Starting phenix.real_space_refine on Mon Sep 23 17:37:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbw_34645/09_2024/8hbw_34645.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbw_34645/09_2024/8hbw_34645.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbw_34645/09_2024/8hbw_34645.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbw_34645/09_2024/8hbw_34645.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbw_34645/09_2024/8hbw_34645.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbw_34645/09_2024/8hbw_34645.cif" } resolution = 2.57 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= 0.003 sd= 0.159 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 7 5.49 5 S 18 5.16 5 C 2109 2.51 5 N 548 2.21 5 O 627 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 3309 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2179 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 15, 'TRANS': 274} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 997 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "A" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 133 Unusual residues: {'ATP': 1, 'CDL': 1, 'PC1': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 102 Time building chain proxies: 3.39, per 1000 atoms: 1.02 Number of scatterers: 3309 At special positions: 0 Unit cell: (65.052, 71.724, 111.756, 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 18 16.00 P 7 15.00 O 627 8.00 N 548 7.00 C 2109 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 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: 1.03 Conformation dependent library (CDL) restraints added in 428.2 milliseconds 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 754 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 3 sheets defined 62.3% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 11 through 42 Proline residue: A 32 - end of helix Processing helix chain 'A' and resid 56 through 69 Processing helix chain 'A' and resid 70 through 75 Processing helix chain 'A' and resid 76 through 94 removed outlier: 4.367A pdb=" N SER A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 104 Processing helix chain 'A' and resid 111 through 143 Proline residue: A 132 - end of helix Processing helix chain 'A' and resid 155 through 167 Processing helix chain 'A' and resid 168 through 174 removed outlier: 3.629A pdb=" N LYS A 174 " --> pdb=" O GLY A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 204 Processing helix chain 'A' and resid 210 through 242 removed outlier: 4.224A pdb=" N HIS A 214 " --> pdb=" O ASP A 210 " (cutoff:3.500A) Proline residue: A 231 - end of helix Processing helix chain 'A' and resid 249 through 262 Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 269 through 298 removed outlier: 3.609A pdb=" N SER A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 32 Processing helix chain 'B' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'B' and resid 11 through 13 removed outlier: 6.892A pdb=" N VAL B 12 " --> pdb=" O SER B 120 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N MET B 34 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ALA B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 11 through 13 removed outlier: 6.892A pdb=" N VAL B 12 " --> pdb=" O SER B 120 " (cutoff:3.500A) 231 hydrogen bonds defined for protein. 627 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.01 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 547 1.32 - 1.44: 902 1.44 - 1.56: 1893 1.56 - 1.68: 13 1.68 - 1.81: 27 Bond restraints: 3382 Sorted by residual: bond pdb=" CA7 CDL A 402 " pdb=" OA8 CDL A 402 " ideal model delta sigma weight residual 1.334 1.454 -0.120 1.10e-02 8.26e+03 1.20e+02 bond pdb=" CB7 CDL A 402 " pdb=" OB8 CDL A 402 " ideal model delta sigma weight residual 1.334 1.446 -0.112 1.10e-02 8.26e+03 1.03e+02 bond pdb=" CA5 CDL A 402 " pdb=" OA6 CDL A 402 " ideal model delta sigma weight residual 1.342 1.454 -0.112 1.50e-02 