Starting phenix.real_space_refine on Fri Aug 22 14:29:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j1n_35928/08_2025/8j1n_35928.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j1n_35928/08_2025/8j1n_35928.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8j1n_35928/08_2025/8j1n_35928.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j1n_35928/08_2025/8j1n_35928.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8j1n_35928/08_2025/8j1n_35928.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j1n_35928/08_2025/8j1n_35928.map" } resolution = 2.51 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= -0.001 sd= 0.146 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 4 5.49 5 S 18 5.16 5 C 2106 2.51 5 N 545 2.21 5 O 619 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3292 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2180 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 15, 'TRANS': 274} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 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: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 115 Unusual residues: {'CDL': 1, 'DNF': 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: 1.18, per 1000 atoms: 0.36 Number of scatterers: 3292 At special positions: 0 Unit cell: (66.72, 68.388, 110.922, 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 4 15.00 O 619 8.00 N 545 7.00 C 2106 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: 0.34 Conformation dependent library (CDL) restraints added in 76.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 14 helices and 3 sheets defined 62.6% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 11 through 43 Proline residue: A 32 - end of helix Processing helix chain 'A' and resid 56 through 69 Processing helix chain 'A' and resid 70 through 73 Processing helix chain 'A' and resid 76 through 107 removed outlier: 4.129A pdb=" N PHE A 101 " --> pdb=" O THR A 97 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LYS A 106 " --> pdb=" O LEU A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 143 removed outlier: 3.512A pdb=" N LYS A 115 " --> pdb=" O SER A 111 " (cutoff:3.500A) Proline residue: A 132 - end of helix Processing helix chain 'A' and resid 155 through 168 Processing helix chain 'A' and resid 169 through 174 removed outlier: 3.603A pdb=" N LYS A 174 " --> pdb=" O GLY A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 205 Processing helix chain 'A' and resid 210 through 242 removed outlier: 3.839A 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 removed outlier: 3.655A pdb=" N LYS A 268 " --> pdb=" O ALA A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 297 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: 6.727A pdb=" N VAL B 12 " --> pdb=" O SER B 120 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N MET B 34 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ALA B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.441A 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: 6.727A pdb=" N VAL B 12 " --> pdb=" O SER B 120 " (cutoff:3.500A) 234 hydrogen bonds defined for protein. 648 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.68 Time building geometry restraints manager: 0.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 517 1.30 - 1.43: 891 1.43 - 1.56: 1920 1.56 - 1.69: 8 1.69 - 1.81: 27 Bond restraints: 3363 Sorted by residual: bond pdb=" CA7 CDL A 402 " pdb=" OA8 CDL A 402 " ideal model delta sigma weight residual 1.334 1.457 -0.123 1.10e-02 8.26e+03 1.26e+02 bond pdb=" CB7 CDL A 402 " pdb=" OB8 CDL A 402 " ideal model delta sigma weight residual 1.334 1.442 -0.108 1.10e-02 8.26e+03 9.61e+01 bond pdb=" CA5 CDL A 402 " pdb=" OA6 CDL A 402 " ideal model delta sigma weight residual 1.342 1.458 -0.116 1.50e-02 4.44e+03 5.93e+01 bond pdb=" CB5 CDL A 402 " pdb=" OB6 CDL A 402 " ideal model delta sigma weight residual 1.342 1.445 -0.103 1.50e-02 4.44e+03 4.74e+01 bond pdb=" C21 PC1 A 403 " pdb=" O21 PC1 A 403 " ideal model delta sigma weight residual 1.331 1.457 -0.126 2.00e-02 2.50e+03 3.96e+01 ... (remaining 3358 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 4345 1.95 - 3.90: 144 