Starting phenix.real_space_refine on Wed Nov 13 23:07:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8spa_40677/11_2024/8spa_40677.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8spa_40677/11_2024/8spa_40677.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8spa_40677/11_2024/8spa_40677.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8spa_40677/11_2024/8spa_40677.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8spa_40677/11_2024/8spa_40677.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8spa_40677/11_2024/8spa_40677.cif" } resolution = 3.0 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 4 Type Number sf(0) Gaussians S 5 5.16 5 C 1210 2.51 5 N 300 2.21 5 O 355 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-5513/modules/chem_data/mon_lib" Total number of atoms: 1870 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 374 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 4, 'TRANS': 44} Restraints were copied for chains: C, B, E, D Time building chain proxies: 2.52, per 1000 atoms: 1.35 Number of scatterers: 1870 At special positions: 0 Unit cell: (63.64, 61.06, 48.16, 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 5 16.00 O 355 8.00 N 300 7.00 C 1210 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: 0.48 Conformation dependent library (CDL) restraints added in 239.0 milliseconds 470 Ramachandran restraints generated. 235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 430 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 1 sheets defined 0.0% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 32 through 37 removed outlier: 6.782A pdb=" N MET A 33 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N GLN C 36 " --> pdb=" O MET A 33 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N PHE A 35 " --> pdb=" O GLN C 36 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N MET C 33 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N GLN E 36 " --> pdb=" O MET C 33 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N PHE C 35 " --> pdb=" O GLN E 36 " (cutoff:3.500A) 10 hydrogen bonds defined for protein. 30 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: 0.31 Time building geometry restraints manager: 0.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 585 1.34 - 1.46: 441 1.46 - 1.57: 904 1.57 - 1.69: 0 1.69 - 1.80: 10 Bond restraints: 1940 Sorted by residual: bond pdb=" CB VAL A 29 " pdb=" CG1 VAL A 29 " ideal model delta sigma weight residual 1.521 1.483 0.038 3.30e-02 9.18e+02 1.30e+00 bond pdb=" CB VAL D 29 " pdb=" CG1 VAL D 29 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.26e+00 bond pdb=" CB VAL E 29 " pdb=" CG1 VAL E 29 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.26e+00 bond pdb=" CB VAL B 29 " pdb=" CG1 VAL B 29 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.25e+00 bond pdb=" CB VAL C 29 " pdb=" CG1 VAL C 29 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.24e+00 ... (remaining 1935 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 2416 1.10 - 2.19: 169 2.19 - 3.29: 54 3.29 - 4.39: 6 4.39 - 5.48: 10 Bond angle restraints: 2655 Sorted by residual: angle pdb=" C PRO D 39 " pdb=" N HIS D 40 " pdb=" CA HIS D 40 " ideal model delta sigma weight residual 122.08 118.87 3.21 1.59e+00 3.96e-01 4.06e+00 angle pdb=" C PRO B 39 " pdb=" N HIS B 40 " pdb=" CA HIS B 40 " ideal model delta sigma weight residual 122.08 118.90 3.18 1.59e+00 3.96e-01 4.01e+00 angle pdb=" C PRO E 39 " pdb=" N HIS E 40 " pdb=" CA HIS E 40 " ideal model delta sigma weight residual 122.08 118.90 3.18 1.59e+00 3.96e-01 4.00e+00 angle pdb=" C PRO A 39 " pdb=" N HIS A 40 " pdb=" CA HIS A 40 " ideal model delta sigma weight residual 122.08 118.94 3.14 1.59e+00 3.96e-01 3.89e+00 angle pdb=" C PRO C 39 " pdb=" N HIS C 40 " pdb=" CA HIS C 40 " ideal model delta sigma weight residual 122.08 118.97 3.11 1.59e+00 3.96e-01 3.83e+00 ... (remaining 2650 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 6.72: 796 6.72 - 13.44: 129 13.44 - 20.17: 75 20.17 - 26.89: 30 26.89 - 33.61: 20 Dihedral angle restraints: 1050 sinusoidal: 380 harmonic: 670 Sorted by residual: dihedral pdb=" CA HIS A 40 " pdb=" C HIS A 40 " pdb=" N HIS A 41 " pdb=" CA HIS A 41 " ideal model delta harmonic sigma weight residual 180.00 160.78 19.22 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA HIS B 40 " pdb=" C HIS B 40 " pdb=" N HIS B 41 " pdb=" CA HIS B 41 " ideal model delta harmonic sigma weight residual 180.00 160.82 19.18 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA HIS D 40 " pdb=" C HIS D 40 " pdb=" N HIS D 41 " pdb=" CA HIS D 41 " ideal model delta harmonic sigma weight residual 180.00 160.83 19.17 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 1047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 151 0.030 - 0.060: 94 0.060 - 0.090: 23 0.090 - 0.120: 7 0.120 - 0.150: 10 Chirality restraints: 285 Sorted by residual: chirality pdb=" CA HIS C 40 " pdb=" N HIS C 40 " pdb=" C HIS C 40 " pdb=" CB HIS C 40 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.61e-01 chirality pdb=" CA HIS B 40 " pdb=" N HIS B 40 " pdb=" C HIS B 40 " pdb=" CB HIS B 40 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.49e-01 chirality pdb=" CA HIS E 40 " pdb=" N HIS E 40 " pdb=" C HIS E 40 " pdb=" CB HIS E 40 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.45e-01 ... (remaining 282 not shown) Planarity restraints: 350 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN E 43 " 0.022 5.00e-02 4.00e+02 3.39e-02 1.84e+00 pdb=" N PRO E 44 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO E 44 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO E 44 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 43 " 0.022 5.00e-02 4.00e+02 3.39e-02 1.84e+00 pdb=" N PRO A 44 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 44 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 44 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 43 " 0.022 5.00e-02 4.00e+02 3.38e-02 1.83e+00 pdb=" N PRO B 44 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO B 44 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 44 " 0.019 5.00e-02 4.00e+02 ... (remaining 347 not shown) Histogram of nonbonded interaction distances: 2.61 - 3.07: 1221 3.07 - 3.53: 1837 3.53 - 3.99: 2653 3.99 - 4.44: 3041 4.44 - 4.90: 5102 Nonbonded interactions: 13854 Sorted by model distance: nonbonded pdb=" O HIS D 40 " pdb=" ND1 HIS D 41 " model vdw 2.614 3.120 nonbonded pdb=" O HIS B 40 " pdb=" ND1 HIS B 41 " model vdw 2.614 3.120 nonbonded pdb=" O HIS E 40 " pdb=" ND1 HIS E 41 " model vdw 2.614 3.120 nonbonded pdb=" O HIS A 40 " pdb=" ND1 HIS A 41 " model vdw 2.614 3.120 nonbonded pdb=" O HIS C 40 " pdb=" ND1 HIS C 41 " model vdw 2.614 3.120 ... (remaining 13849 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' } 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: 3.020 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: 0.020 Process input model: 10.540 Find NCS groups from input model: 0.070 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:14.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 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 : 0.006 0.038 1940 Z= 0.392 Angle : 0.753 5.482 2655 Z= 0.403 Chirality : 0.045 0.150 285 Planarity : 0.005 0.034 350 Dihedral : 10.816 33.609 620 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % 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: -3.14 (0.42), residues: 235 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.38 (0.32), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.001 TRP D 10 HIS 0.005 0.002 HIS D 40 PHE 0.012 0.002 PHE A 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 470 Ramachandran restraints generated. 235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 470 Ramachandran restraints generated. 235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.222 Fit side-chains REVERT: C 10 TRP cc_start: 0.7650 (t-100) cc_final: 0.6809 (t-100) REVERT: D 19 GLU cc_start: 0.7977 (tt0) cc_final: 0.7568 (tm-30) REVERT: E 33 MET cc_start: 0.8984 (mtp) cc_final: 0.8663 (mtt) outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.8243 time to fit residues: 37.3684 Evaluate side-chains 18 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 0.7980 chunk 15 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 5 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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: 0.8056 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 1940 Z= 0.232 Angle : 0.684 5.093 2655 Z= 0.344 Chirality : 0.042 0.145 285 Planarity : 0.003 0.018 350 Dihedral : 6.227 20.563 240 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 2.38 % Allowed : 15.24 % Favored : 82.38 % 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: -2.77 (0.44), residues: 235 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.11 (0.34), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 10 HIS 0.006 0.001 HIS C 40 PHE 0.011 0.001 PHE A 35 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 470 Ramachandran restraints generated. 