Starting phenix.real_space_refine on Mon Sep 23 12:43:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q67_13854/09_2024/7q67_13854.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q67_13854/09_2024/7q67_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q67_13854/09_2024/7q67_13854.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q67_13854/09_2024/7q67_13854.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q67_13854/09_2024/7q67_13854.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q67_13854/09_2024/7q67_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-5461/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: 1.39, per 1000 atoms: 0.53 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: 0.68 Conformation dependent library (CDL) restraints added in 319.1 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: 0.24 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: 0.47 Time building geometry restraints manager: 0.76 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: 0.00 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: 0.760 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 10.340 Find NCS groups from input model: 0.100 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.130 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 22 poor density : 143 time to evaluate : 0.300 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: 0.1117 time to fit residues: 19.4565 Evaluate side-chains 99 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 88 time to evaluate : 0.296 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 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 fitting. rotamer outliers: 43 poor density : 116 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 87 THR cc_start: 0.5910 (p) cc_final: 0.5686 (p) REVERT: C 91 THR cc_start: 0.8620 (p) cc_final: 0.8313 (t) REVERT: F 91 THR cc_start: 0.8454 (p) cc_final: 0.8012 (t) REVERT: G 94 THR cc_start: 0.8637 (p) cc_final: 0.8418 (m) REVERT: H 91 THR cc_start: 0.8422 (p) cc_final: 0.8052 (t) REVERT: J 91 THR cc_start: 0.8329 (p) cc_final: 0.8055 (t) REVERT: K 94 THR cc_start: 0.8757 (p) cc_final: 0.8340 (m) outliers start: 43 outliers final: 28 residues processed: 139 average time/residue: 0.0787 time to fit residues: 14.1996 Evaluate side-chains 112 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 84 time to evaluate : 0.282 ------------------------------------------------------------------------------- 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 20 optimal weight: 8.9990 chunk 8 optimal weight: 6.9990 chunk 30 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 10 optimal weight: 7.9990 chunk 24 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 overall best weight: 3.9586 ------------------------------------------------------------------------------- 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** ** I 102 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 2673 Z= 0.508 Angle : 1.099 9.929 3608 Z= 0.567 Chirality : 0.065 0.226 396 Planarity : 0.004 0.013 484 Dihedral : 8.651 22.922 374 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 24.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.06 % Favored : 80.94 % Rotamer: Outliers : 15.64 % Allowed : 18.55 % Favored : 65.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -5.03 (0.29), residues: 341 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.83 (0.22), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.025 0.003 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 136 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 93 time to evaluate : 0.285 Fit side-chains revert: symmetry clash REVERT: C 91 THR cc_start: 0.8620 (p) cc_final: 0.8321 (t) REVERT: F 91 THR cc_start: 0.8466 (p) cc_final: 0.8087 (t) REVERT: G 106 PHE cc_start: 0.6335 (t80) cc_final: 0.6033 (t80) REVERT: H 91 THR cc_start: 0.8382 (p) cc_final: 0.8034 (t) REVERT: J 91 THR cc_start: 0.8361 (p) cc_final: 0.8051 (t) outliers start: 43 outliers final: 36 residues processed: 119 average time/residue: 0.0741 time to fit residues: 11.6815 Evaluate side-chains 126 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 90 time to evaluate : 0.282 ------------------------------------------------------------------------------- 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 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 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 14 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 30 optimal weight: 0.0470 chunk 31 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 28 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 18 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 overall best weight: 0.7480 ------------------------------------------------------------------------------- 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 ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 103 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6853 moved from start: 0.4401 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= 0.237 Angle : 0.991 10.155 3608 Z= 0.481 Chirality : 0.055 0.194 396 Planarity : 0.003 0.013 484 Dihedral : 6.995 21.525 374 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 19.