3.90 - 5.85: 55 5.85 - 7.80: 6 7.80 - 9.75: 9 Bond angle restraints: 4559 Sorted by residual: angle pdb=" C51 CDL A 402 " pdb=" CB5 CDL A 402 " pdb=" OB6 CDL A 402 " ideal model delta sigma weight residual 111.33 120.79 -9.46 1.32e+00 5.72e-01 5.12e+01 angle pdb=" C11 CDL A 402 " pdb=" CA5 CDL A 402 " pdb=" OA6 CDL A 402 " ideal model delta sigma weight residual 111.33 120.58 -9.25 1.32e+00 5.72e-01 4.90e+01 angle pdb=" C71 CDL A 402 " pdb=" CB7 CDL A 402 " pdb=" OB8 CDL A 402 " ideal model delta sigma weight residual 111.64 121.39 -9.75 1.65e+00 3.69e-01 3.51e+01 angle pdb=" C31 CDL A 402 " pdb=" CA7 CDL A 402 " pdb=" OA8 CDL A 402 " ideal model delta sigma weight residual 111.64 120.78 -9.14 1.65e+00 3.69e-01 3.08e+01 angle pdb=" OB6 CDL A 402 " pdb=" CB5 CDL A 402 " pdb=" OB7 CDL A 402 " ideal model delta sigma weight residual 123.92 118.75 5.17 1.00e+00 9.92e-01 2.65e+01 ... (remaining 4554 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.92: 1835 20.92 - 41.84: 122 41.84 - 62.75: 34 62.75 - 83.67: 4 83.67 - 104.59: 4 Dihedral angle restraints: 1999 sinusoidal: 816 harmonic: 1183 Sorted by residual: dihedral pdb=" CA ARG B 72 " pdb=" C ARG B 72 " pdb=" N ASP B 73 " pdb=" CA ASP B 73 " ideal model delta harmonic sigma weight residual 180.00 155.64 24.36 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA5 CDL A 402 " pdb=" CA4 CDL A 402 " pdb=" OA6 CDL A 402 " pdb=" CA6 CDL A 402 " ideal model delta sinusoidal sigma weight residual 168.24 63.65 104.59 1 3.00e+01 1.11e-03 1.34e+01 dihedral pdb=" CA TRP B 111 " pdb=" C TRP B 111 " pdb=" N GLY B 112 " pdb=" CA GLY B 112 " ideal model delta harmonic sigma weight residual 180.00 163.83 16.17 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 1996 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 337 0.045 - 0.090: 132 0.090 - 0.135: 33 0.135 - 0.180: 3 0.180 - 0.225: 1 Chirality restraints: 506 Sorted by residual: chirality pdb=" CB ILE A 116 " pdb=" CA ILE A 116 " pdb=" CG1 ILE A 116 " pdb=" CG2 ILE A 116 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA VAL A 211 " pdb=" N VAL A 211 " pdb=" C VAL A 211 " pdb=" CB VAL A 211 " both_signs ideal model delta sigma weight residual False 2.44 2.30 0.14 2.00e-01 2.50e+01 5.23e-01 chirality pdb=" CG LEU A 90 " pdb=" CB LEU A 90 " pdb=" CD1 LEU A 90 " pdb=" CD2 LEU A 90 " both_signs ideal model delta sigma weight residual False -2.59 -2.73 0.14 2.00e-01 2.50e+01 4.91e-01 ... (remaining 503 not shown) Planarity restraints: 569 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 101 " 0.025 2.00e-02 2.50e+03 3.82e-02 2.55e+01 pdb=" CG PHE B 101 " -0.086 2.00e-02 2.50e+03 pdb=" CD1 PHE B 101 " 0.039 2.00e-02 2.50e+03 pdb=" CD2 PHE B 101 " 0.024 2.00e-02 2.50e+03 pdb=" CE1 PHE B 101 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE B 101 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE B 101 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 27 " 0.024 5.00e-02 4.00e+02 3.68e-02 2.17e+00 pdb=" N PRO B 28 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 28 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 28 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 96 " -0.007 2.00e-02 2.50e+03 1.35e-02 1.82e+00 pdb=" C ASP A 96 " 0.023 2.00e-02 2.50e+03 pdb=" O ASP A 96 " -0.009 2.00e-02 2.50e+03 pdb=" N THR A 97 " -0.008 2.00e-02 2.50e+03 ... (remaining 566 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 501 2.76 - 3.29: 3101 3.29 - 3.83: 5992 3.83 - 4.36: 6913 4.36 - 4.90: 11952 Nonbonded interactions: 28459 Sorted by model distance: nonbonded pdb=" O TRP A 173 " pdb=" OG1 THR A 176 " model vdw 2.219 3.040 nonbonded pdb=" OG1 THR A 30 " pdb=" NH1 ARG A 276 " model vdw 2.233 3.120 nonbonded pdb=" O GLY A 130 " pdb=" OG1 THR A 133 " model vdw 2.300 3.040 nonbonded pdb=" O ALA A 63 " pdb=" OG1 THR A 67 " model vdw 2.342 3.040 nonbonded pdb=" OE2 GLU B 6 " pdb=" N CYS B 96 " model vdw 2.353 3.120 ... (remaining 28454 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: 2.130 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.560 Find NCS groups from input model: 0.010 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: 0.010 Load rotamer database and sin/cos tables:10.