235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 470 Ramachandran restraints generated. 235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.186 Fit side-chains revert: symmetry clash REVERT: C 10 TRP cc_start: 0.7703 (t-100) cc_final: 0.6948 (t-100) REVERT: D 19 GLU cc_start: 0.7648 (tt0) cc_final: 0.7256 (tm-30) REVERT: E 33 MET cc_start: 0.8833 (mtp) cc_final: 0.8561 (mtt) outliers start: 5 outliers final: 4 residues processed: 32 average time/residue: 0.7685 time to fit residues: 25.4272 Evaluate side-chains 25 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 49 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 17 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1940 Z= 0.224 Angle : 0.653 6.017 2655 Z= 0.324 Chirality : 0.042 0.144 285 Planarity : 0.003 0.018 350 Dihedral : 5.951 19.952 240 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 2.86 % Allowed : 17.14 % Favored : 80.00 % 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: -2.71 (0.44), residues: 235 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.06 (0.33), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 10 HIS 0.005 0.002 HIS A 40 PHE 0.011 0.001 PHE C 35 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 470 Ramachandran restraints generated. 235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 470 Ramachandran restraints generated. 235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 27 time to evaluate : 0.184 Fit side-chains revert: symmetry clash REVERT: C 10 TRP cc_start: 0.7797 (t-100) cc_final: 0.6544 (t-100) REVERT: E 10 TRP cc_start: 0.7205 (t-100) cc_final: 0.5470 (p-90) REVERT: E 33 MET cc_start: 0.8874 (mtp) cc_final: 0.7933 (pmt) outliers start: 6 outliers final: 3 residues processed: 31 average time/residue: 0.4839 time to fit residues: 15.7538 Evaluate side-chains 23 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 20 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain D residue 49 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 9 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN ** B 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 1940 Z= 0.262 Angle : 0.666 7.657 2655 Z= 0.330 Chirality : 0.042 0.146 285 Planarity : 0.003 0.021 350 Dihedral : 6.106 20.215 240 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 3.33 % Allowed : 20.00 % Favored : 76.67 % 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: -2.71 (0.44), residues: 235 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.06 (0.33), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 10 HIS 0.005 0.002 HIS C 40 PHE 0.011 0.002 PHE C 35 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 470 Ramachandran restraints generated. 235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 470 Ramachandran restraints generated. 235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 25 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: C 10 TRP cc_start: 0.7887 (t-100) cc_final: 0.6650 (t-100) REVERT: E 10 TRP cc_start: 0.7180 (t-100) cc_final: 0.5336 (p-90) REVERT: E 33 MET cc_start: 0.8882 (mtp) cc_final: 0.8035 (pmt) outliers start: 7 outliers final: 3 residues processed: 30 average time/residue: 0.5515 time to fit residues: 17.4133 Evaluate side-chains 24 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 49 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 17 optimal weight: 8.9990 chunk 3 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 1940 Z= 0.248 Angle : 0.657 8.925 2655 Z= 0.323 Chirality : 0.041 0.144 285 Planarity : 0.003 0.023 350 Dihedral : 6.042 19.974 240 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 4.76 % Allowed : 18.10 % Favored : 77.14 % 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: -2.71 (0.44), residues: 235 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.06 (0.33), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 10 HIS 0.005 0.002 HIS C 40 PHE 0.010 0.001 PHE C 35 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 470 Ramachandran restraints generated. 235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 470 Ramachandran restraints generated. 