Starting phenix.real_space_refine on Sun Mar 10 17:42:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kge_37218/03_2024/8kge_37218.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kge_37218/03_2024/8kge_37218.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kge_37218/03_2024/8kge_37218.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kge_37218/03_2024/8kge_37218.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kge_37218/03_2024/8kge_37218.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kge_37218/03_2024/8kge_37218.pdb" } resolution = 3.8 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= 0.009 sd= 0.084 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 10 5.16 5 C 2238 2.51 5 N 604 2.21 5 O 732 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "V ASP 33": "OD1" <-> "OD2" Residue "V GLU 53": "OE1" <-> "OE2" Residue "V ASP 79": "OD1" <-> "OD2" Residue "V PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 102": "OE1" <-> "OE2" Residue "V ASP 118": "OD1" <-> "OD2" Residue "V PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 153": "OE1" <-> "OE2" Residue "V PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 192": "OD1" <-> "OD2" Residue "V PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 234": "OE1" <-> "OE2" Residue "V GLU 240": "OE1" <-> "OE2" Residue "v ASP 33": "OD1" <-> "OD2" Residue "v GLU 49": "OE1" <-> "OE2" Residue "v PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v GLU 240": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3584 Number of models: 1 Model: "" Number of chains: 2 Chain: "V" Number of atoms: 1792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1792 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 11, 'TRANS': 231} Chain: "v" Number of atoms: 1792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1792 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 11, 'TRANS': 231} Time building chain proxies: 2.45, per 1000 atoms: 0.68 Number of scatterers: 3584 At special positions: 0 Unit cell: (93.4554, 106.346, 82.7134, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 10 16.00 O 732 8.00 N 604 7.00 C 2238 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: 1.36 Conformation dependent library (CDL) restraints added in 859.1 milliseconds 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 880 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 8 sheets defined 6.2% alpha, 38.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'V' and resid 92 through 103 Processing helix chain 'v' and resid 92 through 103 Processing helix chain 'v' and resid 151 through 156 removed outlier: 3.511A pdb=" N SER v 156 " --> pdb=" O GLU v 153 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'V' and resid 36 through 38 removed outlier: 5.281A pdb=" N ALA V 107 " --> pdb=" O TYR V 20 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LYS V 142 " --> pdb=" O SER V 125 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ILE V 127 " --> pdb=" O THR V 140 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N THR V 140 " --> pdb=" O ILE V 127 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS V 129 " --> pdb=" O THR V 138 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THR V 138 " --> pdb=" O LYS V 129 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ALA V 85 " --> pdb=" O VAL V 42 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL V 42 " --> pdb=" O ALA V 85 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'V' and resid 36 through 38 removed outlier: 5.281A pdb=" N ALA V 107 " --> pdb=" O TYR V 20 " (cutoff:3.500A) removed outlier: 17.128A pdb=" N ARG V 121 " --> pdb=" O ASP v 56 " (cutoff:3.500A) removed outlier: 14.175A pdb=" N ASP v 56 " --> pdb=" O ARG V 121 " (cutoff:3.500A) removed outlier: 12.143A pdb=" N TRP V 123 " --> pdb=" O SER v 54 " (cutoff:3.500A) removed outlier: 9.353A pdb=" N SER v 54 " --> pdb=" O TRP V 123 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N SER V 125 " --> pdb=" O ALA v 52 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLN v 74 " --> pdb=" O GLU v 53 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N TYR v 55 " --> pdb=" O GLN v 72 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N GLN v 72 " --> pdb=" O TYR v 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'V' and resid 51 through 56 removed outlier: 6.569A pdb=" N THR V 51 " --> pdb=" O LYS V 75 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LYS V 75 " --> pdb=" O THR V 51 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N GLU V 53 " --> pdb=" O GLY V 73 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'V' and resid 164 through 166 removed outlier: 3.537A pdb=" N ILE V 214 " --> pdb=" O LEU V 181 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'V' and resid 196 through 197 removed outlier: 3.811A pdb=" N GLY V 222 " --> pdb=" O VAL V 243 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'v' and resid 36 through 38 removed outlier: 5.291A pdb=" N ALA v 107 " --> pdb=" O TYR v 20 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N VAL v 124 " --> pdb=" O THR v 144 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N THR v 144 " --> pdb=" O VAL v 124 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR v 138 " --> pdb=" O ALA v 130 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ALA v 85 " --> pdb=" O VAL v 42 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N VAL v 42 " --> pdb=" O ALA v 85 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'v' and resid 165 through 166 Processing sheet with id=AA8, first strand: chain 'v' and resid 195 through 197 128 hydrogen bonds defined for protein. 