Starting phenix.real_space_refine on Mon Sep 23 11:31:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbs_6478/09_2024/3jbs_6478.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbs_6478/09_2024/3jbs_6478.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbs_6478/09_2024/3jbs_6478.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbs_6478/09_2024/3jbs_6478.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbs_6478/09_2024/3jbs_6478.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbs_6478/09_2024/3jbs_6478.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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 1 5.16 5 C 902 2.51 5 N 251 2.21 5 O 247 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 1401 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1401 Classifications: {'peptide': 175} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 165} Time building chain proxies: 1.89, per 1000 atoms: 1.35 Number of scatterers: 1401 At special positions: 0 Unit cell: (103.49, 69.43, 60.26, 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 1 16.00 O 247 8.00 N 251 7.00 C 902 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: 0.32 Conformation dependent library (CDL) restraints added in 165.4 milliseconds 346 Ramachandran restraints generated. 173 Oldfield, 0 Emsley, 173 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 336 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 1 sheets defined 29.7% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 68 through 73 Processing helix chain 'A' and resid 80 through 82 No H-bonds generated for 'chain 'A' and resid 80 through 82' Processing helix chain 'A' and resid 112 through 122 Processing helix chain 'A' and resid 123 through 126 Processing helix chain 'A' and resid 131 through 150 Processing helix chain 'A' and resid 154 through 161 Processing sheet with id=A, first strand: chain 'A' and resid 77 through 79 removed outlier: 6.418A pdb=" N LEU A 64 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N THR A 38 " --> pdb=" O TYR A 54 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N THR A 89 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N ILE A 41 " --> pdb=" O THR A 87 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N THR A 87 " --> pdb=" O ILE A 41 " (cutoff:3.500A) 41 hydrogen bonds defined for protein. 114 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: 0.28 Time building geometry restraints manager: 0.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.32: 275 1.32 - 1.44: 282 1.44 - 1.56: 866 1.56 - 1.68: 0 1.68 - 1.80: 2 Bond restraints: 1425 Sorted by residual: bond pdb=" CG ASP A 142 " pdb=" OD2 ASP A 142 " ideal model delta sigma weight residual 1.249 1.205 0.044 1.90e-02 2.77e+03 5.32e+00 bond pdb=" CD GLU A 124 " pdb=" OE1 GLU A 124 " ideal model delta sigma weight residual 1.249 1.206 0.043 1.90e-02 2.77e+03 5.13e+00 bond pdb=" CG ASP A 60 " pdb=" OD2 ASP A 60 " ideal model delta sigma weight residual 1.249 1.206 0.043 1.90e-02 2.77e+03 5.07e+00 bond pdb=" CG ASP A 169 " pdb=" OD2 ASP A 169 " ideal model delta sigma weight residual 1.249 1.206 0.043 1.90e-02 2.77e+03 5.03e+00 bond pdb=" CG ASP A 14 " pdb=" OD2 ASP A 14 " ideal model delta sigma weight residual 1.249 1.206 0.043 1.90e-02 2.77e+03 5.02e+00 ... (remaining 1420 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 1740 1.97 - 3.93: 136 3.93 - 5.89: 26 5.89 - 7.86: 8 7.86 - 9.82: 4 Bond angle restraints: 1914 Sorted by residual: angle pdb=" C LYS A 170 " pdb=" N PRO A 171 " pdb=" CA PRO A 171 " ideal model delta sigma weight residual 119.47 129.29 -9.82 1.16e+00 7.43e-01 7.17e+01 angle pdb=" C VAL A 74 " pdb=" N PRO A 75 " pdb=" CA PRO A 75 " ideal model delta sigma weight residual 120.03 127.80 -7.77 9.90e-01 1.02e+00 6.17e+01 angle pdb=" C THR A 152 " pdb=" N PRO A 153 " pdb=" CA PRO A 153 " ideal model delta sigma weight residual 119.56 127.47 -7.91 1.02e+00 9.61e-01 6.01e+01 angle pdb=" C ARG A 26 " pdb=" N PRO A 27 " pdb=" CA PRO A 27 " ideal model delta sigma weight residual 119.78 127.47 -7.69 1.03e+00 9.43e-01 5.58e+01 angle pdb=" C PHE A 122 " pdb=" N PRO A 123 " pdb=" CA PRO A 123 " ideal model delta sigma weight residual 119.28 127.41 -8.13 1.10e+00 8.26e-01 5.47e+01 ... (remaining 1909 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.52: 