Starting phenix.real_space_refine on Sun Apr 27 02:40:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hbw_34645/04_2025/8hbw_34645.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hbw_34645/04_2025/8hbw_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/cci-nas-00/data/ceres_data/8hbw_34645/04_2025/8hbw_34645.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hbw_34645/04_2025/8hbw_34645.map" model { file = "/net/cci-nas-00/data/ceres_data/8hbw_34645/04_2025/8hbw_34645.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hbw_34645/04_2025/8hbw_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-5669/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: 3.35, per 1000 atoms: 1.01 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 416.0 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: 0.41 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: 1.20 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: 1.530 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 14.410 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:14.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.460 ------------------------------------------------------------------------------- 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 3383 Z= 0.619 Angle : 1.055 17.042 4594 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 Details of bonding type rmsd hydrogen bonds : bond 0.10650 ( 227) hydrogen bonds : angle 6.85175 ( 627) SS BOND : bond 0.00499 ( 1) SS BOND : angle 3.02118 ( 2) covalent geometry : bond 0.01032 ( 3382) covalent geometry : angle 1.05315 ( 4592) *********************** 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 to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.489 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: 1.6981 time to fit residues: 107.5368 Evaluate side-chains 53 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.388 ------------------------------------------------------------------------------- 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: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.133669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.119003 restraints weight = 3557.466| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 0.93 r_work: 0.3204 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 2.35 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 3383 Z= 0.151 Angle : 0.543 6.815 4594 Z= 0.287 Chirality : 0.040 0.141 510 Planarity : 0.005 0.051 567 Dihedral : 13.766 78.621 569 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % 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: 2.43 (0.40), residues: 410 helix: 2.64 (0.32), residues: 221 sheet: 0.04 (0.64), 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 147 PHE 0.010 0.002 PHE A 223 TYR 0.008 0.001 TYR A 74 ARG 0.004 0.001 ARG B 72 Details of bonding type rmsd hydrogen bonds : bond 0.03935 ( 227) hydrogen bonds : angle 5.60932 ( 627) SS BOND : bond 0.00276 ( 1) SS BOND : angle 1.68909 ( 2) covalent geometry : bond 0.00346 ( 3382) covalent geometry : angle 0.54184 ( 4592) *********************** 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 63 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.346 Fit side-chains REVERT: A 55 LYS cc_start: 0.8328 (tttp) cc_final: 0.7829 (tptp) REVERT: A 117 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7622 (tt) REVERT: A 161 ARG cc_start: 0.7984 (ttt180) cc_final: 0.6617 (mtt90) REVERT: A 206 ILE cc_start: 0.6792 (mm) cc_final: 0.6406 (mp) REVERT: A 293 ARG cc_start: 0.6389 (ptm-80) cc_final: 0.6002 (tmt-80) outliers start: 5 outliers final: 0 residues processed: 61 average time/residue: 1.4061 time to fit residues: 88.0503 Evaluate side-chains 54 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 0.353 ------------------------------------------------------------------------------- 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 28 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.129812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.115677 restraints weight = 3585.355| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 0.86 r_work: 0.3170 rms_B_bonded: 1.20 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 2.12 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 3383 Z= 0.237 Angle : 0.614 7.516 4594 Z= 0.320 Chirality : 0.044 0.142 510 Planarity : 0.005 0.046 567 Dihedral : 13.814 76.254 569 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.08 % Allowed : 12.46 % Favored : 85.46 % 