342 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: 0.94 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1178 1.34 - 1.46: 837 1.46 - 1.58: 1619 1.58 - 1.70: 0 1.70 - 1.82: 20 Bond restraints: 3654 Sorted by residual: bond pdb=" CG PRO V 168 " pdb=" CD PRO V 168 " ideal model delta sigma weight residual 1.503 1.404 0.099 3.40e-02 8.65e+02 8.54e+00 bond pdb=" CB GLU V 240 " pdb=" CG GLU V 240 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.47e+00 bond pdb=" CB GLU v 102 " pdb=" CG GLU v 102 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.34e+00 bond pdb=" C GLN V 186 " pdb=" N PRO V 187 " ideal model delta sigma weight residual 1.334 1.360 -0.026 2.34e-02 1.83e+03 1.27e+00 bond pdb=" CA GLU V 188 " pdb=" CB GLU V 188 " ideal model delta sigma weight residual 1.530 1.548 -0.018 1.69e-02 3.50e+03 1.17e+00 ... (remaining 3649 not shown) Histogram of bond angle deviations from ideal: 92.89 - 101.10: 8 101.10 - 109.31: 359 109.31 - 117.53: 2428 117.53 - 125.74: 2123 125.74 - 133.95: 70 Bond angle restraints: 4988 Sorted by residual: angle pdb=" N PRO V 168 " pdb=" CD PRO V 168 " pdb=" CG PRO V 168 " ideal model delta sigma weight residual 103.20 92.89 10.31 1.50e+00 4.44e-01 4.72e+01 angle pdb=" CA PRO V 168 " pdb=" N PRO V 168 " pdb=" CD PRO V 168 " ideal model delta sigma weight residual 112.00 104.64 7.36 1.40e+00 5.10e-01 2.77e+01 angle pdb=" CA PRO V 168 " pdb=" CB PRO V 168 " pdb=" CG PRO V 168 " ideal model delta sigma weight residual 104.50 96.47 8.03 1.90e+00 2.77e-01 1.79e+01 angle pdb=" CB MET V 151 " pdb=" CG MET V 151 " pdb=" SD MET V 151 " ideal model delta sigma weight residual 112.70 125.10 -12.40 3.00e+00 1.11e-01 1.71e+01 angle pdb=" CB MET v 151 " pdb=" CG MET v 151 " pdb=" SD MET v 151 " ideal model delta sigma weight residual 112.70 124.70 -12.00 3.00e+00 1.11e-01 1.60e+01 ... (remaining 4983 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.87: 1764 14.87 - 29.73: 263 29.73 - 44.60: 106 44.60 - 59.46: 21 59.46 - 74.33: 6 Dihedral angle restraints: 2160 sinusoidal: 786 harmonic: 1374 Sorted by residual: dihedral pdb=" CA GLN v 186 " pdb=" C GLN v 186 " pdb=" N PRO v 187 " pdb=" CA PRO v 187 " ideal model delta harmonic sigma weight residual -180.00 -161.50 -18.50 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA GLY V 176 " pdb=" C GLY V 176 " pdb=" N GLN V 177 " pdb=" CA GLN V 177 " ideal model delta harmonic sigma weight residual 180.00 -163.01 -16.99 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA ASP V 192 " pdb=" C ASP V 192 " pdb=" N LYS V 193 " pdb=" CA LYS V 193 " ideal model delta harmonic sigma weight residual -180.00 -164.17 -15.83 0 5.00e+00 4.00e-02 1.00e+01 ... (remaining 2157 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 398 0.037 - 0.074: 106 0.074 - 0.111: 66 0.111 - 0.148: 16 0.148 - 0.185: 4 Chirality restraints: 590 Sorted by residual: chirality pdb=" CA ILE V 241 " pdb=" N ILE V 241 " pdb=" C ILE V 241 " pdb=" CB ILE V 241 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.60e-01 chirality pdb=" CB THR V 162 " pdb=" CA THR V 162 " pdb=" OG1 THR V 162 " pdb=" CG2 THR V 162 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 7.95e-01 chirality pdb=" CA GLU V 188 " pdb=" N GLU V 188 " pdb=" C GLU V 188 " pdb=" CB GLU V 188 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.42e-01 ... (remaining 587 not shown) Planarity restraints: 640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN V 186 " 0.047 5.00e-02 4.00e+02 7.28e-02 8.49e+00 pdb=" N PRO V 187 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO V 187 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO V 187 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE v 226 " -0.039 5.00e-02 4.00e+02 5.95e-02 5.66e+00 pdb=" N PRO v 227 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO v 227 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO v 227 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE v 226 " -0.011 2.00e-02 2.50e+03 2.20e-02 4.84e+00 pdb=" C ILE v 226 " 0.038 2.00e-02 2.50e+03 pdb=" O ILE v 226 " -0.014 2.00e-02 2.50e+03 pdb=" N PRO v 227 " -0.013 2.00e-02 2.50e+03 ... (remaining 637 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 104 2.66 - 3.22: 3308 3.22 - 3.78: 5243 3.78 - 4.34: 6751 4.34 - 4.90: 11634 Nonbonded interactions: 27040 Sorted by model distance: nonbonded pdb=" OG1 THR V 180 " pdb=" OG1 THR V 213 " model vdw 2.103 2.440 nonbonded pdb=" OH TYR V 108 " pdb=" OD1 ASN V 145 " model vdw 2.182 2.440 nonbonded pdb=" NE2 GLN V 177 " pdb=" O VAL V 216 " model vdw 2.214 2.520 nonbonded pdb=" OG1 THR v 206 " pdb=" OD1 ASN v 217 " model vdw 2.298 2.440 nonbonded pdb=" NZ LYS V 129 " pdb=" OD2 ASP v 118 " model vdw 2.299 2.520 ... (remaining 27035 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'V' selection = chain 'v' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.680 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: 3.640 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 14.610 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 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 : 0.004 0.099 3654 Z= 0.266 Angle : 0.871 12.404 4988 Z= 0.444 Chirality : 0.048 0.185 590 Planarity : 0.005 0.073 640 Dihedral : 17.206 74.325 1280 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.34 % Favored : 90.46 % Rotamer: Outliers : 10.88 % Allowed : 34.72 % Favored : 54.