4.44e+03 5.57e+01 bond pdb=" C4 ATP A 401 " pdb=" C5 ATP A 401 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.43e+01 bond pdb=" CB5 CDL A 402 " pdb=" OB6 CDL A 402 " ideal model delta sigma weight residual 1.342 1.449 -0.107 1.50e-02 4.44e+03 5.10e+01 ... (remaining 3377 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.41: 4506 3.41 - 6.82: 70 6.82 - 10.22: 14 10.22 - 13.63: 1 13.63 - 17.04: 1 Bond angle restraints: 4592 Sorted by residual: angle pdb=" PB ATP A 401 " pdb=" O3B ATP A 401 " pdb=" PG ATP A 401 " ideal model delta sigma weight residual 139.87 122.83 17.04 1.00e+00 1.00e+00 2.90e+02 angle pdb=" PA ATP A 401 " pdb=" O3A ATP A 401 " pdb=" PB ATP A 401 " ideal model delta sigma weight residual 136.83 124.25 12.58 1.00e+00 1.00e+00 1.58e+02 angle pdb=" C5 ATP A 401 " pdb=" C4 ATP A 401 " pdb=" N3 ATP A 401 " ideal model delta sigma weight residual 126.80 119.46 7.34 1.00e+00 1.00e+00 5.39e+01 angle pdb=" C11 CDL A 402 " pdb=" CA5 CDL A 402 " pdb=" OA6 CDL A 402 " ideal model delta sigma weight residual 111.33 120.23 -8.90 1.32e+00 5.72e-01 4.53e+01 angle pdb=" N3 ATP A 401 " pdb=" C4 ATP A 401 " pdb=" N9 ATP A 401 " ideal model delta sigma weight residual 127.04 134.51 -7.47 1.15e+00 7.59e-01 4.24e+01 ... (remaining 4587 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.12: 1792 17.12 - 34.24: 156 34.24 - 51.36: 64 51.36 - 68.49: 14 68.49 - 85.61: 6 Dihedral angle restraints: 2032 sinusoidal: 849 harmonic: 1183 Sorted by residual: dihedral pdb=" CA ALA A 208 " pdb=" C ALA A 208 " pdb=" N ASP A 209 " pdb=" CA ASP A 209 " ideal model delta harmonic sigma weight residual -180.00 -162.45 -17.55 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA ASP A 209 " pdb=" C ASP A 209 " pdb=" N ASP A 210 " pdb=" CA ASP A 210 " ideal model delta harmonic sigma weight residual 180.00 162.97 17.03 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CB GLU A 100 " pdb=" CG GLU A 100 " pdb=" CD GLU A 100 " pdb=" OE1 GLU A 100 " ideal model delta sinusoidal sigma weight residual 0.00 85.61 -85.61 1 3.00e+01 1.11e-03 9.85e+00 ... (remaining 2029 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 331 0.043 - 0.086: 138 0.086 - 0.129: 33 0.129 - 0.172: 5 0.172 - 0.214: 3 Chirality restraints: 510 Sorted by residual: chirality pdb=" CA LYS A 66 " pdb=" N LYS A 66 " pdb=" C LYS A 66 " pdb=" CB LYS A 66 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA GLU A 261 " pdb=" N GLU A 261 " pdb=" C GLU A 261 " pdb=" CB GLU A 261 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.07e-01 chirality pdb=" CA ARG A 238 " pdb=" N ARG A 238 " pdb=" C ARG A 238 " pdb=" CB ARG A 238 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.49e-01 ... (remaining 507 not shown) Planarity restraints: 567 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 9 " -0.038 5.00e-02 4.00e+02 5.71e-02 5.22e+00 pdb=" N PRO A 10 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 10 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 10 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 84 " 0.011 2.00e-02 2.50e+03 2.23e-02 4.96e+00 pdb=" C GLN A 84 " -0.039 2.00e-02 2.50e+03 pdb=" O GLN A 84 " 0.015 2.00e-02 2.50e+03 pdb=" N ILE A 85 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 101 " -0.009 2.00e-02 2.50e+03 1.76e-02 3.10e+00 pdb=" C PHE B 101 " 0.030 2.00e-02 2.50e+03 pdb=" O PHE B 101 " -0.011 2.00e-02 2.50e+03 pdb=" N GLY B 102 " -0.010 2.00e-02 2.50e+03 ... (remaining 564 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 360 2.74 - 3.28: 3189 3.28 - 3.82: 5979 3.82 - 4.36: 7174 4.36 - 4.90: 12102 Nonbonded interactions: 28804 Sorted by model distance: nonbonded pdb=" OG1 THR A 103 " pdb=" O THR A 108 " model vdw 2.199 3.040 nonbonded pdb=" OE2 GLU A 45 " pdb=" OH TYR A 247 " model vdw 2.266 3.040 nonbonded pdb=" O LYS A 292 " pdb=" OG SER A 296 " model vdw 2.276 3.040 nonbonded pdb=" O GLY A 130 " pdb=" OG1 THR A 133 " model vdw 2.320 3.040 nonbonded pdb=" O TRP A 173 " pdb=" OG1 THR A 176 " model vdw 2.323 3.040 ... (remaining 28799 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: 2.