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 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 : 0.009 0.126 3364 Z= 0.518 Angle : 1.012 9.745 4561 Z= 0.524 Chirality : 0.049 0.225 506 Planarity : 0.005 0.038 569 Dihedral : 15.984 104.588 1242 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.72 (0.39), residues: 410 helix: 1.87 (0.32), residues: 223 sheet: -0.02 (0.64), residues: 59 loop : 0.60 (0.54), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 70 TYR 0.020 0.002 TYR A 157 PHE 0.086 0.004 PHE B 101 TRP 0.011 0.002 TRP B 56 HIS 0.004 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00947 ( 3363) covalent geometry : angle 1.00980 ( 4559) SS BOND : bond 0.00448 ( 1) SS BOND : angle 2.98172 ( 2) hydrogen bonds : bond 0.09917 ( 230) hydrogen bonds : angle 7.47174 ( 648) *********************** 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 69 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.087 Fit side-chains REVERT: A 157 TYR cc_start: 0.7543 (m-80) cc_final: 0.6787 (t80) REVERT: A 169 LEU cc_start: 0.8127 (mm) cc_final: 0.7893 (mt) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.4246 time to fit residues: 30.1720 Evaluate side-chains 61 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.180541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.131316 restraints weight = 3323.525| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.73 r_work: 0.3340 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3364 Z= 0.155 Angle : 0.569 6.756 4561 Z= 0.296 Chirality : 0.042 0.255 506 Planarity : 0.004 0.035 569 Dihedral : 12.798 88.719 535 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.48 % Allowed : 10.65 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.18 (0.39), residues: 410 helix: 2.50 (0.32), residues: 223 sheet: 0.01 (0.64), residues: 54 loop : 0.32 (0.51), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 39 TYR 0.011 0.001 TYR A 157 PHE 0.031 0.002 PHE B 101 TRP 0.012 0.002 TRP B 111 HIS 0.003 0.001 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 3363) covalent geometry : angle 0.56863 ( 4559) SS BOND : bond 0.00210 ( 1) SS BOND : angle 1.54596 ( 2) hydrogen bonds : bond 0.04243 ( 230) hydrogen bonds : angle 5.89371 ( 648) *********************** 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 to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.095 Fit side-chains REVERT: A 150 LYS cc_start: 0.8372 (tptp) cc_final: 0.8085 (tttm) REVERT: A 157 TYR cc_start: 0.7978 (m-80) cc_final: 0.7023 (t80) REVERT: A 169 LEU cc_start: 0.8403 (mm) cc_final: 0.8096 (mt) REVERT: B 71 SER cc_start: 0.8785 (t) cc_final: 0.8405 (t) REVERT: B 78 THR cc_start: 0.9204 (m) cc_final: 0.8878 (t) REVERT: B 83 MET cc_start: 0.8360 (mtp) cc_final: 0.7967 (mtp) REVERT: B 95 TYR cc_start: 0.8426 (m-80) cc_final: 0.8053 (m-80) REVERT: B 119 VAL cc_start: 0.7773 (OUTLIER) cc_final: 0.7525 (p) outliers start: 5 outliers final: 2 residues processed: 61 average time/residue: 0.3825 time to fit residues: 24.1996 Evaluate side-chains 59 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 119 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 39 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.179713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.129806 restraints weight = 3322.051| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.73 r_work: 0.3318 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 3364 Z= 0.166 Angle : 0.554 6.507 4561 Z= 0.286 Chirality : 0.042 0.200 506 Planarity : 0.004 0.033 569 Dihedral : 12.308 81.939 535 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.37 % Allowed : 12.13 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.42 (0.39), residues: 410 helix: 2.69 (0.32), residues: 223 sheet: 0.25 (0.63), residues: 54 loop : 0.35 (0.52), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 83 TYR 0.014 0.001 TYR A 157 PHE 0.014 0.002 PHE B 101 TRP 0.010 0.002 TRP B 56 HIS 0.004 0.001 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 3363) covalent geometry : angle 0.55340 ( 4559) SS BOND : bond 0.00025 ( 1) SS BOND : angle 1.29531 ( 2) hydrogen bonds : bond 