Starting phenix.real_space_refine (version: dev) on Mon Apr 4 11:17:19 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbs_6478/04_2022/3jbs_6478.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbs_6478/04_2022/3jbs_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_6478/04_2022/3jbs_6478.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbs_6478/04_2022/3jbs_6478.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbs_6478/04_2022/3jbs_6478.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbs_6478/04_2022/3jbs_6478.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.003 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/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: {'PTRANS': 8, 'TRANS': 165, 'PCIS': 1} Time building chain proxies: 1.37, per 1000 atoms: 0.98 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.36 Conformation dependent library (CDL) restraints added in 296.2 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: 0.08 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: 0.27 Time building geometry restraints manager: 0.41 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: 100.55 - 107.19: 46 107.19 - 113.83: 812 113.83 - 120.47: 544 120.47 - 127.11: 499 127.11 - 133.75: 13 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 2.440 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 2.440 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 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. 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: 1.800 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: 6.500 Check model and map are aligned: 0.020 Convert atoms to be neutral: 0.010 Process input model: 9.570 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 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:13.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 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 % 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 *********************** 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 : 0.153 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 1.5225 time to fit residues: 84.6330 Evaluate side-chains 19 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.189 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2626 ------------------------------------------------------------------------------- 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: 9.9990 chunk 12 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 9 optimal weight: 7.9990 chunk 15 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN A 167 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.4145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 1425 Z= 0.166 Angle : 0.526 3.804 1914 Z= 0.285 Chirality : 0.042 0.118 217 Planarity : 0.005 0.033 241 Dihedral : 3.604 16.346 190 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 4.61 % 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: 1.55 (0.64), residues: 173 helix: 2.05 (0.77), residues: 45 sheet: -2.30 (1.30), residues: 12 loop : 1.17 (0.60), residues: 116 *********************** 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 35 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 28 time to evaluate : 0.197 Fit side-chains outliers start: 7 outliers final: 1 residues processed: 32 average time/residue: 0.8476 time to fit residues: 27.7679 Evaluate side-chains 25 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 24 time to evaluate : 0.179 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0165 time to fit residues: 0.2750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 4 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 13 optimal weight: 9.9990 chunk 5 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 7 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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: 0.7965 moved from start: 0.5693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.023 1425 Z= 0.238 Angle : 0.562 4.387 1914 Z= 0.294 Chirality : 0.042 0.140 217 Planarity : 0.005 0.031 241 Dihedral : 3.796 12.557 190 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer Outliers : 5.26 % 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: 1.25 (0.63), residues: 173 helix: 2.04 (0.78), residues: 45 sheet: -1.80 (1.19), residues: 18 loop : 0.96 (0.57), residues: 110 *********************** 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 27 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 19 time to evaluate : 0.178 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 24 average time/residue: 0.9715 time to fit residues: 23.8217 Evaluate side-chains 20 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 16 time to evaluate : 0.139 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.0142 time to fit residues: 0.2126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 15 optimal weight: 0.9990 chunk 16 optimal weight: 0.2980 chunk 8 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 9 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.6072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 1425 Z= 0.184 Angle : 0.481 4.799 1914 Z= 0.252 Chirality : 0.041 0.124 217 Planarity : 0.004 0.026 241 Dihedral : 3.661 16.292 190 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer Outliers : 5.26 % 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: 1.19 (0.62), residues: 173 helix: 1.80 (0.75), residues: 45 sheet: -1.58 (1.24), residues: 18 loop : 0.96 (0.58), residues: 110 *********************** 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 26 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 18 time to evaluate : 0.200 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 23 average time/residue: 0.9118 time to fit residues: 21.5312 Evaluate side-chains 23 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 19 time to evaluate : 0.179 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.0163 time to fit residues: 0.2772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 4 optimal weight: 8.9990 chunk 5 optimal weight: 0.9980 chunk 3 optimal weight: 6.9990 chunk 9 optimal weight: 7.9990 chunk 16 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- 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: 0.8062 moved from start: 0.6647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.028 1425 Z= 0.251 Angle : 0.518 4.677 1914 Z= 0.274 Chirality : 0.042 0.125 217 Planarity : 0.004 0.023 241 Dihedral : 4.064 17.313 190 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer Outliers : 3.29 % 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: 1.00 (0.62), residues: 173 helix: 1.78 (0.78), residues: 39 sheet: -1.41 (1.30), residues: 18 loop : 0.77 (0.56), residues: 116 *********************** 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 21 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 16 time to evaluate : 0.177 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 21 average time/residue: 1.1508 time to fit residues: 24.6798 Evaluate side-chains 17 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 14 time to evaluate : 0.180 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.2475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 5 optimal weight: 3.9990 chunk 8 optimal weight: 10.0000 chunk 15 optimal weight: 0.8980 chunk 1 optimal weight: 0.2980 chunk 9 optimal weight: 9.9990 chunk 12 optimal weight: 0.0470 chunk 13 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 overall best weight: 0.8482 ------------------------------------------------------------------------------- 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: 0.7997 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 : 0.002 0.031 1425 Z= 0.141 Angle : 0.474 6.140 1914 Z= 0.248 Chirality : 0.040 