861 11.52 - 23.04: 25 23.04 - 34.57: 5 34.57 - 46.09: 1 46.09 - 57.61: 8 Dihedral angle restraints: 900 sinusoidal: 385 harmonic: 515 Sorted by residual: dihedral pdb=" CA TYR A 54 " pdb=" CB TYR A 54 " pdb=" CG TYR A 54 " pdb=" CD1 TYR A 54 " ideal model delta sinusoidal sigma weight residual 90.00 37.54 52.46 2 2.00e+01 2.50e-03 7.54e+00 dihedral pdb=" C ARG A 82 " pdb=" N ARG A 82 " pdb=" CA ARG A 82 " pdb=" CB ARG A 82 " ideal model delta harmonic sigma weight residual -122.60 -116.51 -6.09 0 2.50e+00 1.60e-01 5.93e+00 dihedral pdb=" CA GLU A 59 " pdb=" CB GLU A 59 " pdb=" CG GLU A 59 " pdb=" CD GLU A 59 " ideal model delta sinusoidal sigma weight residual 60.00 87.37 -27.37 3 1.50e+01 4.44e-03 4.09e+00 ... (remaining 897 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 110 0.040 - 0.079: 66 0.079 - 0.119: 31 0.119 - 0.158: 5 0.158 - 0.198: 5 Chirality restraints: 217 Sorted by residual: chirality pdb=" CA VAL A 91 " pdb=" N VAL A 91 " pdb=" C VAL A 91 " pdb=" CB VAL A 91 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 9.77e-01 chirality pdb=" CA ALA A 81 " pdb=" N ALA A 81 " pdb=" C ALA A 81 " pdb=" CB ALA A 81 " both_signs ideal model delta sigma weight residual False 2.48 2.31 0.18 2.00e-01 2.50e+01 7.68e-01 chirality pdb=" CA VAL A 35 " pdb=" N VAL A 35 " pdb=" C VAL A 35 " pdb=" CB VAL A 35 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.37e-01 ... (remaining 214 not shown) Planarity restraints: 241 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 176 " -0.014 2.00e-02 2.50e+03 2.78e-02 7.72e+00 pdb=" C PHE A 176 " 0.048 2.00e-02 2.50e+03 pdb=" O PHE A 176 " -0.017 2.00e-02 2.50e+03 pdb=" OXT PHE A 176 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 54 " -0.024 2.00e-02 2.50e+03 1.35e-02 3.65e+00 pdb=" CG TYR A 54 " 0.002 2.00e-02 2.50e+03 pdb=" CD1 TYR A 54 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR A 54 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR A 54 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A 54 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR A 54 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 54 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 152 " 0.032 5.00e-02 4.00e+02 4.77e-02 3.64e+00 pdb=" N PRO A 153 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 153 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 153 " 0.024 5.00e-02 4.00e+02 ... (remaining 238 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 681 2.99 - 3.47: 1292 3.47 - 3.94: 2189 3.94 - 4.42: 2289 4.42 - 4.90: 3627 Nonbonded interactions: 10078 Sorted by model distance: nonbonded pdb=" O VAL A 35 " pdb=" OG1 THR A 38 " model vdw 2.510 3.040 nonbonded pdb=" O PHE A 122 " pdb=" CB PHE A 122 " model vdw 2.604 2.752 nonbonded pdb=" O GLY A 67 " pdb=" CD PRO A 68 " model vdw 2.616 2.752 nonbonded pdb=" OH TYR A 105 " pdb=" OD2 ASP A 137 " model vdw 2.628 3.040 nonbonded pdb=" N TYR A 83 " pdb=" N VAL A 84 " model vdw 2.631 2.560 ... (remaining 10073 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: 1.810 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: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.560 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 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 : 0.010 0.044 1425 Z= 0.671 Angle : 1.322 9.824 1914 Z= 0.943 Chirality : 0.061 0.198 217 Planarity : 0.007 0.048 241 Dihedral : 8.674 57.610 564 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.51 (0.60), residues: 173 helix: 0.62 (0.74), residues: 45 sheet: -2.37 (1.27), residues: 11 loop : 0.66 (0.55), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.005 TRP A 9 HIS 0.006 0.002 HIS A 57 PHE 0.020 0.004 PHE A 101 TYR 0.024 0.005 TYR A 54 ARG 0.002 0.000 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 346 Ramachandran restraints generated. 173 Oldfield, 0 Emsley, 173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 346 Ramachandran restraints generated. 