0.04071 ( 230) hydrogen bonds : angle 5.68844 ( 648) *********************** 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 57 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.120 Fit side-chains REVERT: A 150 LYS cc_start: 0.8379 (tptp) cc_final: 0.8105 (tttm) REVERT: A 157 TYR cc_start: 0.7978 (m-80) cc_final: 0.7029 (t80) REVERT: B 71 SER cc_start: 0.8760 (t) cc_final: 0.8435 (t) REVERT: B 83 MET cc_start: 0.8316 (mtp) cc_final: 0.8040 (mtp) REVERT: B 95 TYR cc_start: 0.8478 (m-80) cc_final: 0.8069 (m-80) outliers start: 8 outliers final: 3 residues processed: 54 average time/residue: 0.4601 time to fit residues: 25.6648 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 : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 93 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.7980 chunk 29 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 24 optimal weight: 0.0870 chunk 11 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 2 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 overall best weight: 0.8360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.179093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.129572 restraints weight = 3287.657| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.74 r_work: 0.3323 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 3364 Z= 0.158 Angle : 0.538 6.426 4561 Z= 0.276 Chirality : 0.041 0.203 506 Planarity : 0.004 0.032 569 Dihedral : 12.178 80.648 535 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.37 % Allowed : 12.43 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.62 (0.39), residues: 410 helix: 2.83 (0.32), residues: 223 sheet: 0.43 (0.62), residues: 54 loop : 0.46 (0.53), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 161 TYR 0.012 0.001 TYR A 157 PHE 0.011 0.002 PHE A 128 TRP 0.010 0.001 TRP B 111 HIS 0.004 0.001 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 3363) covalent geometry : angle 0.53735 ( 4559) SS BOND : bond 0.00045 ( 1) SS BOND : angle 1.25828 ( 2) hydrogen bonds : bond 0.03948 ( 230) hydrogen bonds : angle 5.53018 ( 648) *********************** 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 67 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.082 Fit side-chains REVERT: A 150 LYS cc_start: 0.8377 (tptp) cc_final: 0.8103 (tttm) REVERT: A 157 TYR cc_start: 0.7940 (m-80) cc_final: 0.7033 (t80) REVERT: A 169 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8057 (mt) REVERT: B 71 SER cc_start: 0.8696 (t) cc_final: 0.8130 (p) REVERT: B 83 MET cc_start: 0.8296 (mtp) cc_final: 0.7936 (mtp) REVERT: B 95 TYR cc_start: 0.8486 (m-80) cc_final: 0.8107 (m-80) outliers start: 8 outliers final: 4 residues processed: 63 average time/residue: 0.4461 time to fit residues: 28.9905 Evaluate side-chains 62 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 119 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 40 optimal weight: 0.9980 chunk 20 optimal weight: 0.0060 chunk 24 optimal weight: 0.0370 chunk 29 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 overall best weight: 0.4674 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.181194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.131743 restraints weight = 3307.907| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.74 r_work: 0.3356 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3364 Z= 0.119 Angle : 0.495 6.362 4561 Z= 0.253 Chirality : 0.039 0.190 506 Planarity : 0.004 0.030 569 Dihedral : 11.768 80.005 535 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.07 % Allowed : 14.79 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.97 (0.40), residues: 410 helix: 3.14 (0.32), residues: 223 sheet: 0.66 (0.63), residues: 54 loop : 0.53 (0.53), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 161 TYR 0.010 0.001 TYR A 157 PHE 0.008 0.001 PHE A 128 TRP 0.008 0.001 TRP B 111 HIS 0.003 0.001 HIS B 35 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 3363) covalent geometry : angle 0.49513 ( 4559) SS BOND : bond 0.00024 ( 1) SS BOND : angle 0.98053 ( 2) hydrogen bonds : bond 0.03633 ( 230) hydrogen bonds : angle 5.28026 ( 648) *********************** 