Starting phenix.real_space_refine on Sun Mar 10 14:16:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8acc_15346/03_2024/8acc_15346.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8acc_15346/03_2024/8acc_15346.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/8acc_15346/03_2024/8acc_15346.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8acc_15346/03_2024/8acc_15346.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8acc_15346/03_2024/8acc_15346.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8acc_15346/03_2024/8acc_15346.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 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: 5 Type Number sf(0) Gaussians P 5 5.49 5 S 10 5.16 5 C 1104 2.51 5 N 309 2.21 5 O 351 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 1779 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1680 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 10, 'TRANS': 220} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 168 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 5, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 104 Chain: "B" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 99 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 3} Link IDs: {'rna2p': 1, 'rna3p': 3} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.51, per 1000 atoms: 0.85 Number of scatterers: 1779 At special positions: 0 Unit cell: (85.2, 73.485, 123.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 P 5 15.00 O 351 8.00 N 309 7.00 C 1104 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 348.8 milliseconds 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 438 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 1 sheets defined 49.4% alpha, 4.8% beta 0 base pairs and 2 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 81 through 85 removed outlier: 3.518A pdb=" N ARG A 85 " --> pdb=" O ARG A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 98 removed outlier: 3.624A pdb=" N GLU A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 128 Processing helix chain 'A' and resid 130 through 137 Processing helix chain 'A' and resid 137 through 149 removed outlier: 3.882A pdb=" N ALA A 141 " --> pdb=" O THR A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 159 removed outlier: 3.861A pdb=" N ASN A 157 " --> pdb=" O GLU A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 184 Processing helix chain 'A' and resid 189 through 194 removed outlier: 3.544A pdb=" N VAL A 193 " --> pdb=" O THR A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 211 removed outlier: 3.531A pdb=" N ALA A 203 " --> pdb=" O GLU A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 224 Processing helix chain 'A' and resid 245 through 257 removed outlier: 3.992A pdb=" N GLU A 250 " --> pdb=" O THR A 246 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N VAL A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 262 removed outlier: 3.502A pdb=" N ARG A 262 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 161 through 166 removed outlier: 4.034A pdb=" N GLU A 173 " --> pdb=" O ILE A 165 " (cutoff:3.500A) 64 hydrogen bonds defined for protein. 171 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 2 stacking parallelities Total time for adding SS restraints: 0.39 Time building geometry restraints manager: 0.91 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: 538 1.34 - 1.45: 271 1.45 - 1.57: 984 1.57 - 1.69: 9 1.69 - 1.80: 18 Bond restraints: 1820 Sorted by residual: bond pdb=" N PRO A 273 " pdb=" CA PRO A 273 " ideal model delta sigma weight residual 1.468 1.456 0.012 1.20e-02 6.94e+03 9.83e-01 bond pdb=" CA VAL A 286 " pdb=" CB VAL A 286 " ideal model delta sigma weight residual 1.540 1.528 0.012 1.36e-02 5.41e+03 7.88e-01 bond pdb=" CA VAL A 289 " pdb=" CB VAL A 289 " ideal model delta sigma weight residual 1.536 1.526 0.010 1.17e-02 7.31e+03 7.02e-01 bond pdb=" CA VAL A 65 " pdb=" CB VAL A 65 " ideal model delta sigma weight residual 1.540 1.519 0.021 2.70e-02 1.37e+03 6.26e-01 bond pdb=" N GLY A 276 " pdb=" CA GLY A 276 " ideal model delta sigma weight residual 1.449 1.460 -0.011 1.45e-02 4.76e+03 5.73e-01 ... (remaining 1815 not shown) Histogram of bond angle deviations from ideal: 100.64 - 107.31: 77 107.31 - 113.98: 1039 113.98 - 120.65: 704 120.65 - 127.32: 664 127.32 - 133.99: 21 Bond angle restraints: 2505 Sorted by residual: angle pdb=" N PRO A 273 " pdb=" CA PRO A 273 " pdb=" CB PRO A 273 " ideal model delta sigma weight residual 103.27 110.20 -6.93 9.00e-01 1.23e+00 5.93e+01 angle pdb=" N PRO A 69 " pdb=" CA PRO A 69 " pdb=" CB PRO A 69 " ideal model delta sigma weight residual 103.08 110.52 -7.44 9.70e-01 1.06e+00 5.89e+01 angle pdb=" N PRO A 70 " pdb=" CA PRO A 70 " pdb=" CB PRO A 70 " ideal model delta sigma weight residual 103.25 110.45 -7.20 1.05e+00 9.07e-01 4.70e+01 angle pdb=" OP1 U B 6 " pdb=" P U B 6 " pdb=" OP2 U B 6 " ideal model delta sigma weight residual 119.60 109.32 10.28 3.00e+00 1.11e-01 1.17e+01 angle pdb=" OP1 U B 4 " pdb=" P U B 4 " pdb=" OP2 U B 4 " ideal model delta sigma weight residual 119.60 109.53 10.07 3.00e+00 1.11e-01 1.13e+01 ... (remaining 2500 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.33: 979 15.33 - 30.66: 75 30.66 - 45.99: 25 45.99 - 61.32: 10 61.32 - 76.65: 1 Dihedral angle restraints: 1090 sinusoidal: 414 harmonic: 676 Sorted by residual: dihedral pdb=" N PRO A 70 " pdb=" C PRO A 70 " pdb=" CA PRO A 70 " pdb=" CB PRO A 70 " ideal model delta harmonic sigma weight residual 115.10 123.97 -8.87 0 2.50e+00 1.60e-01 1.26e+01 dihedral pdb=" N PRO A 69 " pdb=" C PRO A 69 " pdb=" CA PRO A 69 " pdb=" CB PRO A 69 " ideal model delta harmonic sigma weight residual 115.10 123.48 -8.38 0 2.50e+00 1.60e-01 1.12e+01 dihedral pdb=" CA TRP A 232 " pdb=" C TRP A 232 " pdb=" N LEU A 233 " pdb=" CA LEU A 233 " ideal model delta harmonic sigma weight residual -180.00 -165.06 -14.94 0 5.00e+00 4.00e-02 8.92e+00 ... (remaining 1087 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 251 0.057 - 0.113: 41 0.113 - 0.170: 3 0.170 - 0.227: 1 0.227 - 0.283: 4 Chirality restraints: 300 Sorted by residual: chirality pdb=" CA PRO A 70 " pdb=" N PRO A 70 " pdb=" C PRO A 70 " pdb=" CB PRO A 70 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" P U B 6 " pdb=" OP1 U B 6 " pdb=" OP2 U B 6 " pdb=" O5' U B 6 " both_signs ideal model delta sigma weight residual True 2.41 -2.67 -0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CA PRO A 69 " pdb=" N PRO A 69 " pdb=" C PRO A 69 " pdb=" CB PRO A 69 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.24 2.00e-01 2.50e+01 1.49e+00 ... (remaining 297 not shown) Planarity restraints: 309 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 256 " 0.005 2.00e-02 2.50e+03 1.02e-02 1.04e+00 pdb=" C ILE A 256 " -0.018 2.00e-02 2.50e+03 pdb=" O ILE A 256 " 0.007 2.00e-02 2.50e+03 pdb=" N ALA A 257 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 180 " 0.016 5.00e-02 4.00e+02 2.41e-02 9.33e-01 pdb=" N PRO A 181 " -0.042 5.00e-02 4.00e+02 pdb=" CA PRO A 181 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 181 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 159 " 0.004 2.00e-02 2.50e+03 7.32e-03 5.37e-01 pdb=" C HIS A 159 " -0.013 2.00e-02 2.50e+03 pdb=" O HIS A 159 " 0.005 2.00e-02 2.50e+03 pdb=" N THR A 160 " 0.004 2.00e-02 2.50e+03 ... (remaining 306 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 143 2.74 - 3.28: 1856 3.28 - 3.82: 2587 3.82 - 4.36: 3178 4.36 - 4.90: 5043 Nonbonded interactions: 12807 Sorted by model distance: nonbonded pdb=" O ALA A 258 " pdb=" OG1 THR A 261 " model vdw 2.200 2.440 nonbonded pdb=" O PRO A 181 " pdb=" ND2 ASN A 185 " model vdw 2.265 2.520 nonbonded pdb=" O VAL A 260 " pdb=" NH2 ARG A 263 " model vdw 2.273 2.520 nonbonded pdb=" O PRO A 188 " pdb=" OG1 THR A 189 " model vdw 2.307 2.440 nonbonded pdb=" OE2 GLU A 154 " pdb=" NZ LYS A 264 " model vdw 2.307 2.520 ... (remaining 12802 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 1.930 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.910 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 1820 Z= 0.152 Angle : 0.696 10.278 2505 Z= 0.420 Chirality : 0.051 0.283 300 Planarity : 0.002 0.024 309 Dihedral : 13.616 76.647 652 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 2.18 % Allowed : 11.35 % Favored : 86.46 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.55), residues: 229 helix: -1.18 (0.53), residues: 100 sheet: 1.20 (1.45), residues: 12 loop : -2.40 (0.56), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 161 HIS 0.001 0.000 HIS A 196 PHE 0.007 0.001 PHE A 237 TYR 0.007 0.001 TYR A 205 ARG 0.001 0.000 ARG A 82 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.176 Fit side-chains REVERT: A 97 LYS cc_start: 0.8956 (mttp) cc_final: 0.7965 (tptt) REVERT: A 132 ASP cc_start: 0.7999 (t0) cc_final: 0.7764 (t0) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 1.2316 time to fit residues: 71.2697 Evaluate side-chains 49 residues out of total 197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 19 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 11 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 10 optimal weight: 20.0000 chunk 13 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 14 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN A 104 ASN ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 1820 Z= 0.305 Angle : 0.614 6.331 2505 Z= 0.325 Chirality : 0.048 0.282 300 Planarity : 0.004 0.018 309 Dihedral : 10.739 59.367 323 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.87 % Allowed : 11.79 % Favored : 87.34 % Rotamer: Outliers : 3.95 % Allowed : 14.47 % Favored : 81.58 % 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: -2.03 (0.55), residues: 229 helix: -0.35 (0.56), residues: 89 sheet: -0.19 (1.33), residues: 16 loop : -2.35 (0.54), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 161 HIS 0.004 0.002 HIS A 159 PHE 0.012 0.002 PHE A 237 TYR 0.008 0.001 TYR A 92 ARG 0.003 0.000 ARG A 195 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 55 time to evaluate : 0.212 Fit side-chains REVERT: A 97 LYS cc_start: 0.8907 (mttp) cc_final: 0.7994 (tptt) REVERT: A 173 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7641 (tt0) REVERT: A 262 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.8116 (ptp-110) outliers start: 6 outliers final: 4 residues processed: 58 average time/residue: 1.1144 time to fit residues: 65.7826 Evaluate side-chains 57 residues out of total 197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 51 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 263 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 5 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 22 optimal weight: 20.0000 chunk 18 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 16 optimal weight: 0.1980 chunk 15 optimal weight: 10.0000 chunk 10 optimal weight: 0.1980 chunk 2 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 1820 Z= 0.181 Angle : 0.553 5.698 2505 Z= 0.292 Chirality : 0.044 0.246 300 Planarity : 0.003 0.017 309 Dihedral : 10.663 59.138 323 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.44 % Allowed : 13.97 % Favored : 85.59 % Rotamer: Outliers : 3.95 % Allowed : 21.05 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.55), residues: 229 helix: -0.55 (0.54), residues: 95 sheet: -0.57 (1.29), residues: 16 loop : -2.19 (0.58), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 161 HIS 0.003 0.001 HIS A 159 PHE 0.007 0.001 PHE A 237 TYR 0.010 0.001 TYR A 92 ARG 0.001 0.000 ARG A 263 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 53 time to evaluate : 0.216 Fit side-chains REVERT: A 92 TYR cc_start: 0.8931 (t80) cc_final: 0.8688 (t80) REVERT: A 97 LYS cc_start: 0.8879 (mttp) cc_final: 0.7988 (tptt) REVERT: A 262 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7691 (ptp-110) outliers start: 6 outliers final: 3 residues processed: 57 average time/residue: 1.0961 time to fit residues: 63.5769 Evaluate side-chains 55 residues out of total 197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 51 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 263 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 20 optimal weight: 5.9990 chunk 22 optimal weight: 20.0000 chunk 10 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 12 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 16 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN A 115 GLN A 187 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 1820 Z= 0.227 Angle : 0.563 6.060 2505 Z= 0.298 Chirality : 0.046 0.271 300 Planarity : 0.003 0.017 309 Dihedral : 10.624 59.343 323 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.44 % Allowed : 12.23 % Favored : 87.34 % Rotamer: Outliers : 5.26 % Allowed : 24.34 % Favored : 70.39 % 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 (0.56), residues: 229 helix: -0.06 (0.55), residues: 89 sheet: -0.82 (1.27), residues: 16 loop : -2.21 (0.57), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 161 HIS 0.004 0.001 HIS A 159 PHE 0.009 0.001 PHE A 237 TYR 0.010 0.001 TYR A 92 ARG 0.001 0.000 ARG A 195 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 54 time to evaluate : 0.195 Fit side-chains REVERT: A 92 TYR cc_start: 0.8968 (t80) cc_final: 0.8710 (t80) REVERT: A 97 LYS cc_start: 0.8887 (mttp) cc_final: 0.7994 (tptt) REVERT: A 243 GLN cc_start: 0.7785 (OUTLIER) cc_final: 0.7136 (mp-120) REVERT: A 247 LYS cc_start: 0.8403 (mmmm) cc_final: 0.8058 (mppt) REVERT: A 262 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.7905 (ptp-110) outliers start: 8 outliers final: 4 residues processed: 58 average time/residue: 1.1396 time to fit residues: 67.2353 Evaluate side-chains 59 residues out of total 197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 53 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 243 GLN Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 263 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 0 optimal weight: 30.0000 chunk 11 optimal weight: 5.9990 chunk 19 optimal weight: 0.0070 chunk 5 optimal weight: 5.9990 chunk 7 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 4 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 22 optimal weight: 30.0000 chunk 18 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 overall best weight: 4.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 1820 Z= 0.266 Angle : 0.590 6.269 2505 Z= 0.313 Chirality : 0.047 0.290 300 Planarity : 0.003 0.017 309 Dihedral : 10.731 59.448 323 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.44 % Allowed : 13.10 % Favored : 86.46 % Rotamer: Outliers : 4.61 % Allowed : 26.32 % Favored : 69.08 % 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: -1.84 (0.56), residues: 229 helix: -0.04 (0.55), residues: 89 sheet: -0.92 (1.27), residues: 16 loop : -2.24 (0.57), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 161 HIS 0.005 0.002 HIS A 159 PHE 0.009 0.002 PHE A 237 TYR 0.012 0.002 TYR A 87 ARG 0.002 0.000 ARG A 195 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 54 time to evaluate : 0.175 Fit side-chains REVERT: A 92 TYR cc_start: 0.8973 (t80) cc_final: 0.8766 (t80) REVERT: A 97 LYS cc_start: 0.8883 (mttp) cc_final: 0.8004 (tptt) REVERT: A 243 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.7151 (mp-120) REVERT: A 247 LYS cc_start: 0.8448 (mmmm) cc_final: 0.8091 (mppt) REVERT: A 262 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.7969 (ptp-110) outliers start: 7 outliers final: 4 residues processed: 57 average time/residue: 1.1484 time to fit residues: 66.5587 Evaluate side-chains 58 residues out of total 197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 52 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 243 GLN Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 263 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 1 optimal weight: 8.9990 chunk 7 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 2 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 chunk 18 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 1820 Z= 0.208 Angle : 0.564 5.861 2505 Z= 0.297 Chirality : 0.046 0.267 300 Planarity : 0.003 0.018 309 Dihedral : 10.676 59.265 323 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.87 % Allowed : 11.35 % Favored : 87.77 % Rotamer: Outliers : 6.58 % Allowed : 25.66 % Favored : 67.76 % 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: -1.89 (0.56), residues: 229 helix: -0.28 (0.53), residues: 95 sheet: -1.02 (1.27), residues: 16 loop : -2.17 (0.58), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 161 HIS 0.005 0.001 HIS A 159 PHE 0.007 0.001 PHE A 237 TYR 0.009 0.001 TYR A 92 ARG 0.001 0.000 ARG A 239 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 55 time to evaluate : 0.148 Fit side-chains REVERT: A 92 TYR cc_start: 0.8962 (t80) cc_final: 0.8738 (t80) REVERT: A 97 LYS cc_start: 0.8868 (mttp) cc_final: 0.7994 (tptt) REVERT: A 243 GLN cc_start: 0.7734 (OUTLIER) cc_final: 0.7110 (mp-120) REVERT: A 247 LYS cc_start: 0.8433 (mmmm) cc_final: 0.8074 (mppt) REVERT: A 262 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.7990 (ptp-110) outliers start: 10 outliers final: 4 residues processed: 60 average time/residue: 1.0128 time to fit residues: 61.8072 Evaluate side-chains 60 residues out of total 197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 54 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 243 GLN Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 263 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 13 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 4 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN A 259 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 1820 Z= 0.248 Angle : 0.594 6.091 2505 Z= 0.312 Chirality : 0.047 0.282 300 Planarity : 0.004 0.027 309 Dihedral : 10.735 59.395 323 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.87 % Allowed : 12.23 % Favored : 86.90 % Rotamer: Outliers : 4.61 % Allowed : 28.95 % Favored : 66.45 % 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 (0.55), residues: 229 helix: 0.04 (0.54), residues: 89 sheet: -1.13 (1.28), residues: 16 loop : -2.24 (0.57), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 161 HIS 0.005 0.002 HIS A 159 PHE 0.008 0.001 PHE A 237 TYR 0.010 0.001 TYR A 87 ARG 0.005 0.001 ARG A 82 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 53 time to evaluate : 0.186 Fit side-chains REVERT: A 95 LYS cc_start: 0.9180 (OUTLIER) cc_final: 0.8603 (tmtt) REVERT: A 97 LYS cc_start: 0.8887 (mttp) cc_final: 0.8005 (tptt) REVERT: A 243 GLN cc_start: 0.7751 (OUTLIER) cc_final: 0.7124 (mp-120) REVERT: A 247 LYS cc_start: 0.8449 (mmmm) cc_final: 0.8089 (mtpt) REVERT: A 262 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.8065 (ptp-110) outliers start: 7 outliers final: 5 residues processed: 57 average time/residue: 1.1749 time to fit residues: 68.0822 Evaluate side-chains 60 residues out of total 197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 52 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 243 GLN Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 263 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 19 optimal weight: 2.9990 chunk 20 optimal weight: 20.0000 chunk 21 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 15 optimal weight: 0.3980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN A 168 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 1820 Z= 0.162 Angle : 0.555 5.114 2505 Z= 0.291 Chirality : 0.044 0.222 300 Planarity : 0.003 0.028 309 Dihedral : 10.610 58.993 323 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.87 % Allowed : 11.79 % Favored : 87.34 % Rotamer: Outliers : 6.58 % Allowed : 25.66 % Favored : 67.76 % 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: -1.72 (0.56), residues: 229 helix: 0.00 (0.54), residues: 95 sheet: -1.11 (1.34), residues: 14 loop : -2.18 (0.58), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 161 HIS 0.005 0.001 HIS A 159 PHE 0.005 0.001 PHE A 134 TYR 0.008 0.001 TYR A 92 ARG 0.005 0.001 ARG A 82 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 52 time to evaluate : 0.205 Fit side-chains REVERT: A 97 LYS cc_start: 0.8906 (mttp) cc_final: 0.8000 (tptt) REVERT: A 243 GLN cc_start: 0.7598 (OUTLIER) cc_final: 0.6968 (mp-120) REVERT: A 247 LYS cc_start: 0.8371 (mmmm) cc_final: 0.7852 (mppt) outliers start: 10 outliers final: 6 residues processed: 59 average time/residue: 1.3344 time to fit residues: 79.9081 Evaluate side-chains 55 residues out of total 197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 48 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 243 GLN Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 263 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 22 optimal weight: 20.0000 chunk 21 optimal weight: 40.0000 chunk 18 optimal weight: 0.9980 chunk 1 optimal weight: 7.9990 chunk 14 optimal weight: 9.9990 chunk 11 optimal weight: 4.9990 chunk 19 optimal weight: 8.9990 chunk 5 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 168 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 1820 Z= 0.175 Angle : 0.558 5.163 2505 Z= 0.292 Chirality : 0.043 0.226 300 Planarity : 0.003 0.030 