Starting phenix.real_space_refine on Sun Mar 10 14:38:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3k_29700/03_2024/8g3k_29700.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3k_29700/03_2024/8g3k_29700.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3k_29700/03_2024/8g3k_29700.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3k_29700/03_2024/8g3k_29700.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3k_29700/03_2024/8g3k_29700.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3k_29700/03_2024/8g3k_29700.pdb" } resolution = 2.2 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= 0.003 sd= 0.096 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 10 5.16 5 C 1425 2.51 5 N 386 2.21 5 O 423 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 2244 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1069 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 2, 'TRANS': 133} Chain breaks: 1 Chain: "B" Number of atoms: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1175 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 2, 'TRANS': 146} Time building chain proxies: 1.76, per 1000 atoms: 0.78 Number of scatterers: 2244 At special positions: 0 Unit cell: (56, 72, 73, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 10 16.00 O 423 8.00 N 386 7.00 C 1425 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 - 3.50 Amino acid : False - 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: 0.92 Conformation dependent library (CDL) restraints added in 407.7 milliseconds 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 528 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 0 sheets defined 87.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 24 through 45 Processing helix chain 'A' and resid 46 through 48 No H-bonds generated for 'chain 'A' and resid 46 through 48' Processing helix chain 'A' and resid 49 through 72 Processing helix chain 'A' and resid 80 through 96 removed outlier: 3.692A pdb=" N ILE A 84 " --> pdb=" O SER A 80 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLU A 96 " --> pdb=" O GLU A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 136 Processing helix chain 'A' and resid 138 through 165 Processing helix chain 'B' and resid 24 through 46 Processing helix chain 'B' and resid 48 through 72 Processing helix chain 'B' and resid 79 through 98 removed outlier: 3.678A pdb=" N ILE B 83 " --> pdb=" O THR B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 134 removed outlier: 3.579A pdb=" N GLU B 134 " --> pdb=" O LYS B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 171 removed outlier: 4.001A pdb=" N LEU B 143 " --> pdb=" O ASN B 139 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU B 171 " --> pdb=" O LEU B 167 " (cutoff:3.500A) 201 hydrogen bonds defined for protein. 603 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: 0.57 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 749 1.34 - 1.46: 322 1.46 - 1.58: 1177 1.58 - 1.69: 0 1.69 - 1.81: 19 Bond restraints: 2267 Sorted by residual: bond pdb=" C ALA A 146 " pdb=" O ALA A 146 " ideal model delta sigma weight residual 1.236 1.244 -0.007 1.15e-02 7.56e+03 3.71e-01 bond pdb=" CG1 ILE A 120 " pdb=" CD1 ILE A 120 " ideal model delta sigma weight residual 1.513 1.489 0.024 3.90e-02 6.57e+02 3.69e-01 bond pdb=" C ASP A 25 " pdb=" N PRO A 26 " ideal model delta sigma weight residual 1.335 1.344 -0.008 1.36e-02 5.41e+03 3.60e-01 bond pdb=" C PHE B 56 " pdb=" O PHE B 56 " ideal model delta sigma weight residual 1.237 1.244 -0.007 1.19e-02 7.06e+03 3.51e-01 bond pdb=" C ASP B 61 " pdb=" O ASP B 61 " ideal model delta sigma weight residual 1.236 1.229 0.007 1.26e-02 6.30e+03 3.19e-01 ... (remaining 2262 not shown) Histogram of bond angle deviations from ideal: 100.39 - 107.11: 30 107.11 - 113.82: 1325 113.82 - 120.54: 908 120.54 - 127.25: 769 127.25 - 133.97: 11 Bond angle restraints: 3043 Sorted by residual: angle pdb=" CA LEU B 43 " pdb=" CB LEU B 43 " pdb=" CG LEU B 43 " ideal model delta sigma weight residual 116.30 121.09 -4.79 3.50e+00 8.16e-02 1.88e+00 angle pdb=" CA TRP A 86 " pdb=" CB TRP