173 Oldfield, 0 Emsley, 173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.175 Fit side-chains REVERT: A 80 ASN cc_start: 0.8572 (t0) cc_final: 0.8356 (t0) REVERT: A 82 ARG cc_start: 0.7796 (mmt180) cc_final: 0.7045 (mtt180) REVERT: A 108 LYS cc_start: 0.3358 (mttt) cc_final: 0.2411 (tptp) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 1.5754 time to fit residues: 87.5504 Evaluate side-chains 20 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 14 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN A 57 HIS A 167 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.4268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 1425 Z= 0.195 Angle : 0.563 4.373 1914 Z= 0.301 Chirality : 0.043 0.127 217 Planarity : 0.005 0.035 241 Dihedral : 4.094 27.300 190 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.29 % Allowed : 16.45 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.52 (0.63), residues: 173 helix: 1.92 (0.75), residues: 45 sheet: -1.38 (1.38), residues: 10 loop : 1.04 (0.59), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 9 HIS 0.002 0.001 HIS A 172 PHE 0.005 0.001 PHE A 122 TYR 0.007 0.001 TYR A 158 ARG 0.003 0.001 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 346 Ramachandran restraints generated. 173 Oldfield, 0 Emsley, 173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 346 Ramachandran restraints generated. 173 Oldfield, 0 Emsley, 173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 28 time to evaluate : 0.184 Fit side-chains REVERT: A 82 ARG cc_start: 0.7947 (mmt180) cc_final: 0.7162 (mtt180) REVERT: A 108 LYS cc_start: 0.2465 (mttt) cc_final: 0.1045 (tptp) REVERT: A 122 PHE cc_start: 0.5769 (m-80) cc_final: 0.5361 (m-80) outliers start: 5 outliers final: 1 residues processed: 31 average time/residue: 0.9091 time to fit residues: 28.8209 Evaluate side-chains 24 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 23 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 4 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 16 optimal weight: 0.1980 chunk 13 optimal weight: 9.9990 chunk 5 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 7 optimal weight: 0.5980 chunk 10 optimal weight: 8.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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: 0.7744 moved from start: 0.5080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 1425 Z= 0.167 Angle : 0.503 5.426 1914 Z= 0.259 Chirality : 0.041 0.123 217 Planarity : 0.004 0.029 241 Dihedral : 3.981 28.591 190 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 5.26 % Allowed : 22.37 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.36 (0.66), residues: 173 helix: 1.82 (0.75), residues: 45 sheet: -2.03 (1.15), residues: 18 loop : 1.24 (0.64), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 9 HIS 0.002 0.001 HIS A 57 PHE 0.004 0.001 PHE A 47 TYR 0.005 0.001 TYR A 158 ARG 0.002 0.000 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 346 Ramachandran restraints generated. 173 Oldfield, 0 Emsley, 173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 346 Ramachandran restraints generated. 173 Oldfield, 0 Emsley, 173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 28 time to evaluate : 0.189 Fit side-chains REVERT: A 19 LYS cc_start: 0.8029 (mttt) cc_final: 0.7598 (mttp) REVERT: A 82 ARG cc_start: 0.7927 (mmt180) cc_final: 0.6969 (mtt180) REVERT: A 108 LYS cc_start: 0.2571 (mttt) cc_final: 0.1504 (tptm) REVERT: A 122 PHE cc_start: 0.5354 (OUTLIER) cc_final: 0.4809 (m-80) outliers start: 8 outliers final: 4 residues processed: 32 average time/residue: 1.0038 time to fit residues: 32.7861 Evaluate side-chains 26 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 21 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 15 optimal weight: 10.0000 chunk 16 optimal weight: 0.0270 chunk 8 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 9 optimal weight: 20.0000 chunk 0 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 overall best weight: 2.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN A 167 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.5845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 1425 Z= 0.223 Angle : 0.557 5.380 1914 Z= 0.290 Chirality : 0.043 0.120 217 Planarity : 0.004 0.024 241 Dihedral : 4.119 25.879 190 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 7.24 % Allowed : 20.39 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.94 (0.65), residues: 173 helix: 1.23 (0.75), residues: 45 sheet: -1.94 (1.22), residues: 18 loop : 1.02 (0.62), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 9 HIS 0.003 0.001 HIS A 57 PHE 0.005 0.001 PHE A 47 TYR 0.007 0.001 TYR A 105 ARG 0.003 0.000 ARG A 51 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 346 Ramachandran restraints generated. 