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 70 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.077 Fit side-chains REVERT: A 115 LYS cc_start: 0.7637 (mtpt) cc_final: 0.7427 (mtmt) REVERT: A 150 LYS cc_start: 0.8355 (tptp) cc_final: 0.8092 (tttp) REVERT: A 157 TYR cc_start: 0.7903 (m-80) cc_final: 0.7035 (t80) REVERT: A 169 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7984 (mt) REVERT: A 187 ASN cc_start: 0.8510 (t0) cc_final: 0.7760 (m-40) REVERT: B 71 SER cc_start: 0.8651 (t) cc_final: 0.8223 (p) REVERT: B 83 MET cc_start: 0.8304 (mtp) cc_final: 0.8069 (mtp) REVERT: B 95 TYR cc_start: 0.8476 (m-80) cc_final: 0.8069 (m-80) outliers start: 7 outliers final: 2 residues processed: 66 average time/residue: 0.4221 time to fit residues: 28.7898 Evaluate side-chains 60 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 57 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 119 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 2 optimal weight: 0.0970 chunk 9 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 24 optimal weight: 0.2980 chunk 1 optimal weight: 0.6980 chunk 37 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.181045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.131479 restraints weight = 3313.064| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.75 r_work: 0.3343 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3364 Z= 0.124 Angle : 0.502 6.238 4561 Z= 0.256 Chirality : 0.039 0.192 506 Planarity : 0.004 0.029 569 Dihedral : 11.647 78.935 535 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.07 % Allowed : 16.57 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.09 (0.40), residues: 410 helix: 3.25 (0.31), residues: 222 sheet: 0.77 (0.63), residues: 54 loop : 0.54 (0.54), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 161 TYR 0.011 0.001 TYR A 157 PHE 0.009 0.001 PHE A 128 TRP 0.008 0.001 TRP B 111 HIS 0.002 0.001 HIS B 35 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 3363) covalent geometry : angle 0.50178 ( 4559) SS BOND : bond 0.00026 ( 1) SS BOND : angle 0.99567 ( 2) hydrogen bonds : bond 0.03676 ( 230) hydrogen bonds : angle 5.23738 ( 648) *********************** 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 64 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.085 Fit side-chains REVERT: A 115 LYS cc_start: 0.7606 (mtpt) cc_final: 0.7380 (mtmt) REVERT: A 150 LYS cc_start: 0.8341 (tptp) cc_final: 0.8080 (tttm) REVERT: A 157 TYR cc_start: 0.7921 (m-80) cc_final: 0.7045 (t80) REVERT: A 169 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.7986 (mt) REVERT: A 187 ASN cc_start: 0.8506 (t0) cc_final: 0.7746 (m-40) REVERT: B 71 SER cc_start: 0.8572 (t) cc_final: 0.8138 (p) REVERT: B 83 MET cc_start: 0.8283 (mtp) cc_final: 0.8023 (mtp) REVERT: B 95 TYR cc_start: 0.8472 (m-80) cc_final: 0.8045 (m-80) outliers start: 7 outliers final: 5 residues processed: 61 average time/residue: 0.3986 time to fit residues: 25.3155 Evaluate side-chains 63 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 119 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.179775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.132889 restraints weight = 3372.631| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.14 r_work: 0.3338 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 3364 Z= 0.148 Angle : 0.528 6.257 4561 Z= 0.270 Chirality : 0.041 0.200 506 Planarity : 0.004 0.029 569 Dihedral : 11.714 77.872 535 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.66 % Allowed : 15.98 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.02 (0.40), residues: 410 helix: 3.15 (0.31), residues: 222 sheet: 0.79 (0.64), residues: 54 loop : 0.56 (0.54), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 161 TYR 0.013 0.001 TYR A 157 PHE 0.011 0.002 PHE A 128 TRP 0.008 0.001 TRP B 56 HIS 0.003 0.001 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 3363) covalent geometry : angle 0.52729 ( 4559) SS BOND : bond 0.00001 ( 1) SS BOND : angle 1.06681 ( 2) hydrogen bonds : bond 0.03864 ( 230) hydrogen bonds : angle 5.34393 ( 648) *********************** 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 70 