A 86 " pdb=" CG TRP A 86 " ideal model delta sigma weight residual 113.60 115.97 -2.37 1.90e+00 2.77e-01 1.56e+00 angle pdb=" C ASP A 25 " pdb=" N PRO A 26 " pdb=" CD PRO A 26 " ideal model delta sigma weight residual 125.00 129.81 -4.81 4.10e+00 5.95e-02 1.38e+00 angle pdb=" N GLY A 138 " pdb=" CA GLY A 138 " pdb=" C GLY A 138 " ideal model delta sigma weight residual 113.18 115.93 -2.75 2.37e+00 1.78e-01 1.34e+00 angle pdb=" C VAL B 64 " pdb=" N LEU B 65 " pdb=" CA LEU B 65 " ideal model delta sigma weight residual 120.29 121.61 -1.32 1.42e+00 4.96e-01 8.65e-01 ... (remaining 3038 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 1349 17.96 - 35.93: 38 35.93 - 53.89: 9 53.89 - 71.85: 2 71.85 - 89.82: 1 Dihedral angle restraints: 1399 sinusoidal: 582 harmonic: 817 Sorted by residual: dihedral pdb=" CB ARG B 127 " pdb=" CG ARG B 127 " pdb=" CD ARG B 127 " pdb=" NE ARG B 127 " ideal model delta sinusoidal sigma weight residual -60.00 -112.92 52.92 3 1.50e+01 4.44e-03 9.16e+00 dihedral pdb=" CA ARG A 122 " pdb=" CB ARG A 122 " pdb=" CG ARG A 122 " pdb=" CD ARG A 122 " ideal model delta sinusoidal sigma weight residual -60.00 -106.90 46.90 3 1.50e+01 4.44e-03 8.41e+00 dihedral pdb=" N GLU A 134 " pdb=" CA GLU A 134 " pdb=" CB GLU A 134 " pdb=" CG GLU A 134 " ideal model delta sinusoidal sigma weight residual -180.00 -137.08 -42.92 3 1.50e+01 4.44e-03 7.71e+00 ... (remaining 1396 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 246 0.025 - 0.049: 60 0.049 - 0.074: 36 0.074 - 0.098: 10 0.098 - 0.123: 6 Chirality restraints: 358 Sorted by residual: chirality pdb=" CA ILE B 138 " pdb=" N ILE B 138 " pdb=" C ILE B 138 " pdb=" CB ILE B 138 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.77e-01 chirality pdb=" CA ILE A 76 " pdb=" N ILE A 76 " pdb=" C ILE A 76 " pdb=" CB ILE A 76 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.42e-01 chirality pdb=" CA ILE A 137 " pdb=" N ILE A 137 " pdb=" C ILE A 137 " pdb=" CB ILE A 137 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.11 2.00e-01 2.50e+01 2.96e-01 ... (remaining 355 not shown) Planarity restraints: 384 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 145 " -0.009 2.00e-02 2.50e+03 4.88e-03 4.76e-01 pdb=" CG TYR B 145 " 0.007 2.00e-02 2.50e+03 pdb=" CD1 TYR B 145 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR B 145 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR B 145 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 145 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 145 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 145 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 38 " 0.003 2.00e-02 2.50e+03 6.22e-03 3.86e-01 pdb=" C THR A 38 " -0.011 2.00e-02 2.50e+03 pdb=" O THR A 38 " 0.004 2.00e-02 2.50e+03 pdb=" N SER A 39 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 86 " -0.006 2.00e-02 2.50e+03 3.83e-03 3.66e-01 pdb=" CG TRP A 86 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 TRP A 86 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP A 86 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 86 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 86 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 86 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 86 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 86 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 86 " 0.000 2.00e-02 2.50e+03 ... (remaining 381 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 739 2.86 - 3.37: 2386 3.37 - 3.88: 3896 3.88 - 4.39: 4210 4.39 - 4.90: 7179 Nonbonded interactions: 18410 Sorted by model distance: nonbonded pdb=" OD1 ASP B 49 " pdb=" NH2 ARG B 52 " model vdw 2.348 2.520 nonbonded pdb=" O ILE A 91 " pdb=" OG SER A 95 " model vdw 2.386 2.440 nonbonded pdb=" OE2 GLU A 81 " pdb=" ND2 ASN B 151 " model vdw 2.403 2.520 nonbonded pdb=" OE2 GLU B 126 " pdb=" OG SER B 150 " model vdw 2.478 2.440 nonbonded pdb=" O GLU A 57 " pdb=" ND2 ASN A 61 " model vdw 2.493 2.520 ... (remaining 18405 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.990 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: 4.990 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.310 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:10.