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.35), residues: 482 helix: 1.37 (1.06), residues: 24 sheet: -0.83 (0.34), residues: 222 loop : -2.53 (0.33), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP V 123 PHE 0.014 0.002 PHE V 120 TYR 0.005 0.001 TYR V 55 ARG 0.004 0.000 ARG V 139 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 50 time to evaluate : 0.448 Fit side-chains revert: symmetry clash outliers start: 42 outliers final: 37 residues processed: 89 average time/residue: 0.1223 time to fit residues: 13.9667 Evaluate side-chains 84 residues out of total 386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 47 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 45 LEU Chi-restraints excluded: chain V residue 46 THR Chi-restraints excluded: chain V residue 117 VAL Chi-restraints excluded: chain V residue 127 ILE Chi-restraints excluded: chain V residue 131 VAL Chi-restraints excluded: chain V residue 132 THR Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain V residue 157 THR Chi-restraints excluded: chain V residue 177 GLN Chi-restraints excluded: chain V residue 193 LYS Chi-restraints excluded: chain V residue 204 LYS Chi-restraints excluded: chain V residue 215 THR Chi-restraints excluded: chain V residue 232 ASN Chi-restraints excluded: chain v residue 33 ASP Chi-restraints excluded: chain v residue 51 THR Chi-restraints excluded: chain v residue 70 THR Chi-restraints excluded: chain v residue 79 ASP Chi-restraints excluded: chain v residue 80 THR Chi-restraints excluded: chain v residue 83 THR Chi-restraints excluded: chain v residue 84 LEU Chi-restraints excluded: chain v residue 97 LEU Chi-restraints excluded: chain v residue 105 THR Chi-restraints excluded: chain v residue 110 ILE Chi-restraints excluded: chain v residue 119 VAL Chi-restraints excluded: chain v residue 125 SER Chi-restraints excluded: chain v residue 131 VAL Chi-restraints excluded: chain v residue 138 THR Chi-restraints excluded: chain v residue 156 SER Chi-restraints excluded: chain v residue 157 THR Chi-restraints excluded: chain v residue 158 VAL Chi-restraints excluded: chain v residue 180 THR Chi-restraints excluded: chain v residue 183 VAL Chi-restraints excluded: chain v residue 193 LYS Chi-restraints excluded: chain v residue 201 ASP Chi-restraints excluded: chain v residue 216 VAL Chi-restraints excluded: chain v residue 219 VAL Chi-restraints excluded: chain v residue 228 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 19 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 72 GLN ** V 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3654 Z= 0.273 Angle : 0.673 7.808 4988 Z= 0.338 Chirality : 0.048 0.152 590 Planarity : 0.005 0.055 640 Dihedral : 9.404 76.559 567 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.21 % Allowed : 10.79 % Favored : 89.00 % Rotamer: Outliers : 11.66 % Allowed : 30.57 % Favored : 57.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.35), residues: 482 helix: 1.41 (1.00), residues: 25 sheet: -0.73 (0.34), residues: 222 loop : -2.54 (0.33), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP v 18 PHE 0.015 0.002 PHE V 120 TYR 0.011 0.001 TYR v 55 ARG 0.002 0.000 ARG v 155 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 49 time to evaluate : 0.421 Fit side-chains REVERT: V 90 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7920 (tt0) REVERT: V 111 ARG cc_start: 0.8978 (OUTLIER) cc_final: 0.8244 (mmm-85) REVERT: V 155 ARG cc_start: 0.7214 (OUTLIER) cc_final: 0.6135 (mtt-85) REVERT: V 217 ASN cc_start: 0.7381 (OUTLIER) cc_final: 0.7120 (p0) REVERT: v 72 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.8026 (tt0) REVERT: v 87 MET cc_start: 0.3641 (mmt) cc_final: 0.3186 (mmt) outliers start: 45 outliers final: 32 residues processed: 88 average time/residue: 0.1664 time to fit residues: 17.8045 Evaluate side-chains 85 residues out of total 386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 48 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 45 LEU Chi-restraints excluded: chain V residue 46 THR Chi-restraints excluded: chain V residue 79 ASP Chi-restraints excluded: chain V residue 90 GLU Chi-restraints excluded: chain V residue 111 ARG Chi-restraints excluded: chain V residue 117 VAL Chi-restraints excluded: chain V residue 121 ARG Chi-restraints excluded: chain V residue 127 ILE Chi-restraints excluded: chain V residue 131 VAL Chi-restraints excluded: chain V residue 155 ARG Chi-restraints excluded: chain V residue 157 THR Chi-restraints excluded: chain V residue 177 GLN Chi-restraints excluded: chain V residue 193 LYS Chi-restraints excluded: chain V residue 203 THR Chi-restraints excluded: chain V residue 215 THR Chi-restraints excluded: chain V residue 217 ASN Chi-restraints excluded: chain V residue 232 ASN Chi-restraints excluded: chain V residue 242 THR Chi-restraints excluded: chain v residue 17 LEU Chi-restraints excluded: chain v residue 51 THR Chi-restraints excluded: chain v residue 70 THR Chi-restraints excluded: chain v residue 72 GLN Chi-restraints excluded: chain v residue 83 THR Chi-restraints excluded: chain v residue 84 LEU Chi-restraints excluded: chain v residue 96 LEU Chi-restraints excluded: chain v residue 97 LEU Chi-restraints excluded: chain v residue 117 VAL Chi-restraints excluded: chain v residue 119 VAL Chi-restraints excluded: chain v residue 131 VAL Chi-restraints excluded: chain v residue 138 THR Chi-restraints excluded: chain v residue 157 THR Chi-restraints excluded: chain v residue 162 THR Chi-restraints excluded: chain v residue 180 THR Chi-restraints excluded: chain v residue 183 VAL Chi-restraints excluded: chain v residue 193 LYS Chi-restraints excluded: chain v residue 206 THR Chi-restraints excluded: chain v residue 228 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 0.9980 chunk 13 optimal weight: 6.9990 chunk 36 optimal weight: 0.4980 chunk 29 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 38 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.0960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3654 Z= 0.173 Angle : 0.597 7.068 4988 Z= 0.296 Chirality : 0.046 0.150 590 Planarity : 0.004 0.049 640 Dihedral : 7.899 77.321 546 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.34 % Favored : 90.66 % Rotamer: Outliers : 10.36 % Allowed : 30.83 % Favored : 58.