Starting phenix.real_space_refine on Mon Sep 23 11:44:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8acc_15346/09_2024/8acc_15346.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8acc_15346/09_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_15346/09_2024/8acc_15346.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8acc_15346/09_2024/8acc_15346.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8acc_15346/09_2024/8acc_15346.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8acc_15346/09_2024/8acc_15346.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 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 Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 1.93, per 1000 atoms: 1.08 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.47 Conformation dependent library (CDL) restraints added in 218.0 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: 0.56 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: 0.43 Time building geometry restraints manager: 0.53 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: 0.00 - 2.06: 2459 2.06 - 4.11: 37 4.11 - 6.17: 2 6.17 - 8.22: 5 8.22 - 10.28: 2 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 3.040 nonbonded pdb=" O PRO A 181 " pdb=" ND2 ASN A 185 " model vdw 2.265 3.120 nonbonded pdb=" O VAL A 260 " pdb=" NH2 ARG A 263 " model vdw 2.273 3.120 nonbonded pdb=" O PRO A 188 " pdb=" OG1 THR A 189 " model vdw 2.307 3.040 nonbonded pdb=" OE2 GLU A 154 " pdb=" NZ LYS A 264 " model vdw 2.307 3.120 ... (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 Time spend for trying shortcut: 0.00 ========== 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: 0.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 10.580 Find NCS groups from input model: 0.030 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:13.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.170 ------------------------------------------------------------------------------- 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 : 0.175 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: 1.1923 time to fit residues: 69.0861 Evaluate side-chains 49 residues out of total 197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.191 ------------------------------------------------------------------------------- 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: 0.0060 chunk 17 optimal weight: 8.9990 chunk 9 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 10 optimal weight: 30.0000 chunk 13 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 overall best weight: 3.1402 ------------------------------------------------------------------------------- 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 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1820 Z= 0.214 Angle : 0.582 6.025 2505 Z= 0.308 Chirality : 0.045 0.248 300 Planarity : 0.003 0.021 309 Dihedral : 10.963 59.136 323 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.44 % Allowed : 11.35 % Favored : 88.21 % Rotamer: Outliers : 3.95 % Allowed : 15.13 % Favored : 80.92 % 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: -2.13 (0.55), residues: 229 helix: -0.63 (0.54), residues: 95 sheet: -0.13 (1.36), residues: 16 loop : -2.32 (0.56), 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 0.010 0.002 PHE A 237 TYR 0.009 0.001 TYR A 92 ARG 0.001 0.000 ARG A 239 *********************** 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 65 residues out of total 197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 59 time to evaluate : 0.196 Fit side-chains REVERT: A 97 LYS cc_start: 0.8897 (mttp) cc_final: 0.7984 (tptt) REVERT: A 173 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7659 (tt0) REVERT: A 236 ASP cc_start: 0.7276 (t0) cc_final: 0.7001 (t0) outliers start: 6 outliers final: 4 residues processed: 62 average time/residue: 1.1794 time to fit residues: 74.3256 Evaluate side-chains 58 residues out of total 197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 53 time to evaluate : 0.205 ------------------------------------------------------------------------------- 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 263 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 5 optimal weight: 2.9990 chunk 20 optimal weight: 20.0000 chunk 22 optimal weight: 20.0000 chunk 18 optimal weight: 7.9990 chunk 7 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 0.2980 chunk 10 optimal weight: 0.6980 chunk 2 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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: 0.8000 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 1820 Z= 0.144 Angle : 0.534 4.987 2505 Z= 0.282 Chirality : 0.043 0.196 300 Planarity : 0.003 0.021 309 Dihedral : 10.904 58.900 323 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.87 % Allowed : 10.92 % Favored : 88.21 % Rotamer: Outliers : 3.29 % Allowed : 21.71 % 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: -2.06 (0.55), residues: 229 helix: -0.49 (0.54), residues: 95 sheet: -0.38 (1.38), residues: 14 loop : -2.29 (0.56), residues: 120 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 237 TYR 0.011 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 56 residues out of total 197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 51 time to evaluate : 0.191 Fit side-chains REVERT: A 92 TYR cc_start: 0.8966 (t80) cc_final: 0.8712 (t80) REVERT: A 97 LYS cc_start: 0.8842 (mttp) cc_final: 0.7969 (tptt) outliers start: 5 outliers final: 3 residues processed: 53 average time/residue: 1.1754 time to fit residues: 63.3832 Evaluate side-chains 50 residues out of total 197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 47 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 208 SER 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: 2.9990 chunk 22 optimal weight: 20.0000 chunk 10 optimal weight: 6.9990 chunk 19 optimal weight: 0.0980 chunk 5 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 16 optimal weight: 8.9990 chunk 9 optimal weight: 9.9990 chunk 15 optimal weight: 4.9990 overall best weight: 3.4188 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1820 Z= 0.224 Angle : 0.561 6.020 2505 Z= 0.296 Chirality : 0.045 0.263 300 Planarity : 0.003 0.019 309 Dihedral : 10.689 59.365 323 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.44 % Allowed : 11.79 % Favored : 87.77 % Rotamer: Outliers : 3.95 % Allowed : 25.00 % Favored : 71.05 % 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: -1.96 (0.55), residues: 229 helix: -0.38 (0.53), residues: 95 sheet: -0.70 (1.30), residues: 16 loop : -2.22 (0.58), residues: 118 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 0.010 0.001 PHE A 237 TYR 0.009 0.001 TYR A 92 ARG 0.002 0.000 ARG A 239 *********************** 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 58 residues out of total 197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 52 time to evaluate : 0.213 Fit side-chains REVERT: A 92 TYR cc_start: 0.8970 (t80) cc_final: 0.8705 (t80) REVERT: A 97 LYS cc_start: 0.8904 (mttp) cc_final: 0.8008 (tptt) REVERT: A 194 MET cc_start: 0.8874 (mmm) cc_final: 0.8650 (mmp) REVERT: A 236 ASP cc_start: 0.7364 (t0) cc_final: 0.7096 (t0) REVERT: A 262 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.7883 (ptp-110) outliers start: 6 outliers final: 3 residues processed: 55 average time/residue: 1.0587 time to fit residues: 59.2535 Evaluate side-chains 56 residues out of total 197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 52 time to evaluate : 0.146 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 19 optimal weight: 0.2980 chunk 5 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 20 optimal weight: 30.0000 chunk 4 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 22 optimal weight: 20.0000 chunk 18 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- 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 145 ASN A 259 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2832 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= 0.194 Angle : 0.542 5.627 2505 Z= 0.287 Chirality : 0.044 0.246 300 Planarity : 0.003 0.019 309 Dihedral : 10.671 59.185 323 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.44 % Allowed : 11.35 % Favored : 88.21 % Rotamer: Outliers : 5.26 % Allowed : 22.37 % Favored : 72.37 % 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: -1.83 (0.56), residues: 229 helix: -0.18 (0.54), residues: 95 sheet: -0.72 (1.32), residues: 16 loop : -2.23 (0.58), residues: 118 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 0.008 0.001 PHE A 237 TYR 0.009 0.001 TYR A 92 ARG 0.001 0.000 ARG A 155 *********************** 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 60 residues out of total 197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 52 time to evaluate : 0.183 Fit side-chains REVERT: A 97 LYS cc_start: 0.8879 (mttp) cc_final: 0.7991 (tptt) REVERT: A 194 MET cc_start: 0.8862 (mmm) cc_final: 0.8589 (mmp) REVERT: A 236 ASP cc_start: 0.7249 (t0) cc_final: 0.6976 (t0) REVERT: A 247 LYS cc_start: 0.8367 (mmmm) cc_final: 0.8062 (mppt) REVERT: A 262 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7646 (ptp-110) outliers start: 8 outliers final: 4 residues processed: 55 average time/residue: 1.1261 time to fit residues: 63.0096 Evaluate side-chains 55 residues out of total 197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 50 time to evaluate : 0.192 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 7 optimal weight: 10.0000 chunk 11 optimal weight: 0.9980 chunk 21 optimal weight: 20.0000 chunk 2 optimal weight: 0.0670 chunk 12 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 overall best weight: 1.2124 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 