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: 2.34 (0.40), residues: 410 helix: 2.62 (0.32), residues: 221 sheet: -0.13 (0.64), residues: 54 loop : 0.55 (0.53), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 280 HIS 0.003 0.001 HIS B 124 PHE 0.018 0.003 PHE A 223 TYR 0.011 0.001 TYR A 157 ARG 0.006 0.001 ARG B 72 Details of bonding type rmsd hydrogen bonds : bond 0.04404 ( 227) hydrogen bonds : angle 5.81238 ( 627) SS BOND : bond 0.00378 ( 1) SS BOND : angle 2.33936 ( 2) covalent geometry : bond 0.00565 ( 3382) covalent geometry : angle 0.61213 ( 4592) *********************** 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 63 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.326 Fit side-chains REVERT: A 55 LYS cc_start: 0.8355 (tttp) cc_final: 0.7899 (tptp) REVERT: A 57 VAL cc_start: 0.8573 (OUTLIER) cc_final: 0.8201 (t) REVERT: A 117 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7697 (tt) REVERT: A 161 ARG cc_start: 0.7986 (ttt180) cc_final: 0.6622 (mtt90) REVERT: A 206 ILE cc_start: 0.6919 (mm) cc_final: 0.6534 (mp) REVERT: A 293 ARG cc_start: 0.6445 (ptm-80) cc_final: 0.6062 (tmt-80) outliers start: 7 outliers final: 2 residues processed: 59 average time/residue: 2.6331 time to fit residues: 157.7437 Evaluate side-chains 58 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 0.377 ------------------------------------------------------------------------------- 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 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 9 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 36 optimal weight: 0.0270 chunk 38 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 overall best weight: 0.7038 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.134315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.120380 restraints weight = 3636.795| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 0.93 r_work: 0.3202 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 2.31 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 3383 Z= 0.145 Angle : 0.535 7.973 4594 Z= 0.276 Chirality : 0.040 0.141 510 Planarity : 0.005 0.043 567 Dihedral : 12.827 72.736 569 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.37 % Allowed : 13.06 % 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: 2.65 (0.40), residues: 410 helix: 2.91 (0.32), residues: 221 sheet: 0.01 (0.65), residues: 54 loop : 0.62 (0.53), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 111 HIS 0.001 0.001 HIS A 145 PHE 0.010 0.001 PHE A 223 TYR 0.009 0.001 TYR A 157 ARG 0.004 0.000 ARG B 72 Details of bonding type rmsd hydrogen bonds : bond 0.03755 ( 227) hydrogen bonds : angle 5.49709 ( 627) SS BOND : bond 0.00203 ( 1) SS BOND : angle 1.45274 ( 2) covalent geometry : bond 0.00331 ( 3382) covalent geometry : angle 0.53428 ( 4592) *********************** 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 64 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.665 Fit side-chains REVERT: A 55 LYS cc_start: 0.8350 (tttp) cc_final: 0.7838 (tptp) REVERT: A 57 VAL cc_start: 0.8584 (OUTLIER) cc_final: 0.8181 (t) REVERT: A 117 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7609 (tt) REVERT: A 161 ARG cc_start: 0.8004 (ttt180) cc_final: 0.6675 (mpt-90) REVERT: A 206 ILE cc_start: 0.6736 (mm) cc_final: 0.6368 (mp) REVERT: A 293 ARG cc_start: 0.6463 (ptm-80) cc_final: 0.6093 (tmt-80) outliers start: 8 outliers final: 1 residues processed: 60 average time/residue: 1.7835 time to fit residues: 110.1665 Evaluate side-chains 58 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 55 time to evaluate : 0.390 ------------------------------------------------------------------------------- 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 117 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.6980 chunk 36 optimal weight: 0.4980 chunk 23 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 32 optimal weight: 0.0980 chunk 20 optimal weight: 0.7980 chunk 6 optimal weight: 0.1980 chunk 12 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.136734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.122099 restraints weight = 3577.948| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 0.91 r_work: 0.3241 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 2.26 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 3383 Z= 0.120 Angle : 0.505 8.462 4594 Z= 0.259 Chirality : 0.039 0.128 510 Planarity : 0.004 0.041 567 Dihedral : 11.942 69.576 569 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.37 % Allowed : 12.46 