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.35), residues: 482 helix: 1.89 (1.01), residues: 25 sheet: -0.62 (0.34), residues: 222 loop : -2.48 (0.33), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP v 18 PHE 0.013 0.002 PHE V 120 TYR 0.006 0.001 TYR v 55 ARG 0.002 0.000 ARG V 155 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 50 time to evaluate : 0.418 Fit side-chains REVERT: V 90 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7838 (tt0) REVERT: V 111 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.7338 (mtm-85) REVERT: V 118 ASP cc_start: 0.8443 (t0) cc_final: 0.8171 (t0) REVERT: V 155 ARG cc_start: 0.7076 (OUTLIER) cc_final: 0.6028 (mtt-85) REVERT: V 217 ASN cc_start: 0.7386 (OUTLIER) cc_final: 0.7083 (p0) outliers start: 40 outliers final: 29 residues processed: 85 average time/residue: 0.1629 time to fit residues: 16.8837 Evaluate side-chains 82 residues out of total 386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 49 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 17 LEU Chi-restraints excluded: chain V residue 45 LEU Chi-restraints excluded: chain V residue 46 THR Chi-restraints excluded: chain V residue 90 GLU Chi-restraints excluded: chain V residue 111 ARG Chi-restraints excluded: chain V residue 117 VAL Chi-restraints excluded: chain V residue 121 ARG Chi-restraints excluded: chain V residue 127 ILE Chi-restraints excluded: chain V residue 131 VAL Chi-restraints excluded: chain V residue 155 ARG Chi-restraints excluded: chain V residue 177 GLN Chi-restraints excluded: chain V residue 193 LYS Chi-restraints excluded: chain V residue 206 THR Chi-restraints excluded: chain V residue 215 THR Chi-restraints excluded: chain V residue 217 ASN Chi-restraints excluded: chain V residue 225 ASN Chi-restraints excluded: chain V residue 232 ASN Chi-restraints excluded: chain v residue 17 LEU Chi-restraints excluded: chain v residue 84 LEU Chi-restraints excluded: chain v residue 96 LEU Chi-restraints excluded: chain v residue 97 LEU Chi-restraints excluded: chain v residue 105 THR Chi-restraints excluded: chain v residue 110 ILE Chi-restraints excluded: chain v residue 119 VAL Chi-restraints excluded: chain v residue 131 VAL Chi-restraints excluded: chain v residue 162 THR Chi-restraints excluded: chain v residue 180 THR Chi-restraints excluded: chain v residue 183 VAL Chi-restraints excluded: chain v residue 193 LYS Chi-restraints excluded: chain v residue 201 ASP Chi-restraints excluded: chain v residue 206 THR Chi-restraints excluded: chain v residue 216 VAL Chi-restraints excluded: chain v residue 228 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 22 optimal weight: 9.9990 chunk 4 optimal weight: 7.9990 chunk 20 optimal weight: 8.9990 chunk 29 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 41 optimal weight: 8.9990 chunk 12 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 26 optimal weight: 0.0970 chunk 0 optimal weight: 7.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3654 Z= 0.173 Angle : 0.587 7.054 4988 Z= 0.290 Chirality : 0.046 0.144 590 Planarity : 0.004 0.046 640 Dihedral : 7.501 76.525 540 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.54 % Favored : 90.46 % Rotamer: Outliers : 10.36 % Allowed : 32.64 % Favored : 56.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.35), residues: 482 helix: 2.50 (1.00), residues: 24 sheet: -0.67 (0.35), residues: 212 loop : -2.37 (0.33), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP v 18 PHE 0.011 0.002 PHE V 120 TYR 0.006 0.001 TYR v 55 ARG 0.002 0.000 ARG V 155 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 49 time to evaluate : 0.420 Fit side-chains REVERT: V 90 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7813 (tt0) REVERT: V 111 ARG cc_start: 0.8955 (OUTLIER) cc_final: 0.7312 (mtm-85) REVERT: V 118 ASP cc_start: 0.8432 (t0) cc_final: 0.8223 (t0) REVERT: V 155 ARG cc_start: 0.7077 (OUTLIER) cc_final: 0.6000 (mtt-85) REVERT: V 217 ASN cc_start: 0.7414 (OUTLIER) cc_final: 0.7134 (p0) REVERT: v 49 GLU cc_start: 0.8346 (pm20) cc_final: 0.8042 (pm20) REVERT: v 63 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7180 (mp0) REVERT: v 72 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.7796 (tt0) outliers start: 40 outliers final: 31 residues processed: 82 average time/residue: 0.1645 time to fit residues: 16.5260 Evaluate side-chains 85 residues out of total 386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 48 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 17 LEU Chi-restraints excluded: chain V residue 45 LEU Chi-restraints excluded: chain V residue 46 THR Chi-restraints excluded: chain V residue 79 ASP Chi-restraints excluded: chain V residue 90 GLU Chi-restraints excluded: chain V residue 111 ARG Chi-restraints excluded: chain V residue 117 VAL Chi-restraints excluded: chain V residue 121 ARG Chi-restraints excluded: chain V residue 131 VAL Chi-restraints excluded: chain V residue 155 ARG Chi-restraints excluded: chain V residue 177 GLN Chi-restraints excluded: chain V residue 193 LYS Chi-restraints excluded: chain V residue 206 THR Chi-restraints excluded: chain V residue 215 THR Chi-restraints excluded: chain V residue 217 ASN Chi-restraints excluded: chain V residue 225 ASN Chi-restraints excluded: chain V residue 232 ASN Chi-restraints excluded: chain v residue 17 LEU Chi-restraints excluded: chain v residue 63 GLU Chi-restraints excluded: chain v residue 72 GLN Chi-restraints excluded: chain v residue 79 ASP Chi-restraints excluded: chain v residue 84 LEU Chi-restraints