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.092 Fit side-chains REVERT: A 115 LYS cc_start: 0.7658 (mtpt) cc_final: 0.7439 (mtmt) REVERT: A 150 LYS cc_start: 0.8350 (tptp) cc_final: 0.8098 (tttm) REVERT: A 157 TYR cc_start: 0.7961 (m-80) cc_final: 0.7060 (t80) REVERT: A 169 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8009 (mt) REVERT: B 71 SER cc_start: 0.8650 (t) cc_final: 0.8190 (p) REVERT: B 83 MET cc_start: 0.8273 (mtp) cc_final: 0.7952 (mtp) REVERT: B 95 TYR cc_start: 0.8514 (m-80) cc_final: 0.8064 (m-80) outliers start: 9 outliers final: 4 residues processed: 67 average time/residue: 0.3847 time to fit residues: 26.6139 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 : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 119 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 29 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 chunk 25 optimal weight: 0.1980 chunk 35 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.180375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.130577 restraints weight = 3372.068| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.74 r_work: 0.3336 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3364 Z= 0.132 Angle : 0.515 6.563 4561 Z= 0.262 Chirality : 0.040 0.195 506 Planarity : 0.004 0.031 569 Dihedral : 11.599 76.999 535 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.07 % Allowed : 15.98 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.09 (0.40), residues: 410 helix: 3.22 (0.31), residues: 222 sheet: 0.86 (0.64), residues: 54 loop : 0.56 (0.53), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 104 TYR 0.011 0.001 TYR A 157 PHE 0.009 0.001 PHE A 128 TRP 0.007 0.001 TRP B 56 HIS 0.002 0.001 HIS B 35 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 3363) covalent geometry : angle 0.51502 ( 4559) SS BOND : bond 0.00029 ( 1) SS BOND : angle 1.02176 ( 2) hydrogen bonds : bond 0.03751 ( 230) hydrogen bonds : angle 5.28405 ( 648) *********************** 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 65 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.124 Fit side-chains REVERT: A 115 LYS cc_start: 0.7651 (mtpt) cc_final: 0.7424 (mtmt) REVERT: A 150 LYS cc_start: 0.8339 (tptp) cc_final: 0.8087 (tttm) REVERT: A 157 TYR cc_start: 0.7949 (m-80) cc_final: 0.7062 (t80) REVERT: A 169 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8002 (mt) REVERT: B 71 SER cc_start: 0.8620 (t) cc_final: 0.8166 (p) REVERT: B 83 MET cc_start: 0.8256 (mtp) cc_final: 0.7939 (mtp) REVERT: B 95 TYR cc_start: 0.8509 (m-80) cc_final: 0.8061 (m-80) outliers start: 7 outliers final: 5 residues processed: 62 average time/residue: 0.4238 time to fit residues: 27.2548 Evaluate side-chains 63 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 119 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 29 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.179360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.131787 restraints weight = 3331.517| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.10 r_work: 0.3307 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 3364 Z= 0.155 Angle : 0.541 6.219 4561 Z= 0.278 Chirality : 0.041 0.211 506 Planarity : 0.004 0.031 569 Dihedral : 11.665 76.167 535 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.37 % Allowed : 15.98 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.01 (0.39), residues: 410 helix: 3.13 (0.31), residues: 222 sheet: 0.86 (0.64), residues: 54 loop : 0.57 (0.53), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 161 TYR 0.013 0.001 TYR A 157 PHE 0.011 0.002 PHE A 128 TRP 0.008 0.001 TRP B 56 HIS 0.003 0.001 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 3363) covalent geometry : angle 0.54086 ( 4559) SS BOND : bond 0.00001 ( 1) SS BOND : angle 1.11317 ( 2) hydrogen bonds : bond 0.03958 ( 230) hydrogen bonds : angle 5.35805 ( 648) *********************** 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 : 0.121 Fit side-chains REVERT: A 115 LYS cc_start: 0.7693 (mtpt) cc_final: 0.7485 (mtmt) REVERT: A 150 LYS cc_start: 0.8352 (tptp) cc_final: 0.8114 (tttm) REVERT: A 157 TYR cc_start: 0.7953 (m-80) cc_final: 0.7074 (t80) REVERT: A 169 