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 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 : 0.002 0.024 2267 Z= 0.123 Angle : 0.357 4.810 3043 Z= 0.191 Chirality : 0.033 0.123 358 Planarity : 0.002 0.016 384 Dihedral : 9.977 89.815 871 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % 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: 5.07 (0.45), residues: 279 helix: 3.75 (0.29), residues: 232 sheet: None (None), residues: 0 loop : 1.02 (0.88), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 86 HIS 0.001 0.000 HIS A 46 PHE 0.003 0.001 PHE B 154 TYR 0.009 0.001 TYR B 145 ARG 0.002 0.000 ARG B 127 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.278 Fit side-chains revert: symmetry clash REVERT: A 65 LYS cc_start: 0.8111 (mttt) cc_final: 0.7832 (tptp) REVERT: A 134 GLU cc_start: 0.7443 (tp30) cc_final: 0.7155 (mp0) REVERT: B 164 LYS cc_start: 0.7301 (tppt) cc_final: 0.6543 (ttpt) REVERT: B 165 GLU cc_start: 0.7079 (mt-10) cc_final: 0.6644 (mt-10) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 1.6276 time to fit residues: 140.2757 Evaluate side-chains 59 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 22 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 21 optimal weight: 20.0000 chunk 8 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN B 139 ASN B 151 ASN B 161 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2267 Z= 0.228 Angle : 0.452 4.990 3043 Z= 0.244 Chirality : 0.036 0.121 358 Planarity : 0.004 0.027 384 Dihedral : 3.452 12.131 309 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 2.47 % Allowed : 10.29 % Favored : 87.24 % 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 (0.45), residues: 279 helix: 3.59 (0.29), residues: 232 sheet: None (None), residues: 0 loop : 0.71 (0.87), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 48 HIS 0.002 0.001 HIS B 156 PHE 0.006 0.001 PHE A 40 TYR 0.013 0.002 TYR B 85 ARG 0.002 0.001 ARG B 127 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 58 time to evaluate : 0.308 Fit side-chains REVERT: A 43 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8191 (tt0) REVERT: A 65 LYS cc_start: 0.8269 (mttt) cc_final: 0.7895 (mmmt) REVERT: A 134 GLU cc_start: 0.7500 (tp30) cc_final: 0.7011 (mp0) REVERT: B 164 LYS cc_start: 0.7548 (tppt) cc_final: 0.6833 (tttp) outliers start: 6 outliers final: 2 residues processed: 61 average time/residue: 1.8065 time to fit residues: 111.7629 Evaluate side-chains 57 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 54 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain B residue 77 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 13 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 2267 Z= 0.254 Angle : 0.479 5.502 3043 Z= 0.255 Chirality : 0.037 0.123 358 Planarity : 0.004 0.028 384 Dihedral : 3.561 12.678 309 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 4.12 % Allowed : 11.93 % Favored : 83.95 % 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: 4.47 (0.45), residues: 279 helix: 3.40 (0.29), residues: 232 sheet: None (None), residues: 0 loop : 0.43 (0.86), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP B 48 HIS 0.002 0.001 HIS B 116 PHE 0.006 0.001 PHE A 40 TYR 0.014 0.003 TYR B 85 ARG 0.002 0.000 ARG B 163 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 58 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: A 65 LYS cc_start: 0.8226 (mttt) cc_final: 0.7881 (mmmt) REVERT: A 81 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7585 (mp0) REVERT: A 134 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7202 (mp0) REVERT: B 67 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7699 (mt-10) REVERT: B 137 GLU cc_start: 0.6795 (tp30) cc_final: 0.6510 (tm-30) REVERT: B 164 LYS cc_start: 0.7567 (tppt) cc_final: 0.6898 (tttp) REVERT: B 165 GLU cc_start: 0.7421 (mt-10) cc_final: 0.7127 (mt-10) REVERT: B 166 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6940 (mt-10) outliers start: 10 outliers final: 3 residues processed: 