excluded: chain v residue 96 LEU Chi-restraints excluded: chain v residue 97 LEU Chi-restraints excluded: chain v residue 105 THR Chi-restraints excluded: chain v residue 110 ILE Chi-restraints excluded: chain v residue 119 VAL Chi-restraints excluded: chain v residue 131 VAL Chi-restraints excluded: chain v residue 162 THR Chi-restraints excluded: chain v residue 180 THR Chi-restraints excluded: chain v residue 181 LEU Chi-restraints excluded: chain v residue 183 VAL Chi-restraints excluded: chain v residue 193 LYS Chi-restraints excluded: chain v residue 201 ASP Chi-restraints excluded: chain v residue 206 THR Chi-restraints excluded: chain v residue 216 VAL Chi-restraints excluded: chain v residue 228 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 34 optimal weight: 0.8980 chunk 19 optimal weight: 9.9990 chunk 39 optimal weight: 9.9990 chunk 32 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 41 optimal weight: 9.9990 chunk 11 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 72 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 3654 Z= 0.321 Angle : 0.651 6.732 4988 Z= 0.329 Chirality : 0.048 0.156 590 Planarity : 0.004 0.054 640 Dihedral : 8.013 76.028 538 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.21 % Allowed : 11.00 % Favored : 88.80 % Rotamer: Outliers : 12.95 % Allowed : 31.61 % Favored : 55.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.35), residues: 482 helix: 1.53 (1.02), residues: 25 sheet: -0.82 (0.35), residues: 217 loop : -2.48 (0.33), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP v 123 PHE 0.015 0.002 PHE v 120 TYR 0.013 0.002 TYR v 55 ARG 0.003 0.000 ARG V 155 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 52 time to evaluate : 0.409 Fit side-chains REVERT: V 90 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7964 (tt0) REVERT: V 118 ASP cc_start: 0.8514 (t0) cc_final: 0.8260 (t0) REVERT: V 155 ARG cc_start: 0.7253 (OUTLIER) cc_final: 0.6332 (mtt-85) REVERT: V 217 ASN cc_start: 0.7371 (OUTLIER) cc_final: 0.7080 (p0) REVERT: v 49 GLU cc_start: 0.8547 (pm20) cc_final: 0.8274 (pm20) REVERT: v 63 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7101 (mp0) outliers start: 50 outliers final: 36 residues processed: 94 average time/residue: 0.1434 time to fit residues: 16.8103 Evaluate side-chains 88 residues out of total 386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 48 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 45 LEU Chi-restraints excluded: chain V residue 46 THR Chi-restraints excluded: chain V residue 79 ASP Chi-restraints excluded: chain V residue 87 MET Chi-restraints excluded: chain V residue 90 GLU Chi-restraints excluded: chain V residue 117 VAL Chi-restraints excluded: chain V residue 121 ARG Chi-restraints excluded: chain V residue 127 ILE Chi-restraints excluded: chain V residue 131 VAL Chi-restraints excluded: chain V residue 155 ARG Chi-restraints excluded: chain V residue 177 GLN Chi-restraints excluded: chain V residue 193 LYS Chi-restraints excluded: chain V residue 203 THR Chi-restraints excluded: chain V residue 206 THR Chi-restraints excluded: chain V residue 213 THR Chi-restraints excluded: chain V residue 214 ILE Chi-restraints excluded: chain V residue 215 THR Chi-restraints excluded: chain V residue 217 ASN Chi-restraints excluded: chain V residue 225 ASN Chi-restraints excluded: chain V residue 232 ASN Chi-restraints excluded: chain v residue 17 LEU Chi-restraints excluded: chain v residue 63 GLU Chi-restraints excluded: chain v residue 72 GLN Chi-restraints excluded: chain v residue 79 ASP Chi-restraints excluded: chain v residue 84 LEU Chi-restraints excluded: chain v residue 96 LEU Chi-restraints excluded: chain v residue 97 LEU Chi-restraints excluded: chain v residue 105 THR Chi-restraints excluded: chain v residue 117 VAL Chi-restraints excluded: chain v residue 119 VAL Chi-restraints excluded: chain v residue 131 VAL Chi-restraints excluded: chain v residue 162 THR Chi-restraints excluded: chain v residue 180 THR Chi-restraints excluded: chain v residue 181 LEU Chi-restraints excluded: chain v residue 183 VAL Chi-restraints excluded: chain v residue 191 THR Chi-restraints excluded: chain v residue 193 LYS Chi-restraints excluded: chain v residue 201 ASP Chi-restraints excluded: chain v residue 216 VAL Chi-restraints excluded: chain v residue 228 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 11 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 44 optimal weight: 8.9990 chunk 5 optimal weight: 9.9990 chunk 26 optimal weight: 0.2980 chunk 33 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3654 Z= 0.198 Angle : 0.616 8.468 4988 Z= 0.307 Chirality : 0.047 0.170 590 Planarity : 0.004 0.053 640 Dihedral : 7.684 75.791 538 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.54 % Favored : 90.25 % Rotamer: Outliers : 10.88 % Allowed : 33.68 % Favored : 55.