235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 24 time to evaluate : 0.226 Fit side-chains revert: symmetry clash REVERT: C 10 TRP cc_start: 0.7939 (t-100) cc_final: 0.6699 (t-100) REVERT: E 10 TRP cc_start: 0.7174 (t-100) cc_final: 0.5384 (p-90) REVERT: E 33 MET cc_start: 0.9031 (mtp) cc_final: 0.8062 (pmt) outliers start: 10 outliers final: 7 residues processed: 32 average time/residue: 0.5216 time to fit residues: 17.4933 Evaluate side-chains 27 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 20 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 42 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 2 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 14 optimal weight: 0.3980 chunk 10 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 7 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN B 36 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 1940 Z= 0.195 Angle : 0.634 9.106 2655 Z= 0.307 Chirality : 0.040 0.139 285 Planarity : 0.003 0.025 350 Dihedral : 5.794 20.047 240 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 5.24 % Allowed : 19.05 % Favored : 75.71 % 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: -2.67 (0.44), residues: 235 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.03 (0.34), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 10 HIS 0.005 0.001 HIS C 40 PHE 0.017 0.001 PHE B 50 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 470 Ramachandran restraints generated. 235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 470 Ramachandran restraints generated. 235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 27 time to evaluate : 0.225 Fit side-chains revert: symmetry clash REVERT: B 50 PHE cc_start: 0.6749 (t80) cc_final: 0.6442 (t80) REVERT: C 10 TRP cc_start: 0.7900 (t-100) cc_final: 0.6654 (t-100) REVERT: C 14 THR cc_start: 0.8935 (m) cc_final: 0.8672 (m) REVERT: E 10 TRP cc_start: 0.7152 (t-100) cc_final: 0.5452 (p-90) REVERT: E 33 MET cc_start: 0.8865 (mtp) cc_final: 0.7991 (pmt) outliers start: 11 outliers final: 7 residues processed: 36 average time/residue: 0.4123 time to fit residues: 15.7370 Evaluate side-chains 31 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 24 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 42 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 3 optimal weight: 1.9990 chunk 12 optimal weight: 0.4980 chunk 13 optimal weight: 1.9990 chunk 9 optimal weight: 8.9990 chunk 1 optimal weight: 0.3980 chunk 15 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN B 36 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 1940 Z= 0.213 Angle : 0.657 9.320 2655 Z= 0.310 Chirality : 0.040 0.139 285 Planarity : 0.003 0.025 350 Dihedral : 5.714 19.748 240 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 4.76 % Allowed : 20.95 % Favored : 74.29 % 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: -2.72 (0.44), residues: 235 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.07 (0.34), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 10 HIS 0.005 0.001 HIS C 40 PHE 0.017 0.001 PHE B 50 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 470 Ramachandran restraints generated. 235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 470 Ramachandran restraints generated. 235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 23 time to evaluate : 0.222 Fit side-chains revert: symmetry clash REVERT: C 10 TRP cc_start: 0.7820 (t-100) cc_final: 0.6538 (t-100) REVERT: E 10 TRP cc_start: 0.7168 (t-100) cc_final: 0.5424 (p-90) REVERT: E 33 MET cc_start: 0.9039 (mtp) cc_final: 0.8032 (pmt) REVERT: E 49 THR cc_start: 0.8747 (p) cc_final: 0.8404 (t) outliers start: 10 outliers final: 9 residues processed: 32 average time/residue: 0.4924 time to fit residues: 16.5896 Evaluate side-chains 30 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 21 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain E residue 14 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 14 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 1940 Z= 0.286 Angle : 0.685 9.559 2655 Z= 0.336 Chirality : 0.042 0.150 285 Planarity : 0.003 0.024 350 Dihedral : 6.030 19.362 240 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 5.71 % Allowed : 20.48 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.79 (0.44), residues: 235 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.12 (0.33), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 10 HIS 0.006 0.002 HIS C 40 PHE 0.012 0.002 PHE C 35 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 470 Ramachandran restraints generated. 235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 470 Ramachandran restraints generated. 