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8030 (mt) REVERT: B 71 SER cc_start: 0.8662 (t) cc_final: 0.8204 (p) REVERT: B 83 MET cc_start: 0.8259 (mtp) cc_final: 0.7886 (mtp) REVERT: B 95 TYR cc_start: 0.8542 (m-80) cc_final: 0.8172 (m-80) outliers start: 8 outliers final: 5 residues processed: 65 average time/residue: 0.3738 time to fit residues: 25.2669 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 : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 119 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 12 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 19 optimal weight: 0.4980 chunk 4 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 35 optimal weight: 0.0570 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.180394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.131109 restraints weight = 3311.221| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 1.72 r_work: 0.3341 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3364 Z= 0.128 Angle : 0.546 11.493 4561 Z= 0.270 Chirality : 0.042 0.357 506 Planarity : 0.004 0.031 569 Dihedral : 11.516 75.433 535 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.78 % Allowed : 17.75 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.10 (0.39), residues: 410 helix: 3.22 (0.31), residues: 222 sheet: 0.87 (0.64), residues: 54 loop : 0.57 (0.53), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 161 TYR 0.011 0.001 TYR A 157 PHE 0.012 0.001 PHE A 201 TRP 0.007 0.001 TRP B 56 HIS 0.002 0.001 HIS B 35 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 3363) covalent geometry : angle 0.54579 ( 4559) SS BOND : bond 0.00037 ( 1) SS BOND : angle 0.96749 ( 2) hydrogen bonds : bond 0.03773 ( 230) hydrogen bonds : angle 5.26664 ( 648) ********************** 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: 6 poor density : 59 time to evaluate : 0.084 Fit side-chains REVERT: A 115 LYS cc_start: 0.7666 (mtpt) cc_final: 0.7441 (mtmt) REVERT: A 150 LYS cc_start: 0.8335 (tptp) cc_final: 0.8091 (tttp) REVERT: A 157 TYR cc_start: 0.7936 (m-80) cc_final: 0.7055 (t80) REVERT: A 169 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7997 (mt) REVERT: A 187 ASN cc_start: 0.8519 (t0) cc_final: 0.7754 (m-40) REVERT: B 71 SER cc_start: 0.8653 (t) cc_final: 0.8210 (p) REVERT: B 83 MET cc_start: 0.8271 (mtp) cc_final: 0.7926 (mtp) REVERT: B 95 TYR cc_start: 0.8515 (m-80) cc_final: 0.8101 (m-80) outliers start: 6 outliers final: 5 residues processed: 62 average time/residue: 0.4074 time to fit residues: 26.1400 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 : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 119 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.5980 chunk 25 optimal weight: 0.0980 chunk 14 optimal weight: 0.5980 chunk 29 optimal weight: 5.9990 chunk 19 optimal weight: 0.1980 chunk 9 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 31 optimal weight: 0.0970 chunk 36 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.3178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.182035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.132253 restraints weight = 3325.631| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 1.75 r_work: 0.3364 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 3364 Z= 0.108 Angle : 0.524 11.737 4561 Z= 0.257 Chirality : 0.041 0.350 506 Planarity : 0.004 0.031 569 Dihedral : 11.203 73.154 535 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.18 % Allowed : 18.64 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.22 (0.40), residues: 410 helix: 3.35 (0.31), residues: 222 sheet: 0.87 (0.64), residues: 54 loop : 0.59 (0.53), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 104 TYR 0.009 0.001 TYR A 157 PHE 0.006 0.001 PHE A 128 TRP 0.008 0.001 TRP B 111 HIS 0.002 0.001 HIS B 35 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 3363) covalent geometry : angle 0.52387 ( 4559) SS BOND : bond 0.00080 ( 1) SS BOND : angle 0.84003 ( 2) hydrogen bonds : bond 0.03545 ( 230) hydrogen bonds : angle 5.07487 ( 648) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1488.94 seconds wall clock time: 26 minutes 14.30 seconds (1574.30 seconds total)