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.08 % Favored : 85.92 % 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 (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: -4.72 (0.31), residues: 341 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.59 (0.24), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.019 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 144 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 108 time to evaluate : 0.285 Fit side-chains REVERT: A 88 LEU cc_start: 0.7245 (OUTLIER) cc_final: 0.6388 (mt) REVERT: B 88 LEU cc_start: 0.7110 (OUTLIER) cc_final: 0.6587 (mt) REVERT: B 91 THR cc_start: 0.8188 (p) cc_final: 0.7909 (t) REVERT: C 91 THR cc_start: 0.8575 (p) cc_final: 0.8120 (t) REVERT: D 91 THR cc_start: 0.8389 (p) cc_final: 0.8059 (t) REVERT: E 91 THR cc_start: 0.8615 (p) cc_final: 0.8135 (t) REVERT: F 91 THR cc_start: 0.8574 (p) cc_final: 0.8194 (t) REVERT: H 91 THR cc_start: 0.8398 (p) cc_final: 0.8014 (t) REVERT: J 91 THR cc_start: 0.8316 (p) cc_final: 0.8031 (t) outliers start: 36 outliers final: 28 residues processed: 129 average time/residue: 0.0739 time to fit residues: 12.5725 Evaluate side-chains 126 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 96 time to evaluate : 0.282 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 13 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 8 optimal weight: 0.0970 chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 18 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 104 ASN ** 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 ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.4495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 2673 Z= 0.330 Angle : 0.963 9.748 3608 Z= 0.478 Chirality : 0.056 0.191 396 Planarity : 0.003 0.012 484 Dihedral : 7.232 23.466 374 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 20.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.89 % Favored : 82.11 % Rotamer: Outliers : 13.45 % Allowed : 23.27 % Favored : 63.27 % 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: -4.79 (0.32), residues: 341 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.65 (0.24), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.019 0.003 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 140 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 103 time to evaluate : 0.280 Fit side-chains REVERT: A 88 LEU cc_start: 0.7228 (OUTLIER) cc_final: 0.6343 (mt) REVERT: B 88 LEU cc_start: 0.7107 (OUTLIER) cc_final: 0.6696 (mt) REVERT: B 104 ASN cc_start: 0.6821 (m-40) cc_final: 0.6610 (t0) REVERT: C 91 THR cc_start: 0.8593 (p) cc_final: 0.8295 (t) REVERT: F 91 THR cc_start: 0.8653 (p) cc_final: 0.8266 (t) REVERT: H 91 THR cc_start: 0.8509 (p) cc_final: 0.8073 (t) REVERT: J 91 THR cc_start: 0.8323 (p) cc_final: 0.8006 (t) outliers start: 37 outliers final: 33 residues processed: 124 average time/residue: 0.0708 time to fit residues: 11.8104 Evaluate side-chains 130 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 95 time to evaluate : 0.296 ------------------------------------------------------------------------------- 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 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 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 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 94 THR 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 31 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 14 optimal weight: 0.2980 chunk 2 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 16 optimal weight: 0.8980 chunk 30 optimal weight: 0.1980 chunk 3 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** I 108 GLN K 102 GLN ** K 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6864 moved from start: 0.4831 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= 0.236 Angle : 0.938 9.959 3608 Z= 0.452 Chirality : 0.054 0.185 396 Planarity : 0.003 0.013 484 Dihedral : 6.579 22.416 374 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.84 % Favored : 84.16 % Rotamer: Outliers : 12.36 % Allowed : 26.91 % Favored : 60.73 % 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: -4.83 (0.30), residues: 341 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.67 (0.23), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.002 PHE I 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 139 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 105 time to evaluate : 0.294 Fit side-chains REVERT: A 88 LEU cc_start: 0.7165 (OUTLIER) cc_final: 0.6333 (mt) REVERT: B 88 LEU cc_start: 0.7049 (OUTLIER) cc_final: 0.6703 (mt) REVERT: C 91 THR cc_start: 0.8584 (p) cc_final: 0.8316 (t) REVERT: F 91 THR cc_start: 0.8654 (p) cc_final: 0.8308 (t) REVERT: H 91 THR cc_start: 0.8514 (p) cc_final: 0.8083 (t) REVERT: J 91 THR cc_start: 0.8284 (p) cc_final: 0.7981 (t) outliers start: 34 outliers final: 29 residues processed: 124 average time/residue: 0.0727 time to fit residues: 12.0470 Evaluate side-chains 130 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 99 time to evaluate : 0.283 ------------------------------------------------------------------------------- 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 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 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 31 optimal weight: 4.9990 chunk 19 optimal weight: 10.0000 chunk 14 optimal weight: 0.6980 chunk 12 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 9 optimal weight: 9.9990 chunk 6 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 2 optimal weight: 0.0050 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6822 moved from start: 0.5066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2673 Z= 0.215 Angle : 0.910 9.886 3608 Z= 0.437 Chirality : 0.053 0.185 396 Planarity : 0.003 0.015 484 Dihedral : 6.342 21.325 374 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.42 % Favored : 83.58 % Rotamer: Outliers : 12.36 % Allowed : 28.00 % Favored : 59.64 % 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: -4.79 (0.31), residues: 341 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.64 (0.24), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.018 0.002 PHE I 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 142 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 108 time to evaluate : 0.309 Fit side-chains REVERT: A 88 LEU cc_start: 0.7009 (OUTLIER) cc_final: 0.6238 (mt) REVERT: B 88 LEU cc_start: 0.6990 (OUTLIER) cc_final: 0.6571 (mt) REVERT: C 91 THR cc_start: 0.8591 (p) cc_final: 0.8195 (t) REVERT: E 91 THR cc_start: 0.8651 (p) cc_final: 0.8194 (t) REVERT: F 91 THR cc_start: 0.8634 (p) cc_final: 0.8305 (t) REVERT: H 91 THR cc_start: 0.8494 (p) cc_final: 0.8054 (t) REVERT: J 91 THR cc_start: 0.8298 (p) cc_final: 0.7978 (t) REVERT: J 99 PHE cc_start: 0.6966 (OUTLIER) cc_final: 0.6304 (m-80) outliers start: 34 outliers final: 30 residues processed: 125 average time/residue: 0.0714 time to fit residues: 11.9741 Evaluate side-chains 132 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 99 time to evaluate : 0.277 ------------------------------------------------------------------------------- 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 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 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 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 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 25 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 chunk 27 optimal weight: 10.0000 chunk 29 optimal weight: 0.3980 chunk 17 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 23 optimal weight: 0.1980 chunk 9 optimal weight: 8.9990 chunk 26 optimal weight: 0.3980 chunk 19 optimal weight: 5.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 104 ASN ** 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** ** J 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6793 moved from start: 0.5249 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= 0.216 Angle : 0.899 9.840 3608 Z= 0.428 Chirality : 0.051 0.182 396 Planarity : 0.003 0.020 484 Dihedral : 6.075 21.093 374 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 18.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.96 % Favored : 85.04 % Rotamer: Outliers : 12.36 % Allowed : 28.00 % Favored : 59.64 % 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: -4.75 (0.31), residues: 341 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.62 (0.24), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.002 PHE I 99 *********************** 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 143 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 109 time to evaluate : 0.303 Fit side-chains REVERT: A 88 LEU cc_start: 0.7004 (OUTLIER) cc_final: 0.6294 (mt) REVERT: B 88 LEU cc_start: 0.7135 (OUTLIER) cc_final: 0.6863 (mt) REVERT: C 91 THR cc_start: 0.8600 (p) cc_final: 0.8207 (t) REVERT: E 91 THR cc_start: 0.8679 (p) cc_final: 0.8263 (t) REVERT: F 91 THR cc_start: 0.8643 (p) cc_final: 0.8304 (t) REVERT: H 91 THR cc_start: 0.8518 (p) cc_final: 0.8096 (t) REVERT: J 91 THR cc_start: 0.8254 (p) cc_final: 0.7945 (t) REVERT: J 99 PHE cc_start: 0.6822 (OUTLIER) cc_final: 0.6112 (m-80) outliers start: 34 outliers final: 27 residues processed: 124 average time/residue: 0.0716 time to fit residues: 11.9120 Evaluate side-chains 130 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 100 time to evaluate : 0.293 ------------------------------------------------------------------------------- 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 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 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 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 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 31 optimal weight: 8.9990 chunk 19 optimal weight: 9.9990 chunk 14 optimal weight: 8.9990 chunk 21 optimal weight: 8.9990 chunk 32 optimal weight: 0.9980 chunk 30 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.0000 chunk 20 optimal weight: 0.9980 chunk 16 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 104 ASN ** 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 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6805 moved from start: 0.5440 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= 0.224 Angle : 0.881 9.795 3608 Z= 0.423 Chirality : 0.051 0.183 396 Planarity : 0.003 0.027 484 Dihedral : 6.058 21.049 374 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 17.