0.124 217 Planarity : 0.004 0.023 241 Dihedral : 3.596 21.431 190 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer Outliers : 3.95 % 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: 1.19 (0.64), residues: 173 helix: 1.98 (0.80), residues: 39 sheet: -1.41 (1.24), residues: 18 loop : 0.91 (0.60), residues: 116 *********************** 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 23 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 17 time to evaluate : 0.186 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 21 average time/residue: 1.0075 time to fit residues: 21.6839 Evaluate side-chains 20 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 17 time to evaluate : 0.180 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 0.0219 time to fit residues: 0.2807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 9 optimal weight: 10.0000 chunk 4 optimal weight: 8.9990 chunk 3 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 12 optimal weight: 0.0970 chunk 14 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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: 0.8011 moved from start: 0.6884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 1425 Z= 0.173 Angle : 0.507 6.247 1914 Z= 0.267 Chirality : 0.042 0.170 217 Planarity : 0.004 0.024 241 Dihedral : 3.633 19.413 190 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer Outliers : 3.29 % 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: 1.16 (0.64), residues: 173 helix: 2.05 (0.83), residues: 39 sheet: -1.47 (1.24), residues: 18 loop : 0.85 (0.59), residues: 116 *********************** 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 19 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 14 time to evaluate : 0.179 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 18 average time/residue: 1.0214 time to fit residues: 18.8721 Evaluate side-chains 15 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 13 time to evaluate : 0.182 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.2604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 11 optimal weight: 6.9990 chunk 4 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 16 optimal weight: 0.0000 chunk 9 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 1 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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: 0.8050 moved from start: 0.6982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 1425 Z= 0.216 Angle : 0.524 6.159 1914 Z= 0.279 Chirality : 0.042 0.164 217 Planarity : 0.004 0.024 241 Dihedral : 3.960 20.546 190 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer Outliers : 3.29 % 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: 0.97 (0.64), residues: 173 helix: 1.85 (0.83), residues: 39 sheet: -1.51 (1.21), residues: 18 loop : 0.73 (0.59), residues: 116 *********************** 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 17 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 12 time to evaluate : 0.162 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 16 average time/residue: 0.9810 time to fit residues: 16.1383 Evaluate side-chains 14 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 12 time to evaluate : 0.176 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.2425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 4 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 5 optimal weight: 0.9990 chunk 2 optimal weight: 0.0770 chunk 11 optimal weight: 8.9990 chunk 0 optimal weight: 4.9990 overall best weight: 2.2146 ------------------------------------------------------------------------------- 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: 0.8045 moved from start: 0.7026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 1425 Z= 0.201 Angle : 0.535 8.057 1914 Z= 0.283 Chirality : 0.042 0.163 217 Planarity : 0.004 0.023 241 Dihedral : 3.909 21.770 190 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer Outliers : 3.29 % 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: 1.63 (0.81), residues: 42 sheet: -1.42 (1.20), residues: 18 loop : 0.83 (0.61), residues: 113 *********************** 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 18 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 13 time to evaluate : 0.182 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 16 average time/residue: 0.9415 time to fit residues: 15.5278 Evaluate side-chains 17 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 13 time to evaluate : 0.174 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 1.4145 time to fit residues: 1.6690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 9 optimal weight: 6.9990 chunk 15 optimal weight: 7.9990 chunk 11 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 chunk 16 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 overall best weight: 2.7186 ------------------------------------------------------------------------------- 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: 0.8066 moved from start: 0.7261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 1425 Z= 0.226 Angle : 0.548 7.489 1914 Z= 0.293 Chirality : 0.043 0.155 217 Planarity : 0.004 0.023 241 Dihedral : 4.122 21.928 190 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer Outliers : 2.63 % 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: 0.84 (0.64), residues: 173 helix: 1.41 (0.79), residues: 42 sheet: -1.40 (1.22), residues: 18 loop : 0.72 (0.61), residues: 113 ********************** 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 18 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 14 time to evaluate : 0.183 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 17 average time/residue: 1.0353 time to fit residues: 18.0918 Evaluate side-chains 15 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 12 time to evaluate : 0.196 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.2661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 1 optimal weight: 6.9990 chunk 4 optimal weight: 9.9990 chunk 3 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 chunk 8 optimal weight: 0.4980 chunk 0 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 chunk 12 optimal weight: 8.9990 chunk 14 optimal weight: 0.9980 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.137923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.114354 restraints weight = 2692.697| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.21 r_work: 0.3502 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3493 rms_B_bonded: 1.98 restraints_weight: 0.2500 r_work: 0.3483 rms_B_bonded: 2.04 restraints_weight: 0.1250 r_work: 0.3472 rms_B_bonded: 2.15 restraints_weight: 0.0625 r_work: 0.3461 rms_B_bonded: 2.32 restraints_weight: 0.0312 r_work: 0.3448 rms_B_bonded: 2.54 restraints_weight: 0.0156 r_work: 0.3433 rms_B_bonded: 2.82 restraints_weight: 0.0078 r_work: 0.3418 rms_B_bonded: 3.16 restraints_weight: 0.0039 r_work: 0.3400 rms_B_bonded: 3.58 restraints_weight: 0.0020 r_work: 0.3381 rms_B_bonded: 4.08 restraints_weight: 0.0010 r_work: 0.3359 rms_B_bonded: 4.67 restraints_weight: 0.0005 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.7333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 1425 Z= 0.213 Angle : 0.550 7.684 1914 Z= 0.293 Chirality : 0.042 0.155 217 Planarity : 0.004 0.023 241 Dihedral : 4.106 23.332 190 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer Outliers : 2.63 % 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: 0.84 (0.65), residues: 173 helix: 1.37 (0.80), residues: 42 sheet: -1.46 (1.21), residues: 18 loop : 0.75 (0.62), residues: 113 =============================================================================== Job complete usr+sys time: 995.62 seconds wall clock time: 20 minutes 20.47 seconds (1220.47 seconds total)