1820 Z= 0.136 Angle : 0.512 4.849 2505 Z= 0.270 Chirality : 0.042 0.179 300 Planarity : 0.003 0.019 309 Dihedral : 10.675 58.797 323 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.87 % Allowed : 10.04 % Favored : 89.08 % Rotamer: Outliers : 3.95 % Allowed : 26.32 % Favored : 69.74 % 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: -1.46 (0.56), residues: 229 helix: 0.58 (0.56), residues: 89 sheet: -0.60 (1.39), residues: 14 loop : -2.29 (0.55), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 161 HIS 0.003 0.001 HIS A 159 PHE 0.006 0.001 PHE A 237 TYR 0.009 0.001 TYR A 92 ARG 0.001 0.000 ARG A 85 *********************** 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 57 residues out of total 197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 51 time to evaluate : 0.192 Fit side-chains REVERT: A 92 TYR cc_start: 0.9022 (t80) cc_final: 0.8794 (t80) REVERT: A 97 LYS cc_start: 0.8859 (mttp) cc_final: 0.7970 (tptt) REVERT: A 194 MET cc_start: 0.8856 (mmm) cc_final: 0.8560 (mmp) outliers start: 6 outliers final: 3 residues processed: 55 average time/residue: 1.0452 time to fit residues: 58.5264 Evaluate side-chains 53 residues out of total 197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 50 time to evaluate : 0.193 ------------------------------------------------------------------------------- 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 263 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 13 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 10 optimal weight: 8.9990 chunk 2 optimal weight: 7.9990 chunk 17 optimal weight: 4.9990 chunk 20 optimal weight: 8.9990 chunk 21 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 1820 Z= 0.351 Angle : 0.640 6.746 2505 Z= 0.338 Chirality : 0.048 0.311 300 Planarity : 0.004 0.030 309 Dihedral : 10.790 59.656 323 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.87 % Allowed : 12.23 % Favored : 86.90 % Rotamer: Outliers : 4.61 % Allowed : 28.29 % 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: -1.77 (0.55), residues: 229 helix: 0.19 (0.55), residues: 89 sheet: -0.85 (1.34), residues: 16 loop : -2.36 (0.55), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 161 HIS 0.004 0.002 HIS A 159 PHE 0.014 0.002 PHE A 237 TYR 0.012 0.002 TYR A 92 ARG 0.004 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 : 0.189 Fit side-chains REVERT: A 92 TYR cc_start: 0.9066 (t80) cc_final: 0.8840 (t80) REVERT: A 97 LYS cc_start: 0.8922 (mttp) cc_final: 0.8023 (tptt) REVERT: A 173 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7624 (tt0) REVERT: A 236 ASP cc_start: 0.7504 (t0) cc_final: 0.7298 (t0) REVERT: A 247 LYS cc_start: 0.8282 (mmmm) cc_final: 0.7952 (mppt) REVERT: A 256 ILE cc_start: 0.9151 (mm) cc_final: 0.8874 (mt) REVERT: A 262 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.8030 (ptp-110) outliers start: 7 outliers final: 4 residues processed: 56 average time/residue: 1.0962 time to fit residues: 62.4853 Evaluate side-chains 55 residues out of total 197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 49 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 208 SER 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: 0.5980 chunk 20 optimal weight: 0.6980 chunk 21 optimal weight: 0.1980 chunk 12 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 1820 Z= 0.149 Angle : 0.555 5.026 2505 Z= 0.291 Chirality : 0.043 0.205 300 Planarity : 0.003 0.030 309 Dihedral : 10.684 58.900 323 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.87 % Allowed : 10.04 % Favored : 89.08 % Rotamer: Outliers : 3.95 % Allowed : 30.26 % 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: -1.52 (0.56), residues: 229 helix: 0.62 (0.57), residues: 89 sheet: -0.97 (1.38), residues: 14 loop : -2.35 (0.55), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 161 HIS 0.003 0.001 HIS A 159 PHE 0.006 0.001 PHE A 134 TYR 0.009 0.001 TYR A 92 ARG 0.005 0.000 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 55 residues out of total 197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 49 time to evaluate : 0.205 Fit side-chains REVERT: A 95 LYS cc_start: 0.9166 (OUTLIER) cc_final: 0.8522 (tmtt) REVERT: A 97 LYS cc_start: 0.8846 (mttp) cc_final: 0.7984 (tptt) REVERT: A 236 ASP cc_start: 0.7188 (t0) cc_final: 0.6898 (t0) REVERT: A 247 LYS cc_start: 0.7945 (mmmm) cc_final: 0.7486 (mtmt) outliers start: 6 outliers final: 3 residues processed: 52 average time/residue: 1.1571 time to fit residues: 61.2264 Evaluate side-chains 54 residues out of total 197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 50 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 208 SER 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: 7.9990 chunk 1 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 7 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3276 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= 