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.60 % Favored : 82.40 % Rotamer: Outliers : 12.00 % Allowed : 28.00 % Favored : 60.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.77 (0.31), residues: 341 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.63 (0.24), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.002 PHE I 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 144 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 111 time to evaluate : 0.238 Fit side-chains REVERT: A 88 LEU cc_start: 0.6703 (OUTLIER) cc_final: 0.6057 (mt) REVERT: B 88 LEU cc_start: 0.7180 (OUTLIER) cc_final: 0.6944 (mt) REVERT: C 91 THR cc_start: 0.8609 (p) cc_final: 0.8348 (t) REVERT: F 91 THR cc_start: 0.8634 (p) cc_final: 0.8303 (t) REVERT: H 91 THR cc_start: 0.8517 (p) cc_final: 0.8055 (t) REVERT: J 91 THR cc_start: 0.8257 (p) cc_final: 0.7914 (t) REVERT: J 99 PHE cc_start: 0.6717 (OUTLIER) cc_final: 0.6009 (m-80) outliers start: 33 outliers final: 28 residues processed: 125 average time/residue: 0.0707 time to fit residues: 11.7653 Evaluate side-chains 141 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 110 time to evaluate : 0.279 ------------------------------------------------------------------------------- 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 98 LEU Chi-restraints excluded: chain B residue 101 SER 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 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 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 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 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 8 optimal weight: 2.9990 chunk 24 optimal weight: 20.0000 chunk 3 optimal weight: 20.0000 chunk 7 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 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 102 GLN ** K 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6828 moved from start: 0.5475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2673 Z= 0.243 Angle : 0.886 9.731 3608 Z= 0.428 Chirality : 0.051 0.183 396 Planarity : 0.003 0.026 484 Dihedral : 6.112 21.904 374 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 19.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.30 % Favored : 82.70 % Rotamer: Outliers : 12.00 % Allowed : 28.73 % 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: -4.82 (0.30), residues: 341 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.66 (0.23), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.002 PHE I 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 140 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 107 time to evaluate : 0.295 Fit side-chains REVERT: A 88 LEU cc_start: 0.6627 (OUTLIER) cc_final: 0.6031 (mt) REVERT: B 88 LEU cc_start: 0.7161 (OUTLIER) cc_final: 0.6934 (mt) REVERT: C 91 THR cc_start: 0.8617 (p) cc_final: 0.8355 (t) REVERT: F 91 THR cc_start: 0.8618 (p) cc_final: 0.8283 (t) REVERT: H 91 THR cc_start: 0.8525 (p) cc_final: 0.8140 (t) REVERT: J 99 PHE cc_start: 0.6832 (OUTLIER) cc_final: 0.6092 (m-80) outliers start: 33 outliers final: 28 residues processed: 120 average time/residue: 0.0712 time to fit residues: 11.4675 Evaluate side-chains 134 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 103 time to evaluate : 0.281 ------------------------------------------------------------------------------- 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 98 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 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 17 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 19 optimal weight: 0.8980 chunk 12 optimal weight: 7.9990 chunk 32 optimal weight: 0.1980 chunk 1 optimal weight: 0.3980 chunk 31 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 102 GLN ** J 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 102 GLN ** 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 = 0.4482 r_free = 0.4482 target = 0.189641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.171998 restraints weight = 3967.437| |-----------------------------------------------------------------------------| r_work (start): 0.4301 rms_B_bonded: 3.11 r_work: 0.4187 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.4187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.5417 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= 0.303 Angle : 0.905 9.615 3608 Z= 0.449 Chirality : 0.053 0.186 396 Planarity : 0.003 0.023 484 Dihedral : 6.531 23.606 374 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 19.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.18 % Favored : 81.82 % 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: -4.80 (0.31), residues: 341 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.65 (0.23), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.002 PHE D 114 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1085.47 seconds wall clock time: 19 minutes 53.29 seconds (1193.29 seconds total)