235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 20 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 33 MET cc_start: 0.9037 (mtp) cc_final: 0.8086 (pmt) outliers start: 12 outliers final: 12 residues processed: 29 average time/residue: 0.3473 time to fit residues: 10.8504 Evaluate side-chains 31 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 19 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 42 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 12 optimal weight: 0.0980 chunk 9 optimal weight: 8.9990 chunk 16 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 0 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN B 36 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 1940 Z= 0.182 Angle : 0.643 9.502 2655 Z= 0.300 Chirality : 0.040 0.133 285 Planarity : 0.003 0.025 350 Dihedral : 5.660 19.902 240 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.29 % Allowed : 22.38 % Favored : 73.33 % 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: -2.84 (0.44), residues: 235 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.15 (0.34), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.004 TRP A 10 HIS 0.005 0.001 HIS C 40 PHE 0.025 0.001 PHE B 50 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 470 Ramachandran restraints generated. 235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 470 Ramachandran restraints generated. 235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 26 time to evaluate : 0.224 Fit side-chains revert: symmetry clash REVERT: E 10 TRP cc_start: 0.7142 (t-100) cc_final: 0.5541 (p-90) REVERT: E 22 PHE cc_start: 0.8305 (m-10) cc_final: 0.7393 (m-10) REVERT: E 33 MET cc_start: 0.8669 (mtp) cc_final: 0.7932 (pmt) REVERT: E 49 THR cc_start: 0.8444 (p) cc_final: 0.8125 (t) outliers start: 9 outliers final: 8 residues processed: 34 average time/residue: 0.4709 time to fit residues: 16.8574 Evaluate side-chains 30 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 22 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain E residue 14 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 18 optimal weight: 0.4980 chunk 10 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 12 optimal weight: 0.0980 chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN D 40 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 1940 Z= 0.207 Angle : 0.649 9.692 2655 Z= 0.306 Chirality : 0.041 0.137 285 Planarity : 0.003 0.022 350 Dihedral : 5.566 19.199 240 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 4.29 % Allowed : 23.81 % Favored : 71.90 % 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: -2.86 (0.44), residues: 235 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.17 (0.34), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A 10 HIS 0.005 0.001 HIS C 40 PHE 0.010 0.001 PHE C 35 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 470 Ramachandran restraints generated. 235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 470 Ramachandran restraints generated. 235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 22 time to evaluate : 0.250 Fit side-chains revert: symmetry clash REVERT: E 10 TRP cc_start: 0.7219 (t-100) cc_final: 0.5507 (p-90) REVERT: E 33 MET cc_start: 0.9037 (mtp) cc_final: 0.8020 (pmt) REVERT: E 49 THR cc_start: 0.8482 (p) cc_final: 0.8146 (t) outliers start: 9 outliers final: 9 residues processed: 30 average time/residue: 0.3439 time to fit residues: 11.1006 Evaluate side-chains 29 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 20 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 40 HIS Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain E residue 14 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 40 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.106833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.090626 restraints weight = 4819.537| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 3.49 r_work: 0.3816 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 1940 Z= 0.226 Angle : 0.669 9.642 2655 Z= 0.312 Chirality : 0.041 0.138 285 Planarity : 0.003 0.022 350 Dihedral : 5.614 19.264 240 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 4.76 % Allowed : 23.81 % Favored : 71.43 % 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: -2.86 (0.44), residues: 235 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.17 (0.34), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 10 HIS 0.005 0.001 HIS C 40 PHE 0.024 0.002 PHE B 50 =============================================================================== Job complete usr+sys time: 1184.46 seconds wall clock time: 26 minutes 14.53 seconds (1574.53 seconds total)