62 average time/residue: 1.7766 time to fit residues: 111.7350 Evaluate side-chains 63 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 56 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 166 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 12 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 23 optimal weight: 0.8980 chunk 7 optimal weight: 7.9990 chunk 21 optimal weight: 0.4980 chunk 14 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 2267 Z= 0.162 Angle : 0.421 6.308 3043 Z= 0.225 Chirality : 0.034 0.123 358 Planarity : 0.003 0.019 384 Dihedral : 3.381 11.505 309 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 2.06 % Allowed : 13.58 % Favored : 84.36 % 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: 4.68 (0.45), residues: 279 helix: 3.53 (0.29), residues: 232 sheet: None (None), residues: 0 loop : 0.55 (0.88), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP B 48 HIS 0.001 0.001 HIS B 116 PHE 0.003 0.001 PHE A 40 TYR 0.011 0.002 TYR B 145 ARG 0.001 0.000 ARG B 163 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 60 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: A 43 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8223 (tt0) REVERT: A 65 LYS cc_start: 0.8212 (mttt) cc_final: 0.7863 (mmmt) REVERT: A 81 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7586 (mp0) REVERT: B 164 LYS cc_start: 0.7507 (tppt) cc_final: 0.6844 (tttp) REVERT: B 166 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6942 (mt-10) outliers start: 5 outliers final: 2 residues processed: 64 average time/residue: 1.7102 time to fit residues: 111.0486 Evaluate side-chains 64 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 59 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain B residue 166 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 19 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 18 optimal weight: 0.0970 chunk 0 optimal weight: 8.9990 chunk 13 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 6 optimal weight: 0.3980 chunk 8 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 15 optimal weight: 8.9990 overall best weight: 1.0380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 2267 Z= 0.151 Angle : 0.419 7.342 3043 Z= 0.222 Chirality : 0.034 0.122 358 Planarity : 0.002 0.016 384 Dihedral : 3.311 11.313 309 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 2.47 % Allowed : 14.81 % Favored : 82.72 % 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 (0.45), residues: 279 helix: 3.58 (0.29), residues: 233 sheet: None (None), residues: 0 loop : 0.76 (0.91), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP B 48 HIS 0.001 0.001 HIS B 156 PHE 0.003 0.000 PHE A 40 TYR 0.010 0.002 TYR B 145 ARG 0.001 0.000 ARG B 163 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 60 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: A 43 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8206 (tt0) REVERT: A 65 LYS cc_start: 0.8235 (mttt) cc_final: 0.7872 (mmmt) REVERT: A 81 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7577 (mp0) REVERT: B 67 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7597 (mt-10) REVERT: B 164 LYS cc_start: 0.7490 (tppt) cc_final: 0.6804 (tttp) outliers start: 6 outliers final: 3 residues processed: 64 average time/residue: 1.7453 time to fit residues: 113.2931 Evaluate side-chains 64 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 58 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 77 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 6 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2267 Z= 0.139 Angle : 0.415 7.845 3043 Z= 0.218 Chirality : 0.033 0.122 358 Planarity : 0.002 0.014 384 Dihedral : 3.248 10.924 309 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 2.88 % Allowed : 14.81 % Favored : 82.30 % 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 (0.46), residues: 279 helix: 3.51 (0.30), residues: 236 sheet: None (None), residues: 0 loop : 0.57 (0.94), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP B 48 HIS 0.001 0.000 HIS B 156 PHE 0.003 0.000 PHE A 135 TYR 0.010 0.002 TYR B 85 