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 14.270 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.124 3382 Z= 0.670 Angle : 1.053 17.042 4592 Z= 0.645 Chirality : 0.050 0.214 510 Planarity : 0.005 0.057 567 Dihedral : 16.265 85.607 1275 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % 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: 1.60 (0.39), residues: 410 helix: 1.83 (0.32), residues: 221 sheet: -0.32 (0.61), residues: 60 loop : 0.59 (0.54), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 173 HIS 0.003 0.001 HIS B 124 PHE 0.018 0.003 PHE A 223 TYR 0.014 0.002 TYR A 157 ARG 0.021 0.002 ARG B 104 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.374 Fit side-chains REVERT: A 55 LYS cc_start: 0.8108 (tttp) cc_final: 0.7810 (tptp) REVERT: A 161 ARG cc_start: 0.7447 (ttt180) cc_final: 0.6715 (mtt90) REVERT: A 206 ILE cc_start: 0.6885 (mm) cc_final: 0.6564 (mp) REVERT: A 248 LYS cc_start: 0.8664 (ptmm) cc_final: 0.8426 (ptmt) REVERT: A 293 ARG cc_start: 0.6520 (ptm-80) cc_final: 0.6132 (tmt-80) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 1.4263 time to fit residues: 90.6844 Evaluate side-chains 53 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 0.1980 chunk 23 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 3382 Z= 0.211 Angle : 0.537 6.816 4592 Z= 0.284 Chirality : 0.040 0.139 510 Planarity : 0.005 0.051 567 Dihedral : 13.653 78.242 569 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.48 % Allowed : 9.20 % Favored : 89.32 % 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 (0.40), residues: 410 helix: 2.66 (0.32), residues: 221 sheet: 0.05 (0.65), residues: 54 loop : 0.65 (0.54), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 111 HIS 0.002 0.001 HIS A 145 PHE 0.009 0.002 PHE A 223 TYR 0.008 0.001 TYR A 74 ARG 0.005 0.001 ARG B 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 60 time to evaluate : 0.378 Fit side-chains REVERT: A 55 LYS cc_start: 0.8050 (tttp) cc_final: 0.7723 (tptp) REVERT: A 117 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7639 (tt) REVERT: A 161 ARG cc_start: 0.7430 (ttt180) cc_final: 0.6674 (mtt90) REVERT: A 206 ILE cc_start: 0.6742 (mm) cc_final: 0.6479 (mp) REVERT: A 293 ARG cc_start: 0.6375 (ptm-80) cc_final: 0.6008 (tmt-80) outliers start: 5 outliers final: 0 residues processed: 63 average time/residue: 1.3106 time to fit residues: 84.8247 Evaluate side-chains 56 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 55 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 0.1980 chunk 11 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 33 optimal weight: 0.0040 chunk 36 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 3382 Z= 0.174 Angle : 0.509 7.427 4592 Z= 0.264 Chirality : 0.039 0.134 510 Planarity : 0.005 0.047 567 Dihedral : 12.362 71.428 569 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.08 % Allowed : 11.57 % Favored : 86.35 % 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: 2.81 (0.40), residues: 410 helix: 3.04 (0.32), residues: 221 sheet: 0.13 (0.66), residues: 54 loop : 0.68 (0.53), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 111 HIS 0.001 0.000 HIS A 145 PHE 0.008 0.001 PHE A 223 TYR 0.007 0.001 TYR A 157 ARG 0.003 0.000 ARG B 72 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 60 time to evaluate : 0.338 Fit side-chains REVERT: A 55 LYS cc_start: 0.8020 (tttp) cc_final: 0.7705 (tptp) REVERT: A 117 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7629 (tt) REVERT: A 161 ARG cc_start: 0.7417 (ttt180) cc_final: 0.6669 (mtt90) REVERT: A 206 ILE cc_start: 0.6447 (mm) cc_final: 0.6204 (mp) REVERT: A 293 ARG cc_start: 0.6394 (ptm-80) cc_final: 0.6035 (tmt-80) outliers start: 7 outliers final: 4 residues processed: 62 average time/residue: 1.0450 time to fit residues: 66.7022 Evaluate