173 Oldfield, 0 Emsley, 173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 346 Ramachandran restraints generated. 173 Oldfield, 0 Emsley, 173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 21 time to evaluate : 0.175 Fit side-chains REVERT: A 60 ASP cc_start: 0.7316 (p0) cc_final: 0.6940 (p0) REVERT: A 82 ARG cc_start: 0.7822 (mmt180) cc_final: 0.6807 (mtt180) REVERT: A 108 LYS cc_start: 0.3010 (mttt) cc_final: 0.1607 (tptm) REVERT: A 122 PHE cc_start: 0.5439 (OUTLIER) cc_final: 0.4920 (m-80) REVERT: A 124 GLU cc_start: 0.4689 (mm-30) cc_final: 0.3792 (pt0) outliers start: 11 outliers final: 4 residues processed: 27 average time/residue: 1.0899 time to fit residues: 30.0402 Evaluate side-chains 25 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 20 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 14 optimal weight: 0.6980 chunk 4 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 9 optimal weight: 8.9990 chunk 16 optimal weight: 0.0470 chunk 13 optimal weight: 9.9990 chunk 7 optimal weight: 0.8980 chunk 1 optimal weight: 10.0000 overall best weight: 2.7282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.6437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 1425 Z= 0.224 Angle : 0.558 6.691 1914 Z= 0.287 Chirality : 0.042 0.125 217 Planarity : 0.004 0.024 241 Dihedral : 4.228 25.877 190 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 6.58 % Allowed : 23.68 % Favored : 69.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.01 (0.65), residues: 173 helix: 1.82 (0.80), residues: 39 sheet: -1.88 (1.20), residues: 18 loop : 0.86 (0.60), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.001 TRP A 9 HIS 0.002 0.001 HIS A 57 PHE 0.005 0.001 PHE A 47 TYR 0.007 0.001 TYR A 105 ARG 0.003 0.000 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 346 Ramachandran restraints generated. 173 Oldfield, 0 Emsley, 173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 346 Ramachandran restraints generated. 173 Oldfield, 0 Emsley, 173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 22 time to evaluate : 0.170 Fit side-chains REVERT: A 5 LYS cc_start: 0.3923 (mttt) cc_final: 0.3399 (mtmt) REVERT: A 28 GLN cc_start: 0.8030 (OUTLIER) cc_final: 0.6769 (tp-100) REVERT: A 60 ASP cc_start: 0.7469 (p0) cc_final: 0.7236 (p0) REVERT: A 82 ARG cc_start: 0.7957 (mmt180) cc_final: 0.6834 (mtt180) REVERT: A 108 LYS cc_start: 0.2940 (mttt) cc_final: 0.1424 (tptm) REVERT: A 122 PHE cc_start: 0.5429 (OUTLIER) cc_final: 0.4891 (m-80) outliers start: 10 outliers final: 5 residues processed: 28 average time/residue: 1.2352 time to fit residues: 35.2342 Evaluate side-chains 27 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 20 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 28 GLN Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 155 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 5 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 12 optimal weight: 0.0050 chunk 13 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 6 optimal weight: 6.9990 overall best weight: 2.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.6651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 1425 Z= 0.194 Angle : 0.548 5.941 1914 Z= 0.284 Chirality : 0.043 0.158 217 Planarity : 0.004 0.024 241 Dihedral : 4.196 26.577 190 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 5.26 % Allowed : 25.00 % Favored : 69.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.85 (0.64), residues: 173 helix: 1.55 (0.80), residues: 39 sheet: -1.93 (1.17), residues: 18 loop : 0.80 (0.60), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 9 HIS 0.002 0.001 HIS A 57 PHE 0.004 0.001 PHE A 47 TYR 0.006 0.001 TYR A 105 ARG 0.002 0.000 ARG A 51 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 346 Ramachandran restraints generated. 173 Oldfield, 0 Emsley, 173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 346 Ramachandran restraints generated. 