ARG 0.001 0.000 ARG B 163 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 59 time to evaluate : 0.273 Fit side-chains revert: symmetry clash REVERT: A 65 LYS cc_start: 0.8233 (mttt) cc_final: 0.7885 (mmtm) REVERT: A 81 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7581 (mp0) REVERT: B 67 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7407 (mt-10) REVERT: B 164 LYS cc_start: 0.7489 (tppt) cc_final: 0.6800 (tttp) outliers start: 7 outliers final: 4 residues processed: 64 average time/residue: 1.6094 time to fit residues: 104.7176 Evaluate side-chains 64 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 58 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 77 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 15 optimal weight: 7.9990 chunk 12 optimal weight: 9.9990 chunk 16 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 5 optimal weight: 0.0030 chunk 17 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2267 Z= 0.133 Angle : 0.412 8.023 3043 Z= 0.216 Chirality : 0.033 0.120 358 Planarity : 0.002 0.013 384 Dihedral : 3.204 10.803 309 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 2.88 % Allowed : 14.81 % Favored : 82.30 % 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 (0.46), residues: 279 helix: 3.54 (0.30), residues: 236 sheet: None (None), residues: 0 loop : 0.59 (0.94), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP B 48 HIS 0.001 0.000 HIS B 156 PHE 0.003 0.000 PHE A 135 TYR 0.009 0.001 TYR B 145 ARG 0.001 0.000 ARG B 119 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 59 time to evaluate : 0.272 Fit side-chains revert: symmetry clash REVERT: A 43 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8207 (tt0) REVERT: A 49 ASP cc_start: 0.7721 (p0) cc_final: 0.7455 (p0) REVERT: A 65 LYS cc_start: 0.8218 (mttt) cc_final: 0.7871 (mmtm) REVERT: A 81 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7586 (mp0) REVERT: B 67 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7385 (mt-10) REVERT: B 164 LYS cc_start: 0.7466 (tppt) cc_final: 0.6791 (tttp) REVERT: B 165 GLU cc_start: 0.7221 (mt-10) cc_final: 0.6792 (mt-10) outliers start: 7 outliers final: 4 residues processed: 64 average time/residue: 1.7416 time to fit residues: 113.1584 Evaluate side-chains 66 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 59 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 77 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 22 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 19 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 21 optimal weight: 0.2980 chunk 15 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2267 Z= 0.194 Angle : 0.472 9.119 3043 Z= 0.247 Chirality : 0.035 0.120 358 Planarity : 0.003 0.016 384 Dihedral : 3.406 12.044 309 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 2.88 % Allowed : 15.23 % Favored : 81.89 % 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: 4.57 (0.46), residues: 279 helix: 3.50 (0.30), residues: 233 sheet: None (None), residues: 0 loop : 0.12 (0.86), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP B 48 HIS 0.001 0.001 HIS B 116 PHE 0.006 0.001 PHE A 135 TYR 0.014 0.002 TYR B 85 ARG 0.001 0.000 ARG B 163 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 58 time to evaluate : 0.286 Fit side-chains revert: symmetry clash REVERT: A 43 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8169 (tt0) REVERT: A 65 LYS cc_start: 0.8230 (mttt) cc_final: 0.7874 (mmtm) REVERT: A 81 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7580 (mp0) REVERT: B 67 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7619 (mt-10) REVERT: B 164 LYS cc_start: 0.7488 (tppt) cc_final: 0.6762 (tttp) outliers start: 7 outliers final: 4 residues processed: 63 average time/residue: 1.6937 time to fit residues: 108.2923 Evaluate side-chains 65 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 58 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 77 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 26 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 21 optimal weight: 0.0020 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 6 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 overall best weight: 0.