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.87 (0.40), residues: 410 helix: 3.10 (0.32), residues: 221 sheet: 0.16 (0.66), residues: 54 loop : 0.66 (0.53), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 280 HIS 0.001 0.000 HIS A 145 PHE 0.007 0.001 PHE A 223 TYR 0.007 0.001 TYR A 157 ARG 0.003 0.000 ARG B 72 Details of bonding type rmsd hydrogen bonds : bond 0.03426 ( 227) hydrogen bonds : angle 5.24659 ( 627) SS BOND : bond 0.00121 ( 1) SS BOND : angle 1.15791 ( 2) covalent geometry : bond 0.00266 ( 3382) covalent geometry : angle 0.50423 ( 4592) *********************** 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 69 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.297 Fit side-chains REVERT: A 55 LYS cc_start: 0.8297 (tttp) cc_final: 0.7779 (tptp) REVERT: A 57 VAL cc_start: 0.8590 (OUTLIER) cc_final: 0.8139 (t) REVERT: A 70 ARG cc_start: 0.7351 (OUTLIER) cc_final: 0.6484 (mtp-110) REVERT: A 117 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7579 (tt) REVERT: A 161 ARG cc_start: 0.8000 (ttt180) cc_final: 0.6577 (mtt90) REVERT: A 206 ILE cc_start: 0.6395 (mm) cc_final: 0.6057 (mp) REVERT: A 293 ARG cc_start: 0.6402 (ptm-80) cc_final: 0.6036 (tmt-80) outliers start: 8 outliers final: 2 residues processed: 65 average time/residue: 1.2597 time to fit residues: 84.1065 Evaluate side-chains 61 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.330 ------------------------------------------------------------------------------- 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 70 ARG Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 190 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 6 optimal weight: 0.6980 chunk 33 optimal weight: 0.0270 chunk 24 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.5438 ------------------------------------------------------------------------------- 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 = 0.3476 r_free = 0.3476 target = 0.135863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.121457 restraints weight = 3730.353| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 0.89 r_work: 0.3231 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 2.25 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 3383 Z= 0.127 Angle : 0.515 8.309 4594 Z= 0.265 Chirality : 0.039 0.125 510 Planarity : 0.004 0.039 567 Dihedral : 11.821 70.107 569 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.37 % Allowed : 14.84 % 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: 2.97 (0.40), residues: 410 helix: 3.11 (0.32), residues: 222 sheet: 0.32 (0.68), residues: 54 loop : 0.77 (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 145 PHE 0.012 0.002 PHE A 285 TYR 0.008 0.001 TYR A 157 ARG 0.003 0.000 ARG B 72 Details of bonding type rmsd hydrogen bonds : bond 0.03531 ( 227) hydrogen bonds : angle 5.22089 ( 627) SS BOND : bond 0.00100 ( 1) SS BOND : angle 1.54419 ( 2) covalent geometry : bond 0.00287 ( 3382) covalent geometry : angle 0.51419 ( 4592) *********************** 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 69 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.341 Fit side-chains REVERT: A 53 ARG cc_start: 0.7648 (tmt170) cc_final: 0.7405 (mmm160) REVERT: A 55 LYS cc_start: 0.8321 (tttp) cc_final: 0.7842 (tptp) REVERT: A 57 VAL cc_start: 0.8630 (OUTLIER) cc_final: 0.8164 (t) REVERT: A 70 ARG cc_start: 0.7398 (OUTLIER) cc_final: 0.6578 (mtp-110) REVERT: A 117 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7657 (tt) REVERT: A 161 ARG cc_start: 0.8014 (ttt180) cc_final: 0.6689 (mtt90) REVERT: A 206 ILE cc_start: 0.6539 (mm) cc_final: 0.6209 (mp) REVERT: A 293 ARG cc_start: 0.6462 (ptm-80) cc_final: 0.6093 (tmt-80) outliers start: 8 outliers final: 3 residues processed: 65 average time/residue: 1.3505 time to fit residues: 90.0999 Evaluate side-chains 64 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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 70 ARG Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 190 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 4 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3486 r_free = 0.3486 target = 0.136043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.120393 restraints weight = 3710.050| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.06 r_work: 0.3230 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 3383 Z= 0.155 Angle : 0.552 8.191 4594 Z= 0.284 Chirality : 0.041 0.131 510 Planarity : 0.005 0.038 567 Dihedral : 12.134 71.698 569 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % 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: 2.84 (0.40), residues: 410 helix: 3.02 (0.32), residues: 222 sheet: 0.09 (0.66), residues: 54 loop : 0.76 (0.53), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 103 HIS 0.002 0.001 HIS A 147 PHE 0.013 0.002 PHE B 101 TYR 0.010 0.001 TYR A 157 ARG 0.004 0.000 ARG B 72 Details of bonding type rmsd hydrogen bonds : bond 0.03816 ( 227) hydrogen bonds : angle 5.34762 ( 627) SS BOND : bond 0.00177 ( 1) SS BOND : angle 1.79487 ( 2) covalent geometry : bond 0.00359 ( 3382) covalent geometry : angle 0.55074 ( 4592) *********************** 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 67 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.384 Fit side-chains REVERT: A 53 ARG cc_start: 0.7639 (tmt170) cc_final: 0.7413 (mmm160) REVERT: A 55 LYS cc_start: 0.8376 (tttp) cc_final: 0.7901 (tptp) REVERT: A 70 ARG cc_start: 0.7447 (OUTLIER) cc_final: 0.6699 (mtp-110) REVERT: A 117 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7693 (tt) REVERT: A 161 ARG cc_start: 0.8079 (ttt180) cc_final: 0.6721 (mtt90) REVERT: A 206 ILE cc_start: 0.6617 (mm) cc_final: 0.6288 (mp) REVERT: A 293 ARG cc_start: 0.6500 (ptm-80) cc_final: 0.6137 (tmt-80) outliers start: 7 outliers final: 3 residues processed: 63 average time/residue: 1.3852 time to fit residues: 89.6424 Evaluate side-chains 63 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 190 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 17 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 26 optimal weight: 0.0870 chunk 9 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- 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 = 0.3495 r_free = 0.3495 target = 0.136877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.121249 restraints weight = 3694.620| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.06 r_work: 0.3243 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 3383 Z= 0.141 Angle : 0.538 8.445 4594 Z= 0.277 Chirality : 0.040 0.127 510 Planarity : 0.004 0.037 567 Dihedral : 12.037 71.602 569 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % 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: 2.88 (0.40), residues: 410 helix: 3.09 (0.32), residues: 222 sheet: 0.10 (0.66), residues: 54 loop : 0.72 (0.53), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 280 HIS 0.001 0.001 HIS A 147 PHE 0.010 0.002 PHE A 223 TYR 0.009 0.001 TYR A 157 ARG 0.004 0.000 ARG B 72 Details of bonding type rmsd hydrogen bonds : bond 0.03695 ( 227) hydrogen bonds : angle 5.28410 ( 627) SS BOND : bond 0.00122 ( 1) SS BOND : angle 1.57281 ( 2) covalent geometry : bond 0.00325 ( 3382) covalent geometry : angle 0.53704 ( 4592) *********************** 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 to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.381 Fit side-chains REVERT: A 53 ARG cc_start: 0.7658 (tmt170) cc_final: 0.7445 (mmm160) REVERT: A 55 LYS cc_start: 0.8385 (tttp) cc_final: 0.7908 (tptp) REVERT: A 70 ARG cc_start: 0.7443 (OUTLIER) cc_final: 0.6679 (mtp-110) REVERT: A 117 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7676 (tt) REVERT: A 161 ARG cc_start: 0.8075 (ttt180) cc_final: 0.6719 (mtt90) REVERT: A 206 ILE cc_start: 0.6545 (mm) cc_final: 0.6215 (mp) REVERT: A 293 ARG cc_start: 0.6503 (ptm-80) cc_final: 0.6143 (tmt-80) outliers start: 7 outliers final: 3 residues processed: 62 average time/residue: 1.3355 time to fit residues: 85.0490 Evaluate side-chains 63 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 190 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 37 optimal weight: 0.1980 chunk 33 optimal weight: 0.2980 chunk 35 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3508 r_free = 0.3508 target = 0.137867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.122268 restraints weight = 3696.143| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.06 r_work: 0.3263 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 3383 Z= 0.128 Angle : 0.528 8.703 4594 Z= 0.270 Chirality : 0.039 0.128 510 Planarity : 0.004 0.037 567 Dihedral : 11.816 71.384 569 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.37 % Allowed : 15.43 % Favored : 82.20 % 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: 3.13 (0.32), residues: 222 sheet: 0.10 (0.67), residues: 54 loop : 0.75 (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 145 PHE 0.010 0.002 PHE A 285 TYR 0.008 0.001 TYR A 157 ARG 0.004 0.000 ARG A 238 Details of bonding type rmsd hydrogen bonds : bond 0.03570 ( 227) hydrogen bonds : angle 5.19943 ( 627) SS BOND : bond 0.00083 ( 1) SS BOND : angle 1.39527 ( 2) covalent geometry : bond 0.00289 ( 3382) covalent geometry : angle 0.52722 ( 4592) *********************** 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 68 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.390 Fit side-chains REVERT: A 53 ARG cc_start: 0.7651 (tmt170) cc_final: 0.7449 (mmm160) REVERT: A 55 LYS cc_start: 0.8354 (tttp) cc_final: 0.7879 (tptp) REVERT: A 70 ARG cc_start: 0.7439 (OUTLIER) cc_final: 0.6665 (mtp-110) REVERT: A 117 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7668 (tt) REVERT: A 161 ARG cc_start: 0.8051 (ttt180) cc_final: 0.6707 (mtt90) REVERT: A 206 ILE cc_start: 0.6512 (mm) cc_final: 0.6183 (mp) REVERT: A 293 ARG cc_start: 0.6490 (ptm-80) cc_final: 0.6131 (tmt-80) outliers start: 8 outliers final: 4 residues processed: 65 average time/residue: 1.1847 time to fit residues: 79.3393 Evaluate side-chains 65 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain B residue 29 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 30 optimal weight: 0.0070 chunk 24 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 9 optimal weight: 8.9990 chunk 35 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 overall best weight: 0.5998 ------------------------------------------------------------------------------- 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 = 0.3505 r_free = 0.3505 target = 0.137720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.122190 restraints weight = 3699.145| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.05 r_work: 0.3261 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 3383 Z= 0.135 Angle : 0.537 8.789 4594 Z= 0.276 Chirality : 0.040 0.129 510 Planarity : 0.004 0.037 567 Dihedral : 11.769 71.119 569 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % 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: 2.94 (0.40), residues: 410 helix: 3.13 (0.32), residues: 222 sheet: 0.10 (0.68), residues: 54 loop : 0.78 (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 145 PHE 0.009 0.001 PHE A 223 TYR 0.008 0.001 TYR A 157 ARG 0.003 0.000 ARG A 238 Details of bonding type rmsd hydrogen bonds : bond 0.03619 ( 227) hydrogen bonds : angle 5.27605 ( 627) SS BOND : bond 0.00400 ( 1) SS BOND : angle 3.03874 ( 2) covalent geometry : bond 0.00310 ( 3382) covalent geometry : angle 0.53288 ( 4592) ********************** 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 65 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.403 Fit side-chains REVERT: A 55 LYS cc_start: 0.8367 (tttp) cc_final: 0.7885 (tptp) REVERT: A 70 ARG cc_start: 0.7449 (OUTLIER) cc_final: 0.6657 (mtp-110) REVERT: A 117 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7668 (tt) REVERT: A 161 ARG cc_start: 0.8059 (ttt180) cc_final: 0.6708 (mtt90) REVERT: A 206 ILE cc_start: 0.6512 (mm) cc_final: 0.6178 (mp) REVERT: A 293 ARG cc_start: 0.6478 (ptm-80) cc_final: 0.6117 (tmt-80) outliers start: 7 outliers final: 4 residues processed: 62 average time/residue: 1.2513 time to fit residues: 79.9215 Evaluate side-chains 64 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain B residue 29 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 13 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 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 = 0.3497 r_free = 0.3497 target = 0.136971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.121304 restraints weight = 3717.781| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.07 r_work: 0.3242 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 3383 Z= 0.149 Angle : 0.548 8.681 4594 Z= 0.282 Chirality : 0.040 0.127 510 Planarity : 0.004 0.037 567 Dihedral : 11.864 71.263 569 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.78 % Allowed : 16.02 % Favored : 82.20 % 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: 2.90 (0.40), residues: 410 helix: 3.07 (0.32), residues: 222 sheet: 0.11 (0.68), residues: 54 loop : 0.79 (0.53), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 280 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 0.004 0.000 ARG B 72 Details of bonding type rmsd hydrogen bonds : bond 0.03731 ( 227) hydrogen bonds : angle 5.33013 ( 627) SS BOND : bond 0.00597 ( 1) SS BOND : angle 3.04640 ( 2) covalent geometry : bond 0.00347 ( 3382) covalent geometry : angle 0.54426 ( 4592) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3463.97 seconds wall clock time: 60 minutes 55.22 seconds (3655.22 seconds total)