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.35), residues: 482 helix: 2.07 (1.02), residues: 24 sheet: -0.60 (0.35), residues: 213 loop : -2.43 (0.33), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP v 123 PHE 0.013 0.002 PHE v 195 TYR 0.007 0.001 TYR v 55 ARG 0.002 0.000 ARG V 155 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 45 time to evaluate : 0.412 Fit side-chains REVERT: V 90 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7919 (tt0) REVERT: V 111 ARG cc_start: 0.8936 (OUTLIER) cc_final: 0.7530 (mtm180) REVERT: V 155 ARG cc_start: 0.7057 (OUTLIER) cc_final: 0.6134 (mtt-85) REVERT: V 217 ASN cc_start: 0.7387 (OUTLIER) cc_final: 0.7088 (p0) REVERT: v 49 GLU cc_start: 0.8509 (pm20) cc_final: 0.8203 (pm20) REVERT: v 63 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7067 (mp0) REVERT: v 72 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.7981 (tt0) outliers start: 42 outliers final: 35 residues processed: 81 average time/residue: 0.1642 time to fit residues: 16.1980 Evaluate side-chains 86 residues out of total 386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 45 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 17 LEU Chi-restraints excluded: chain V residue 45 LEU Chi-restraints excluded: chain V residue 46 THR Chi-restraints excluded: chain V residue 79 ASP Chi-restraints excluded: chain V residue 90 GLU Chi-restraints excluded: chain V residue 111 ARG Chi-restraints excluded: chain V residue 117 VAL Chi-restraints excluded: chain V residue 121 ARG Chi-restraints excluded: chain V residue 127 ILE Chi-restraints excluded: chain V residue 131 VAL Chi-restraints excluded: chain V residue 155 ARG Chi-restraints excluded: chain V residue 177 GLN Chi-restraints excluded: chain V residue 193 LYS Chi-restraints excluded: chain V residue 206 THR Chi-restraints excluded: chain V residue 213 THR Chi-restraints excluded: chain V residue 215 THR Chi-restraints excluded: chain V residue 217 ASN Chi-restraints excluded: chain V residue 225 ASN Chi-restraints excluded: chain V residue 232 ASN Chi-restraints excluded: chain v residue 17 LEU Chi-restraints excluded: chain v residue 63 GLU Chi-restraints excluded: chain v residue 72 GLN Chi-restraints excluded: chain v residue 79 ASP Chi-restraints excluded: chain v residue 83 THR Chi-restraints excluded: chain v residue 84 LEU Chi-restraints excluded: chain v residue 96 LEU Chi-restraints excluded: chain v residue 97 LEU Chi-restraints excluded: chain v residue 105 THR Chi-restraints excluded: chain v residue 110 ILE Chi-restraints excluded: chain v residue 117 VAL Chi-restraints excluded: chain v residue 119 VAL Chi-restraints excluded: chain v residue 131 VAL Chi-restraints excluded: chain v residue 162 THR Chi-restraints excluded: chain v residue 180 THR Chi-restraints excluded: chain v residue 181 LEU Chi-restraints excluded: chain v residue 183 VAL Chi-restraints excluded: chain v residue 193 LYS Chi-restraints excluded: chain v residue 201 ASP Chi-restraints excluded: chain v residue 216 VAL Chi-restraints excluded: chain v residue 228 VAL Chi-restraints excluded: chain v residue 241 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 26 optimal weight: 0.0470 chunk 39 optimal weight: 9.9990 chunk 25 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 18 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 9 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 overall best weight: 0.6880 ------------------------------------------------------------------------------- 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: 0.7795 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3654 Z= 0.144 Angle : 0.585 8.856 4988 Z= 0.286 Chirality : 0.046 0.157 590 Planarity : 0.004 0.052 640 Dihedral : 7.325 75.556 538 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.71 % Favored : 91.08 % Rotamer: Outliers : 9.07 % Allowed : 34.97 % Favored : 55.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.36), residues: 482 helix: 2.78 (1.03), residues: 24 sheet: -0.50 (0.36), residues: 203 loop : -2.28 (0.33), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP v 18 PHE 0.009 0.001 PHE V 82 TYR 0.004 0.001 TYR V 108 ARG 0.002 0.000 ARG V 139 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 54 time to evaluate : 0.412 Fit side-chains REVERT: V 90 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7702 (tt0) REVERT: V 111 ARG cc_start: 0.8929 (OUTLIER) cc_final: 0.8233 (mmm-85) REVERT: V 155 ARG cc_start: 0.6727 (OUTLIER) cc_final: 0.5783 (mtt-85) REVERT: V 217 ASN cc_start: 0.7471 (OUTLIER) cc_final: 0.7160 (p0) REVERT: v 49 GLU cc_start: 0.8386 (pm20) cc_final: 0.8102 (pm20) outliers start: 35 outliers final: 26 residues processed: 81 average time/residue: 0.1428 time to fit residues: 14.4871 Evaluate side-chains 82 residues out of total 386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 52 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 45 LEU Chi-restraints excluded: chain V residue 46 THR Chi-restraints excluded: chain V residue 90 GLU Chi-restraints excluded: chain V residue 111 ARG Chi-restraints excluded: chain V residue 127 ILE Chi-restraints excluded: chain V residue 131 VAL Chi-restraints excluded: chain V residue 155 ARG Chi-restraints excluded: chain V residue 177 GLN Chi-restraints excluded: chain V residue 193 LYS Chi-restraints excluded: chain V residue 206 THR Chi-restraints excluded: chain V residue 215 THR Chi-restraints excluded: chain V residue 217 ASN Chi-restraints excluded: chain V residue 225 ASN Chi-restraints excluded: chain V residue 232 ASN Chi-restraints excluded: chain v residue 17 LEU Chi-restraints excluded: chain v residue 79 ASP Chi-restraints excluded: chain v residue 83 THR Chi-restraints excluded: chain v residue 97 LEU Chi-restraints excluded: chain v residue 119 VAL Chi-restraints excluded: chain v residue 131 VAL Chi-restraints excluded: chain v residue 162 THR Chi-restraints excluded: chain v residue 180 THR Chi-restraints excluded: chain v residue 181 LEU Chi-restraints excluded: chain v residue 183 VAL Chi-restraints excluded: chain v residue 193 LYS Chi-restraints excluded: chain v residue 201 ASP Chi-restraints excluded: chain v residue 206 THR Chi-restraints excluded: chain v residue 216 VAL Chi-restraints excluded: chain v residue 228 VAL Chi-restraints excluded: chain v residue 241 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 22 optimal weight: 0.4980 chunk 4 optimal weight: 8.9990 chunk 36 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3654 Z= 0.258 Angle : 0.637 8.896 4988 Z= 0.314 Chirality : 0.048 0.160 590 Planarity : 0.004 0.054 640 Dihedral : 7.617 75.993 535 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.75 % Favored : 90.04 % Rotamer: Outliers : 10.36 % Allowed : 32.64 % Favored : 56.