173 Oldfield, 0 Emsley, 173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 21 time to evaluate : 0.172 Fit side-chains REVERT: A 5 LYS cc_start: 0.3852 (mttt) cc_final: 0.3447 (mttt) REVERT: A 82 ARG cc_start: 0.7872 (mmt180) cc_final: 0.6793 (mtt180) REVERT: A 108 LYS cc_start: 0.3177 (mttt) cc_final: 0.1633 (tptm) REVERT: A 122 PHE cc_start: 0.5405 (OUTLIER) cc_final: 0.4877 (m-80) REVERT: A 124 GLU cc_start: 0.4672 (mm-30) cc_final: 0.3654 (pt0) outliers start: 8 outliers final: 5 residues processed: 26 average time/residue: 1.1345 time to fit residues: 30.0731 Evaluate side-chains 27 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 21 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 9 optimal weight: 0.9980 chunk 4 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 1 optimal weight: 8.9990 chunk 12 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.6822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 1425 Z= 0.194 Angle : 0.536 6.333 1914 Z= 0.277 Chirality : 0.042 0.143 217 Planarity : 0.004 0.025 241 Dihedral : 4.173 26.392 190 Min Nonbonded Distance : 2.651 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 4.61 % Allowed : 25.00 % Favored : 70.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.87 (0.66), residues: 173 helix: 1.70 (0.85), residues: 39 sheet: -1.99 (1.16), residues: 18 loop : 0.78 (0.60), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 9 HIS 0.002 0.001 HIS A 57 PHE 0.004 0.001 PHE A 47 TYR 0.006 0.001 TYR A 105 ARG 0.003 0.000 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 346 Ramachandran restraints generated. 173 Oldfield, 0 Emsley, 173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 346 Ramachandran restraints generated. 173 Oldfield, 0 Emsley, 173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 20 time to evaluate : 0.181 Fit side-chains REVERT: A 5 LYS cc_start: 0.3752 (mttt) cc_final: 0.3270 (mttt) REVERT: A 82 ARG cc_start: 0.7973 (mmt180) cc_final: 0.6874 (mtt180) REVERT: A 108 LYS cc_start: 0.3074 (mttt) cc_final: 0.1621 (tptm) REVERT: A 122 PHE cc_start: 0.5393 (OUTLIER) cc_final: 0.4841 (m-80) outliers start: 7 outliers final: 5 residues processed: 24 average time/residue: 1.0093 time to fit residues: 24.7908 Evaluate side-chains 26 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 20 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 11 optimal weight: 7.9990 chunk 4 optimal weight: 9.9990 chunk 13 optimal weight: 8.9990 chunk 14 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.7063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 1425 Z= 0.247 Angle : 0.561 6.123 1914 Z= 0.295 Chirality : 0.043 0.137 217 Planarity : 0.004 0.026 241 Dihedral : 4.340 23.846 190 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 3.95 % Allowed : 26.32 % Favored : 69.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.70 (0.65), residues: 173 helix: 1.58 (0.86), residues: 39 sheet: -1.99 (1.19), residues: 18 loop : 0.63 (0.59), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.001 TRP A 9 HIS 0.002 0.001 HIS A 57 PHE 0.005 0.001 PHE A 47 TYR 0.009 0.001 TYR A 105 ARG 0.002 0.000 ARG A 51 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 346 Ramachandran restraints generated. 173 Oldfield, 0 Emsley, 173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 346 Ramachandran restraints generated. 173 Oldfield, 0 Emsley, 173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 19 time to evaluate : 0.184 Fit side-chains REVERT: A 5 LYS cc_start: 0.3770 (mttt) cc_final: 0.3322 (mttt) REVERT: A 82 ARG cc_start: 0.8098 (mmt180) cc_final: 0.6904 (mtt180) REVERT: A 108 LYS cc_start: 0.2699 (mttt) cc_final: 0.1174 (tptm) REVERT: A 122 PHE cc_start: 0.5603 (OUTLIER) cc_final: 0.5022 (m-80) REVERT: A 124 GLU cc_start: 0.4804 (mm-30) cc_final: 0.3819 (pt0) outliers start: 6 outliers final: 4 residues processed: 24 average time/residue: 1.1305 time to fit residues: 27.6952 Evaluate side-chains 22 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 17 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 155 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 10 optimal weight: 7.9990 chunk 14 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 3 optimal weight: 0.2980 chunk 13 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 11 optimal weight: 40.0000 chunk 0 optimal weight: 4.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.7111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 1425 Z= 0.184 Angle : 0.572 6.842 1914 Z= 0.300 Chirality : 0.042 0.145 217 Planarity : 0.004 0.026 241 Dihedral : 4.211 26.970 190 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 4.61 % Allowed : 26.32 % Favored : 69.