR cc_start: 0.8831 (p) cc_final: 0.8432 (t) REVERT: C 91 THR cc_start: 0.8818 (p) cc_final: 0.8415 (t) REVERT: F 106 PHE cc_start: 0.6452 (t80) cc_final: 0.6059 (t80) REVERT: H 91 THR cc_start: 0.8767 (p) cc_final: 0.8186 (t) REVERT: I 100 SER cc_start: 0.9091 (p) cc_final: 0.8790 (p) REVERT: J 91 THR cc_start: 0.8770 (p) cc_final: 0.8420 (t) REVERT: J 99 PHE cc_start: 0.7642 (OUTLIER) cc_final: 0.6955 (m-80) outliers start: 36 outliers final: 30 residues processed: 129 average time/residue: 0.0774 time to fit residues: 13.1326 Evaluate side-chains 134 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 101 time to evaluate : 0.290 ------------------------------------------------------------------------------- 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 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 98 LEU 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 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 94 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 10 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 8 optimal weight: 8.9990 chunk 28 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 chunk 16 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 GLN ** 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 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 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 = 0.4369 r_free = 0.4369 target = 0.176921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.159558 restraints weight = 4238.683| |-----------------------------------------------------------------------------| r_work (start): 0.4185 rms_B_bonded: 3.16 r_work: 0.4080 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.4080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.4809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.054 2673 Z= 0.602 Angle : 1.040 9.698 3608 Z= 0.548 Chirality : 0.064 0.203 396 Planarity : 0.004 0.016 484 Dihedral : 8.037 26.711 374 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 23.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.11 % Favored : 78.89 % Rotamer: Outliers : 14.18 % Allowed : 27.64 % Favored : 58.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.26 (0.28), residues: 341 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.00 (0.21), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.034 0.005 PHE K 114 *********************** 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 133 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 94 time to evaluate : 0.323 Fit side-chains REVERT: A 99 PHE cc_start: 0.7590 (OUTLIER) cc_final: 0.7047 (t80) REVERT: B 88 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7146 (mt) REVERT: F 106 PHE cc_start: 0.6820 (t80) cc_final: 0.6486 (t80) REVERT: I 100 SER cc_start: 0.9037 (p) cc_final: 0.8751 (p) outliers start: 39 outliers final: 32 residues processed: 123 average time/residue: 0.0803 time to fit residues: 13.0530 Evaluate side-chains 126 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 92 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 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 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 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 100 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 94 THR 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 94 THR 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 26 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 12 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 chunk 4 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 17 optimal weight: 0.3980 chunk 11 optimal weight: 0.0070 chunk 6 optimal weight: 5.9990 chunk 19 optimal weight: 0.1980 overall best weight: 0.4800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 108 GLN ** J 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 102 GLN ** K 103 ASN ** 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 = 0.4522 r_free = 0.4522 target = 0.195031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.177715 restraints weight = 3841.837| |-----------------------------------------------------------------------------| r_work (start): 0.4361 rms_B_bonded: 3.16 r_work: 0.4250 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.4250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6845 moved from start: 0.5456 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= 0.218 Angle : 0.925 10.254 3608 Z= 0.440 Chirality : 0.053 0.192 396 Planarity : 0.003 0.017 484 Dihedral : 6.685 24.854 374 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 18.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.37 % Favored : 85.63 % Rotamer: Outliers : 9.82 % Allowed : 34.55 % Favored : 55.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.00 (0.28), residues: 341 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.80 (0.22), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.023 0.002 PHE G 99 *********************** 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 132 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 0.269 Fit side-chains REVERT: A 88 LEU cc_start: 0.7681 (OUTLIER) cc_final: 0.6823 (mt) REVERT: A 110 LYS cc_start: 0.6099 (pttp) cc_final: 0.5848 (mmtt) REVERT: B 88 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7343 (mt) REVERT: B 91 THR cc_start: 0.8872 (p) cc_final: 0.8467 (t) REVERT: F 106 PHE cc_start: 0.6360 (t80) cc_final: 0.5959 (t80) REVERT: J 99 PHE cc_start: 0.7615 (OUTLIER) cc_final: 0.6953 (m-80) REVERT: K 114 PHE cc_start: 0.6798 (m-10) cc_final: 0.6491 (m-10) outliers start: 27 outliers final: 23 residues processed: 118 average time/residue: 0.0787 time to fit residues: 12.1889 Evaluate side-chains 129 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 103 time to evaluate : 0.261 ------------------------------------------------------------------------------- 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 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 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 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 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 Chi-restraints excluded: chain K residue 102 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 20 optimal weight: 0.0010 chunk 26 optimal weight: 0.9980 chunk 22 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 chunk 2 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 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 = 0.4481 r_free = 0.4481 target = 0.189888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.173057 restraints weight = 4007.992| |-----------------------------------------------------------------------------| r_work (start): 0.4311 rms_B_bonded: 3.13 r_work: 0.4203 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.4203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.5351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2673 Z= 0.281 Angle : 0.911 9.985 3608 Z= 0.445 Chirality : 0.053 0.187 396 Planarity : 0.003 0.017 484 Dihedral : 6.628 24.492 374 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 20.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.89 % Favored : 82.11 % Rotamer: Outliers : 9.82 % Allowed : 34.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.98 (0.29), residues: 341 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.78 (0.22), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.022 0.002 PHE G 99 ********************** 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 130 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 103 time to evaluate : 0.264 Fit side-chains REVERT: A 88 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.6757 (mt) REVERT: A 110 LYS cc_start: 0.5960 (pttp) cc_final: 0.5710 (mmtt) REVERT: B 88 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7319 (mt) REVERT: B 91 THR cc_start: 0.8880 (p) cc_final: 0.8475 (t) REVERT: F 106 PHE cc_start: 0.6346 (t80) cc_final: 0.5975 (t80) REVERT: J 99 PHE cc_start: 0.7741 (OUTLIER) cc_final: 0.6980 (m-80) outliers start: 27 outliers final: 24 residues processed: 117 average time/residue: 0.0761 time to fit residues: 11.7553 Evaluate side-chains 128 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 101 time to evaluate : 0.252 ------------------------------------------------------------------------------- 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 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 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 98 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 7 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 2 optimal weight: 0.0970 chunk 24 optimal weight: 20.0000 chunk 30 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 9 optimal weight: 20.0000 chunk 22 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 chunk 5 optimal weight: 0.0670 chunk 12 optimal weight: 7.9990 overall best weight: 2.4120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 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 = 0.4464 r_free = 0.4464 target = 0.187447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.169988 restraints weight = 4086.053| |-----------------------------------------------------------------------------| r_work (start): 0.4299 rms_B_bonded: 3.20 r_work: 0.4181 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.4181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.5334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 2673 Z= 0.326 Angle : 0.926 9.926 3608 Z= 0.457 Chirality : 0.054 0.188 396 Planarity : 0.003 0.015 484 Dihedral : 6.898 25.955 374 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 21.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.48 % Favored : 81.52 % Rotamer: Outliers : 10.18 % Allowed : 34.55 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.05 (0.27), residues: 341 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.84 (0.21), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.023 0.002 PHE G 99 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1492.79 seconds wall clock time: 27 minutes 17.23 seconds (1637.23 seconds total)