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.35), residues: 482 helix: 2.29 (1.02), residues: 24 sheet: -0.54 (0.36), residues: 203 loop : -2.33 (0.33), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP v 123 PHE 0.013 0.002 PHE v 120 TYR 0.010 0.001 TYR v 55 ARG 0.002 0.000 ARG V 155 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 52 time to evaluate : 0.415 Fit side-chains REVERT: V 90 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7941 (tt0) REVERT: V 111 ARG cc_start: 0.8918 (OUTLIER) cc_final: 0.7295 (mtm-85) REVERT: V 155 ARG cc_start: 0.7046 (OUTLIER) cc_final: 0.6072 (mtt-85) REVERT: V 217 ASN cc_start: 0.7392 (OUTLIER) cc_final: 0.7060 (p0) REVERT: v 49 GLU cc_start: 0.8572 (pm20) cc_final: 0.8297 (pm20) REVERT: v 63 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7052 (mp0) REVERT: v 72 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.7914 (tt0) outliers start: 40 outliers final: 32 residues processed: 84 average time/residue: 0.1455 time to fit residues: 15.2099 Evaluate side-chains 87 residues out of total 386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 49 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 16 THR Chi-restraints excluded: chain V residue 17 LEU Chi-restraints excluded: chain V residue 45 LEU Chi-restraints excluded: chain V residue 46 THR Chi-restraints excluded: chain V residue 79 ASP Chi-restraints excluded: chain V residue 90 GLU Chi-restraints excluded: chain V residue 111 ARG Chi-restraints excluded: chain V residue 127 ILE Chi-restraints excluded: chain V residue 131 VAL Chi-restraints excluded: chain V residue 155 ARG Chi-restraints excluded: chain V residue 177 GLN Chi-restraints excluded: chain V residue 178 SER Chi-restraints excluded: chain V residue 193 LYS Chi-restraints excluded: chain V residue 206 THR Chi-restraints excluded: chain V residue 215 THR Chi-restraints excluded: chain V residue 217 ASN Chi-restraints excluded: chain V residue 225 ASN Chi-restraints excluded: chain V residue 232 ASN Chi-restraints excluded: chain v residue 17 LEU Chi-restraints excluded: chain v residue 63 GLU Chi-restraints excluded: chain v residue 72 GLN Chi-restraints excluded: chain v residue 79 ASP Chi-restraints excluded: chain v residue 83 THR Chi-restraints excluded: chain v residue 84 LEU Chi-restraints excluded: chain v residue 97 LEU Chi-restraints excluded: chain v residue 105 THR Chi-restraints excluded: chain v residue 110 ILE Chi-restraints excluded: chain v residue 119 VAL Chi-restraints excluded: chain v residue 131 VAL Chi-restraints excluded: chain v residue 162 THR Chi-restraints excluded: chain v residue 180 THR Chi-restraints excluded: chain v residue 181 LEU Chi-restraints excluded: chain v residue 183 VAL Chi-restraints excluded: chain v residue 193 LYS Chi-restraints excluded: chain v residue 201 ASP Chi-restraints excluded: chain v residue 216 VAL Chi-restraints excluded: chain v residue 228 VAL Chi-restraints excluded: chain v residue 241 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 33 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 28 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3654 Z= 0.248 Angle : 0.641 9.000 4988 Z= 0.316 Chirality : 0.048 0.161 590 Planarity : 0.004 0.054 640 Dihedral : 7.657 75.216 535 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.21 % Allowed : 10.17 % Favored : 89.63 % Rotamer: Outliers : 10.62 % Allowed : 32.90 % Favored : 56.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.35), residues: 482 helix: 2.07 (1.01), residues: 24 sheet: -0.52 (0.36), residues: 204 loop : -2.31 (0.33), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP v 123 PHE 0.017 0.002 PHE v 195 TYR 0.010 0.001 TYR v 55 ARG 0.002 0.000 ARG V 155 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 51 time to evaluate : 0.424 Fit side-chains REVERT: V 90 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7937 (tt0) REVERT: V 111 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.7296 (mtm-85) REVERT: V 155 ARG cc_start: 0.7004 (OUTLIER) cc_final: 0.6109 (mtt-85) REVERT: V 217 ASN cc_start: 0.7364 (OUTLIER) cc_final: 0.7082 (p0) REVERT: v 49 GLU cc_start: 0.8588 (pm20) cc_final: 0.8325 (pm20) REVERT: v 63 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7134 (mp0) REVERT: v 72 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.7877 (tt0) REVERT: v 87 MET cc_start: 0.3754 (mmt) cc_final: 0.3317 (mmt) outliers start: 41 outliers final: 32 residues processed: 85 average time/residue: 0.1474 time to fit residues: 15.5362 Evaluate side-chains 86 residues out of total 386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 48 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 17 LEU Chi-restraints excluded: chain V residue 45 LEU Chi-restraints excluded: chain V residue 46 THR Chi-restraints excluded: chain V residue 79 ASP Chi-restraints excluded: chain V residue 90 GLU Chi-restraints excluded: chain V residue 111 ARG Chi-restraints excluded: chain V residue 127 ILE Chi-restraints excluded: chain V residue 131 VAL Chi-restraints excluded: chain V residue 132 THR Chi-restraints excluded: chain V residue 155 ARG Chi-restraints excluded: chain V residue 177 GLN Chi-restraints excluded: chain V residue 178 SER Chi-restraints excluded: chain V residue 193 LYS Chi-restraints excluded: chain V residue 206 THR Chi-restraints excluded: chain V residue 215 THR Chi-restraints excluded: chain V residue 217 ASN Chi-restraints excluded: chain V residue 225 