side-chains 59 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 54 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 179 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.4980 chunk 28 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 33 optimal weight: 0.0470 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN A 187 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3382 Z= 0.171 Angle : 0.505 8.106 4592 Z= 0.260 Chirality : 0.039 0.133 510 Planarity : 0.004 0.043 567 Dihedral : 11.901 70.136 569 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.08 % Allowed : 12.17 % Favored : 85.76 % 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: 2.93 (0.40), residues: 410 helix: 3.11 (0.33), residues: 221 sheet: 0.34 (0.67), residues: 54 loop : 0.70 (0.53), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 111 HIS 0.001 0.000 HIS A 145 PHE 0.008 0.001 PHE A 223 TYR 0.007 0.001 TYR A 157 ARG 0.003 0.000 ARG B 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 58 time to evaluate : 0.407 Fit side-chains REVERT: A 53 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.7298 (tpt-90) REVERT: A 55 LYS cc_start: 0.8016 (tttp) cc_final: 0.7719 (tptp) REVERT: A 117 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7617 (tt) REVERT: A 161 ARG cc_start: 0.7443 (ttt180) cc_final: 0.6683 (mtt90) REVERT: A 206 ILE cc_start: 0.6423 (mm) cc_final: 0.6176 (mp) REVERT: A 293 ARG cc_start: 0.6419 (ptm-80) cc_final: 0.6082 (tmt-80) outliers start: 7 outliers final: 3 residues processed: 60 average time/residue: 1.2711 time to fit residues: 78.5243 Evaluate side-chains 60 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 55 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 117 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 33 optimal weight: 0.0870 chunk 27 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN A 187 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 3382 Z= 0.189 Angle : 0.511 8.244 4592 Z= 0.264 Chirality : 0.039 0.127 510 Planarity : 0.004 0.040 567 Dihedral : 11.819 70.637 569 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.08 % Allowed : 13.35 % Favored : 84.57 % 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: 3.00 (0.40), residues: 410 helix: 3.12 (0.32), residues: 222 sheet: 0.34 (0.66), residues: 54 loop : 0.82 (0.53), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 57 HIS 0.001 0.000 HIS A 147 PHE 0.010 0.002 PHE A 285 TYR 0.008 0.001 TYR A 157 ARG 0.004 0.000 ARG B 72 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 57 time to evaluate : 0.386 Fit side-chains REVERT: A 53 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.7368 (tpt-90) REVERT: A 55 LYS cc_start: 0.8053 (tttp) cc_final: 0.7716 (tptp) REVERT: A 117 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7628 (tt) REVERT: A 161 ARG cc_start: 0.7440 (ttt180) cc_final: 0.6678 (mtt90) REVERT: A 206 ILE cc_start: 0.6517 (mm) cc_final: 0.6258 (mp) REVERT: A 293 ARG cc_start: 0.6461 (ptm-80) cc_final: 0.6114 (tmt-80) outliers start: 7 outliers final: 4 residues processed: 60 average time/residue: 1.2715 time to fit residues: 78.5205 Evaluate side-chains 63 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 57 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 129 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.9990 chunk 9 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 3 optimal weight: 0.0980 chunk 13 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN A 187 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 3382 Z= 0.219 Angle : 0.527 8.064 4592 Z= 0.273 Chirality : 0.040 0.124 510 Planarity : 0.004 0.039 567 Dihedral : 12.050 72.023 569 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.97 % Allowed : 13.95 % Favored : 83.09 % 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: 2.95 (0.40), residues: 410 helix: 3.08 (0.32), residues: 222 sheet: 0.24 (0.66), residues: 54 loop : 0.82 (0.53), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 57 HIS 0.002 0.000 HIS A 147 PHE 0.011 0.002 PHE A 223 TYR 0.009 0.001 TYR A 157 ARG 0.004 0.000 ARG B 72 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 57 time to evaluate : 0.362 Fit side-chains REVERT: A 53 ARG cc_start: 0.7706 (OUTLIER) cc_final: 0.7422 (tpt-90) REVERT: A 55 LYS cc_start: 0.8091 (tttp) cc_final: 0.7756 (tptp) REVERT: A 57 VAL cc_start: 0.8575 (OUTLIER) cc_final: 0.8123 (t) REVERT: A 117 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7638 (tt) REVERT: A 161 ARG cc_start: 0.7445 (ttt180) cc_final: 0.6662 (mtt90) REVERT: A 206 ILE cc_start: 0.6595 (mm) cc_final: 0.6326 (mp) REVERT: A 293 ARG cc_start: 0.6455 (ptm-80) cc_final: 0.6117 (tmt-80) outliers start: 10 outliers final: 4 residues processed: 60 average time/residue: 1.2245 time to fit residues: 75.7062 Evaluate side-chains 62 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 55 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 179 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 33 optimal weight: 0.0040 chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN A 187 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 3382 Z= 0.186 Angle : 0.519 8.321 4592 Z= 0.267 Chirality : 0.039 0.125 510 Planarity : 0.004 0.038 567 Dihedral : 11.825 71.656 569 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.67 % Allowed : 14.54 % Favored : 82.79 % 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: 3.04 (0.40), residues: 410 helix: 3.13 (0.32), residues: 222 sheet: 0.41 (0.68), residues: 54 loop : 0.85 (0.53), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 280 HIS 0.001 0.000 HIS A 147 PHE 0.009 0.001 PHE A 223 TYR 0.008 0.001 TYR A 157 ARG 0.005 0.001 ARG A 70 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 60 time to evaluate : 0.367 Fit side-chains REVERT: A 53 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.7413 (tpt-90) REVERT: A 55 LYS cc_start: 0.8079 (tttp) cc_final: 0.7737 (tptp) REVERT: A 57 VAL cc_start: 0.8555 (OUTLIER) cc_final: 0.8107 (t) REVERT: A 117 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7616 (tt) REVERT: A 161 ARG cc_start: 0.7441 (ttt180) cc_final: 0.6657 (mtt90) REVERT: A 206 ILE cc_start: 0.6483 (mm) cc_final: 0.6209 (mp) REVERT: A 293 ARG cc_start: 0.6452 (ptm-80) cc_final: 0.6125 (tmt-80) outliers start: 9 outliers final: 4 residues processed: 65 average time/residue: 1.2964 time to fit residues: 86.5707 Evaluate side-chains 64 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 57 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 179 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 chunk 3 optimal weight: 0.0970 chunk 31 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN A 187 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 3382 Z= 0.183 Angle : 0.524 8.528 4592 Z= 0.270 Chirality : 0.039 0.125 510 Planarity : 0.005 0.040 567 Dihedral : 11.656 71.007 569 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.08 % Allowed : 15.13 % Favored : 82.79 % 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: 3.05 (0.40), residues: 410 helix: 3.16 (0.32), residues: 222 sheet: 0.42 (0.68), residues: 54 loop : 0.82 (0.52), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 280 HIS 0.001 0.000 HIS A 147 PHE 0.013 0.001 PHE A 285 TYR 0.008 0.001 TYR A 157 ARG 0.008 0.001 ARG B 104 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 59 time to evaluate : 0.390 Fit side-chains REVERT: A 55 LYS cc_start: 0.8064 (tttp) cc_final: 0.7720 (tptp) REVERT: A 117 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7630 (tt) REVERT: A 161 ARG cc_start: 0.7453 (ttt180) cc_final: 0.6657 (mtt90) REVERT: A 293 ARG cc_start: 0.6432 (ptm-80) cc_final: 0.6109 (tmt-80) outliers start: 7 outliers final: 4 residues processed: 62 average time/residue: 1.3868 time to fit residues: 88.3046 Evaluate side-chains 61 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 56 