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.72 (0.65), residues: 173 helix: 1.55 (0.86), residues: 39 sheet: -1.98 (1.15), residues: 18 loop : 0.66 (0.60), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 9 HIS 0.002 0.001 HIS A 57 PHE 0.003 0.001 PHE A 163 TYR 0.006 0.001 TYR A 105 ARG 0.001 0.000 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 346 Ramachandran restraints generated. 173 Oldfield, 0 Emsley, 173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 346 Ramachandran restraints generated. 173 Oldfield, 0 Emsley, 173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 18 time to evaluate : 0.301 Fit side-chains REVERT: A 5 LYS cc_start: 0.3746 (mttt) cc_final: 0.3182 (mtmt) REVERT: A 82 ARG cc_start: 0.8086 (mmt180) cc_final: 0.6947 (mtt180) REVERT: A 108 LYS cc_start: 0.2948 (mttt) cc_final: 0.1624 (tptm) REVERT: A 122 PHE cc_start: 0.5687 (OUTLIER) cc_final: 0.5120 (m-80) REVERT: A 124 GLU cc_start: 0.4799 (mm-30) cc_final: 0.3747 (pt0) outliers start: 7 outliers final: 4 residues processed: 24 average time/residue: 1.2669 time to fit residues: 31.2035 Evaluate side-chains 21 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 16 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 155 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 9 optimal weight: 30.0000 chunk 15 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 7 optimal weight: 8.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.7193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 1425 Z= 0.204 Angle : 0.576 7.165 1914 Z= 0.302 Chirality : 0.043 0.129 217 Planarity : 0.004 0.026 241 Dihedral : 4.206 25.578 190 Min Nonbonded Distance : 2.652 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 3.29 % Allowed : 28.95 % Favored : 67.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.72 (0.65), residues: 173 helix: 1.51 (0.86), residues: 39 sheet: -1.94 (1.16), residues: 18 loop : 0.68 (0.60), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 9 HIS 0.002 0.001 HIS A 57 PHE 0.004 0.001 PHE A 47 TYR 0.007 0.001 TYR A 105 ARG 0.002 0.000 ARG A 51 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 346 Ramachandran restraints generated. 173 Oldfield, 0 Emsley, 173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 346 Ramachandran restraints generated. 173 Oldfield, 0 Emsley, 173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 15 time to evaluate : 0.176 Fit side-chains REVERT: A 5 LYS cc_start: 0.3748 (mttt) cc_final: 0.3382 (mttt) REVERT: A 82 ARG cc_start: 0.8120 (mmt180) cc_final: 0.6972 (mtt180) REVERT: A 108 LYS cc_start: 0.2967 (mttt) cc_final: 0.1573 (tptm) REVERT: A 122 PHE cc_start: 0.5923 (OUTLIER) cc_final: 0.5338 (m-80) REVERT: A 124 GLU cc_start: 0.4936 (mm-30) cc_final: 0.3767 (pt0) outliers start: 5 outliers final: 4 residues processed: 19 average time/residue: 1.1851 time to fit residues: 23.0729 Evaluate side-chains 20 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 15 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 155 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 1 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 0 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.140605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.117408 restraints weight = 2612.455| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.19 r_work: 0.3472 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.7254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 1425 Z= 0.165 Angle : 0.548 7.243 1914 Z= 0.287 Chirality : 0.042 0.127 217 Planarity : 0.004 0.027 241 Dihedral : 4.050 28.890 190 Min Nonbonded Distance : 2.655 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.29 % Allowed : 28.95 % Favored : 67.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.92 (0.67), residues: 173 helix: 1.62 (0.83), residues: 41 sheet: -1.88 (1.16), residues: 18 loop : 0.83 (0.63), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 9 HIS 0.002 0.001 HIS A 57 PHE 0.003 0.000 PHE A 163 TYR 0.004 0.001 TYR A 105 ARG 0.001 0.000 ARG A 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1176.88 seconds wall clock time: 21 minutes 20.45 seconds (1280.45 seconds total)