309 Dihedral : 10.580 59.098 323 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.87 % Allowed : 11.79 % Favored : 87.34 % Rotamer: Outliers : 3.95 % Allowed : 28.95 % Favored : 67.11 % 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: -1.61 (0.56), residues: 229 helix: 0.16 (0.54), residues: 95 sheet: -1.23 (1.36), residues: 14 loop : -2.14 (0.58), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 161 HIS 0.004 0.001 HIS A 159 PHE 0.006 0.001 PHE A 237 TYR 0.010 0.001 TYR A 92 ARG 0.006 0.001 ARG A 82 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 52 time to evaluate : 0.196 Fit side-chains REVERT: A 97 LYS cc_start: 0.8897 (mttp) cc_final: 0.8057 (tptt) REVERT: A 247 LYS cc_start: 0.8021 (mmmm) cc_final: 0.7666 (mppt) REVERT: A 256 ILE cc_start: 0.9162 (mm) cc_final: 0.8900 (mt) outliers start: 6 outliers final: 5 residues processed: 56 average time/residue: 1.2901 time to fit residues: 73.4139 Evaluate side-chains 58 residues out of total 197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 53 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 263 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 18 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 13 optimal weight: 10.0000 chunk 20 optimal weight: 20.0000 chunk 12 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 14 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN A 115 GLN ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 168 ASN A 187 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 1820 Z= 0.133 Angle : 0.528 4.850 2505 Z= 0.275 Chirality : 0.041 0.160 300 Planarity : 0.003 0.032 309 Dihedral : 10.485 58.644 323 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.87 % Allowed : 10.92 % Favored : 88.21 % Rotamer: Outliers : 3.29 % Allowed : 30.92 % Favored : 65.79 % 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: -1.25 (0.57), residues: 229 helix: 0.88 (0.57), residues: 89 sheet: -1.43 (1.35), residues: 14 loop : -2.14 (0.56), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 161 HIS 0.004 0.001 HIS A 159 PHE 0.006 0.001 PHE A 134 TYR 0.011 0.001 TYR A 92 ARG 0.007 0.001 ARG A 82 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 58 time to evaluate : 0.178 Fit side-chains REVERT: A 82 ARG cc_start: 0.8831 (ttm110) cc_final: 0.8401 (ttm110) REVERT: A 97 LYS cc_start: 0.8890 (mttp) cc_final: 0.8053 (tptt) REVERT: A 247 LYS cc_start: 0.7844 (mmmm) cc_final: 0.7444 (mtmt) REVERT: A 256 ILE cc_start: 0.9144 (mm) cc_final: 0.8883 (mt) outliers start: 5 outliers final: 3 residues processed: 61 average time/residue: 1.1465 time to fit residues: 71.0880 Evaluate side-chains 54 residues out of total 197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 51 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 263 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 13 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 22 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 4 optimal weight: 1.9990 chunk 2 optimal weight: 8.9990 chunk 18 optimal weight: 0.7980 chunk 21 optimal weight: 40.0000 chunk 9 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN A 115 GLN ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 168 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.131373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.115230 restraints weight = 2807.376| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.07 r_work: 0.3264 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 1820 Z= 0.204 Angle : 0.564 5.143 2505 Z= 0.294 Chirality : 0.044 0.226 300 Planarity : 0.003 0.027 309 Dihedral : 10.592 59.149 323 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.87 % Allowed : 10.92 % Favored : 88.21 % Rotamer: Outliers : 3.29 % Allowed : 33.55 % Favored : 63.16 % 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: -1.53 (0.56), residues: 229 helix: 0.30 (0.56), residues: 95 sheet: -1.60 (1.36), residues: 14 loop : -2.11 (0.57), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 161 HIS 0.002 0.001 HIS A 159 PHE 0.008 0.001 PHE A 237 TYR 0.012 0.001 TYR A 92 ARG 0.007 0.001 ARG A 82 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1472.16 seconds wall clock time: 27 minutes 33.21 seconds (1653.21 seconds total)