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 179 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 2.9990 chunk 33 optimal weight: 0.0030 chunk 34 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN A 187 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 3382 Z= 0.212 Angle : 0.556 9.947 4592 Z= 0.283 Chirality : 0.040 0.151 510 Planarity : 0.004 0.037 567 Dihedral : 11.751 71.552 569 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.08 % Allowed : 15.43 % Favored : 82.49 % 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: 3.06 (0.40), residues: 410 helix: 3.12 (0.32), residues: 222 sheet: 0.45 (0.69), residues: 54 loop : 0.89 (0.53), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 280 HIS 0.001 0.000 HIS A 147 PHE 0.010 0.001 PHE A 223 TYR 0.008 0.001 TYR A 157 ARG 0.005 0.001 ARG A 70 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 55 time to evaluate : 0.366 Fit side-chains REVERT: A 55 LYS cc_start: 0.8079 (tttp) cc_final: 0.7737 (tptp) REVERT: A 117 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7629 (tt) REVERT: A 161 ARG cc_start: 0.7457 (ttt180) cc_final: 0.6671 (mtt90) REVERT: A 293 ARG cc_start: 0.6441 (ptm-80) cc_final: 0.6109 (tmt-80) outliers start: 7 outliers final: 3 residues processed: 59 average time/residue: 1.2972 time to fit residues: 78.7323 Evaluate side-chains 58 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 54 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 179 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 0.3980 chunk 34 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN A 187 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 3382 Z= 0.228 Angle : 0.562 9.591 4592 Z= 0.288 Chirality : 0.040 0.147 510 Planarity : 0.005 0.037 567 Dihedral : 11.872 71.459 569 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.48 % Allowed : 16.02 % Favored : 82.49 % 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: 3.04 (0.40), residues: 410 helix: 3.12 (0.32), residues: 222 sheet: 0.37 (0.69), residues: 54 loop : 0.89 (0.53), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 57 HIS 0.002 0.001 HIS A 147 PHE 0.014 0.002 PHE A 285 TYR 0.009 0.001 TYR A 157 ARG 0.006 0.001 ARG A 70 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 54 time to evaluate : 0.394 Fit side-chains REVERT: A 55 LYS cc_start: 0.8097 (tttp) cc_final: 0.7758 (tptp) REVERT: A 117 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7643 (tt) REVERT: A 161 ARG cc_start: 0.7461 (ttt180) cc_final: 0.6660 (mtt90) REVERT: A 293 ARG cc_start: 0.6445 (ptm-80) cc_final: 0.6109 (tmt-80) outliers start: 5 outliers final: 3 residues processed: 56 average time/residue: 1.3060 time to fit residues: 75.2492 Evaluate side-chains 57 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 53 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 179 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 37 optimal weight: 0.4980 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN A 187 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.137627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.122348 restraints weight = 3732.959| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.03 r_work: 0.3263 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 3382 Z= 0.226 Angle : 0.560 9.535 4592 Z= 0.287 Chirality : 0.041 0.147 510 Planarity : 0.005 0.036 567 Dihedral : 11.898 71.649 569 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.19 % Allowed : 16.32 % Favored : 82.49 % 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: 3.03 (0.40), residues: 410 helix: 3.11 (0.32), residues: 222 sheet: 0.43 (0.69), residues: 54 loop : 0.87 (0.53), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 103 HIS 0.002 0.001 HIS A 147 PHE 0.011 0.002 PHE A 223 TYR 0.009 0.001 TYR A 157 ARG 0.006 0.001 ARG A 70 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1925.49 seconds wall clock time: 36 minutes 50.35 seconds (2210.35 seconds total)