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN B 139 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2267 Z= 0.146 Angle : 0.438 9.156 3043 Z= 0.227 Chirality : 0.033 0.121 358 Planarity : 0.002 0.014 384 Dihedral : 3.259 11.029 309 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 2.88 % Allowed : 15.64 % Favored : 81.48 % 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: 4.65 (0.46), residues: 279 helix: 3.53 (0.30), residues: 234 sheet: None (None), residues: 0 loop : 0.21 (0.89), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B 48 HIS 0.001 0.001 HIS B 156 PHE 0.003 0.000 PHE A 40 TYR 0.009 0.001 TYR B 145 ARG 0.001 0.000 ARG B 128 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 57 time to evaluate : 0.275 Fit side-chains revert: symmetry clash REVERT: A 43 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8121 (tt0) REVERT: A 65 LYS cc_start: 0.8216 (mttt) cc_final: 0.7875 (mmtm) REVERT: A 81 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7569 (mp0) REVERT: B 67 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7422 (mt-10) REVERT: B 164 LYS cc_start: 0.7485 (tppt) cc_final: 0.6786 (tttp) outliers start: 7 outliers final: 4 residues processed: 62 average time/residue: 1.7444 time to fit residues: 109.7158 Evaluate side-chains 63 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 56 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 77 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 5 optimal weight: 5.9990 chunk 21 optimal weight: 0.0670 chunk 8 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 18 optimal weight: 0.1980 chunk 1 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2267 Z= 0.132 Angle : 0.433 9.243 3043 Z= 0.223 Chirality : 0.033 0.120 358 Planarity : 0.002 0.012 384 Dihedral : 3.183 10.573 309 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 2.47 % Allowed : 16.87 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.46), residues: 279 helix: 3.55 (0.30), residues: 236 sheet: None (None), residues: 0 loop : 0.28 (0.93), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP B 48 HIS 0.001 0.000 HIS B 156 PHE 0.002 0.000 PHE A 135 TYR 0.008 0.001 TYR B 145 ARG 0.001 0.000 ARG B 128 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 58 time to evaluate : 0.275 Fit side-chains revert: symmetry clash REVERT: A 49 ASP cc_start: 0.7736 (p0) cc_final: 0.7430 (p0) REVERT: A 65 LYS cc_start: 0.8203 (mttt) cc_final: 0.7884 (mmtp) REVERT: A 133 ARG cc_start: 0.7175 (mtm110) cc_final: 0.6628 (mtt-85) REVERT: B 67 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7363 (mt-10) REVERT: B 164 LYS cc_start: 0.7456 (tppt) cc_final: 0.6757 (tttp) REVERT: B 165 GLU cc_start: 0.7219 (mt-10) cc_final: 0.6801 (mt-10) outliers start: 6 outliers final: 4 residues processed: 62 average time/residue: 1.6837 time to fit residues: 105.9763 Evaluate side-chains 62 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 57 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 77 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 18 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.149878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.123781 restraints weight = 2032.849| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.21 r_work: 0.3232 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2267 Z= 0.180 Angle : 0.472 9.674 3043 Z= 0.242 Chirality : 0.034 0.118 358 Planarity : 0.003 0.015 384 Dihedral : 3.311 11.754 309 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 2.88 % Allowed : 16.05 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 4.64 (0.46), residues: 279 helix: 3.55 (0.29), residues: 233 sheet: None (None), residues: 0 loop : 0.14 (0.89), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.004 TRP B 48 HIS 0.001 0.001 HIS A 46 PHE 0.005 0.001 PHE A 135 TYR 0.010 0.002 TYR B 145 ARG 0.001 0.000 ARG B 163 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1972.20 seconds wall clock time: 35 minutes 28.84 seconds (2128.84 seconds total)