ASN Chi-restraints excluded: chain V residue 232 ASN Chi-restraints excluded: chain v residue 17 LEU Chi-restraints excluded: chain v residue 63 GLU Chi-restraints excluded: chain v residue 70 THR Chi-restraints excluded: chain v residue 72 GLN Chi-restraints excluded: chain v residue 79 ASP Chi-restraints excluded: chain v residue 83 THR Chi-restraints excluded: chain v residue 84 LEU Chi-restraints excluded: chain v residue 97 LEU Chi-restraints excluded: chain v residue 119 VAL Chi-restraints excluded: chain v residue 131 VAL Chi-restraints excluded: chain v residue 162 THR Chi-restraints excluded: chain v residue 180 THR Chi-restraints excluded: chain v residue 181 LEU Chi-restraints excluded: chain v residue 183 VAL Chi-restraints excluded: chain v residue 191 THR Chi-restraints excluded: chain v residue 193 LYS Chi-restraints excluded: chain v residue 201 ASP Chi-restraints excluded: chain v residue 216 VAL Chi-restraints excluded: chain v residue 228 VAL Chi-restraints excluded: chain v residue 241 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 44 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 3 optimal weight: 8.9990 chunk 29 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 30 optimal weight: 0.0980 chunk 40 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 5 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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: 0.7817 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3654 Z= 0.167 Angle : 0.616 9.471 4988 Z= 0.299 Chirality : 0.047 0.166 590 Planarity : 0.004 0.054 640 Dihedral : 7.392 74.963 535 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.54 % Favored : 90.25 % Rotamer: Outliers : 8.55 % Allowed : 34.97 % Favored : 56.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.36), residues: 482 helix: 2.50 (1.02), residues: 24 sheet: -0.50 (0.35), residues: 209 loop : -2.21 (0.34), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP v 123 PHE 0.019 0.002 PHE v 195 TYR 0.006 0.001 TYR v 55 ARG 0.002 0.000 ARG V 155 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 53 time to evaluate : 0.419 Fit side-chains REVERT: V 90 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7874 (tt0) REVERT: V 111 ARG cc_start: 0.8913 (OUTLIER) cc_final: 0.7315 (mtm-85) REVERT: V 155 ARG cc_start: 0.6756 (OUTLIER) cc_final: 0.5838 (mtt-85) REVERT: V 217 ASN cc_start: 0.7393 (OUTLIER) cc_final: 0.7101 (p0) REVERT: v 49 GLU cc_start: 0.8562 (pm20) cc_final: 0.8257 (pm20) outliers start: 33 outliers final: 29 residues processed: 78 average time/residue: 0.1506 time to fit residues: 14.7255 Evaluate side-chains 85 residues out of total 386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 52 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 45 LEU Chi-restraints excluded: chain V residue 46 THR Chi-restraints excluded: chain V residue 90 GLU Chi-restraints excluded: chain V residue 111 ARG Chi-restraints excluded: chain V residue 127 ILE Chi-restraints excluded: chain V residue 131 VAL Chi-restraints excluded: chain V residue 132 THR Chi-restraints excluded: chain V residue 155 ARG Chi-restraints excluded: chain V residue 177 GLN Chi-restraints excluded: chain V residue 193 LYS Chi-restraints excluded: chain V residue 206 THR Chi-restraints excluded: chain V residue 215 THR Chi-restraints excluded: chain V residue 217 ASN Chi-restraints excluded: chain V residue 225 ASN Chi-restraints excluded: chain V residue 232 ASN Chi-restraints excluded: chain v residue 17 LEU Chi-restraints excluded: chain v residue 51 THR Chi-restraints excluded: chain v residue 79 ASP Chi-restraints excluded: chain v residue 83 THR Chi-restraints excluded: chain v residue 84 LEU Chi-restraints excluded: chain v residue 96 LEU Chi-restraints excluded: chain v residue 97 LEU Chi-restraints excluded: chain v residue 119 VAL Chi-restraints excluded: chain v residue 131 VAL Chi-restraints excluded: chain v residue 162 THR Chi-restraints excluded: chain v residue 180 THR Chi-restraints excluded: chain v residue 181 LEU Chi-restraints excluded: chain v residue 183 VAL Chi-restraints excluded: chain v residue 193 LYS Chi-restraints excluded: chain v residue 201 ASP Chi-restraints excluded: chain v residue 216 VAL Chi-restraints excluded: chain v residue 228 VAL Chi-restraints excluded: chain v residue 241 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 38 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 39 optimal weight: 10.0000 chunk 4 optimal weight: 8.9990 chunk 7 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 25 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 72 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.112652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.097461 restraints weight = 8795.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.099098 restraints weight = 4551.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.100077 restraints weight = 2844.994| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 3654 Z= 0.290 Angle : 0.676 10.031 4988 Z= 0.337 Chirality : 0.048 0.167 590 Planarity : 0.004 0.055 640 Dihedral : 7.762 74.865 535 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.21 % Allowed : 10.79 % Favored : 89.00 % Rotamer: Outliers : 10.36 % Allowed : 33.42 % Favored : 56.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.36), residues: 482 helix: 2.10 (1.03), residues: 24 sheet: -0.56 (0.35), residues: 207 loop : -2.26 (0.34), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP v 123 PHE 0.014 0.002 PHE v 120 TYR 0.010 0.001 TYR v 55 ARG 0.003 0.000 ARG V 155 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1122.21 seconds wall clock time: 21 minutes 2.22 seconds (1262.22 seconds total)