0.222 Angle : 0.584 5.626 2505 Z= 0.305 Chirality : 0.045 0.250 300 Planarity : 0.004 0.031 309 Dihedral : 10.634 59.254 323 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.87 % Allowed : 12.23 % Favored : 86.90 % Rotamer: Outliers : 2.63 % Allowed : 32.24 % Favored : 65.13 % 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: -1.64 (0.57), residues: 229 helix: 0.20 (0.56), residues: 95 sheet: -1.08 (1.38), residues: 14 loop : -2.25 (0.57), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 161 HIS 0.003 0.001 HIS A 159 PHE 0.009 0.002 PHE A 237 TYR 0.010 0.002 TYR A 87 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 56 residues out of total 197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 52 time to evaluate : 0.192 Fit side-chains REVERT: A 97 LYS cc_start: 0.8915 (mttp) cc_final: 0.8007 (tptt) REVERT: A 236 ASP cc_start: 0.7313 (t0) cc_final: 0.7046 (t0) REVERT: A 247 LYS cc_start: 0.8124 (mmmm) cc_final: 0.7674 (mtmt) REVERT: A 256 ILE cc_start: 0.9194 (mm) cc_final: 0.8914 (mt) REVERT: A 262 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.7916 (ptp-110) outliers start: 4 outliers final: 4 residues processed: 55 average time/residue: 1.1183 time to fit residues: 62.5953 Evaluate side-chains 57 residues out of total 197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 52 time to evaluate : 0.197 ------------------------------------------------------------------------------- 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 208 SER Chi-restraints excluded: chain A residue 262 ARG 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: 6.9990 chunk 2 optimal weight: 8.9990 chunk 3 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 1 optimal weight: 0.0000 chunk 13 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 14 optimal weight: 2.9990 overall best weight: 2.3390 ------------------------------------------------------------------------------- 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 168 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3246 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= 0.180 Angle : 0.578 5.458 2505 Z= 0.302 Chirality : 0.044 0.238 300 Planarity : 0.003 0.033 309 Dihedral : 10.649 59.118 323 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.87 % Allowed : 10.48 % Favored : 88.65 % 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: -1.58 (0.57), residues: 229 helix: 0.28 (0.56), residues: 95 sheet: -1.18 (1.37), residues: 14 loop : -2.22 (0.58), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 161 HIS 0.003 0.001 HIS A 159 PHE 0.007 0.001 PHE A 237 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 57 residues out of total 197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 52 time to evaluate : 0.207 Fit side-chains REVERT: A 97 LYS cc_start: 0.8901 (mttp) cc_final: 0.7998 (tptt) REVERT: A 236 ASP cc_start: 0.7210 (t0) cc_final: 0.6935 (t0) REVERT: A 247 LYS cc_start: 0.8012 (mmmm) cc_final: 0.7568 (mtmt) REVERT: A 262 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7825 (ptp-110) outliers start: 5 outliers final: 3 residues processed: 55 average time/residue: 1.1205 time to fit residues: 62.7149 Evaluate side-chains 56 residues out of total 197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 52 time to evaluate : 0.197 ------------------------------------------------------------------------------- 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 262 ARG 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: 8.9990 chunk 22 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 4 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 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: 5.9990 ------------------------------------------------------------------------------- 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 168 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.126807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.110620 restraints weight = 2826.222| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.13 r_work: 0.3192 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 1820 Z= 0.351 Angle : 0.654 6.618 2505 Z= 0.342 Chirality : 0.049 0.315 300 Planarity : 0.004 0.035 309 Dihedral : 10.892 59.622 323 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.87 % Allowed : 12.66 % Favored : 86.46 % Rotamer: Outliers : 3.95 % Allowed : 30.92 % Favored : 65.13 % 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: -1.75 (0.56), residues: 229 helix: 0.32 (0.56), residues: 89 sheet: -1.16 (1.41), residues: 14 loop : -2.39 (0.56), residues: 126 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 0.014 0.002 PHE A 237 TYR 0.010 0.002 TYR A 92 ARG 0.006 0.001 ARG A 82 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1446.26 seconds wall clock time: 30 minutes 31.09 seconds (1831.09 seconds total)