Starting phenix.real_space_refine on Fri Aug 22 12:39:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v4n_42974/08_2025/8v4n_42974.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v4n_42974/08_2025/8v4n_42974.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8v4n_42974/08_2025/8v4n_42974.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v4n_42974/08_2025/8v4n_42974.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8v4n_42974/08_2025/8v4n_42974.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v4n_42974/08_2025/8v4n_42974.map" } resolution = 2.43 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= 0.005 sd= 0.075 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: 4 Type Number sf(0) Gaussians S 9 5.16 5 C 1303 2.51 5 N 373 2.21 5 O 382 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 2067 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2067 Classifications: {'peptide': 263} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 251} Chain breaks: 1 Time building chain proxies: 0.88, per 1000 atoms: 0.43 Number of scatterers: 2067 At special positions: 0 Unit cell: (93.636, 65.892, 84.099, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 9 16.00 O 382 8.00 N 373 7.00 C 1303 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.16 Conformation dependent library (CDL) restraints added in 79.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 482 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 3 sheets defined 36.5% alpha, 18.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'A' and resid 13 through 32 Processing helix chain 'A' and resid 33 through 37 Processing helix chain 'A' and resid 95 through 106 removed outlier: 3.518A pdb=" N ASN A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 132 Processing helix chain 'A' and resid 159 through 174 Processing helix chain 'A' and resid 186 through 193 Processing helix chain 'A' and resid 203 through 212 Processing helix chain 'A' and resid 271 through 273 No H-bonds generated for 'chain 'A' and resid 271 through 273' Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 41 removed outlier: 7.069A pdb=" N ALA A 240 " --> pdb=" O ARG A 268 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ARG A 268 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N SER A 242 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 9.434A pdb=" N LEU A 266 " --> pdb=" O SER A 242 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N ASP A 244 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N ALA A 264 " --> pdb=" O ASP A 244 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 52 Processing sheet with id=AA3, first strand: chain 'A' and resid 148 through 149 removed outlier: 3.980A pdb=" N GLY A 215 " --> pdb=" O TYR A 181 " (cutoff:3.500A) 92 hydrogen bonds defined for protein. 261 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: 0.23 Time building geometry restraints manager: 0.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 710 1.34 - 1.46: 420 1.46 - 1.58: 964 1.58 - 1.69: 0 1.69 - 1.81: 16 Bond restraints: 2110 Sorted by residual: bond pdb=" N LEU A 278 " pdb=" CA LEU A 278 " ideal model delta sigma weight residual 1.462 1.486 -0.024 1.44e-02 4.82e+03 2.79e+00 bond pdb=" N GLU A 279 " pdb=" CA GLU A 279 " ideal model delta sigma weight residual 1.458 1.484 -0.026 1.90e-02 2.77e+03 1.92e+00 bond pdb=" C GLU A 279 " pdb=" O GLU A 279 " ideal model delta sigma weight residual 1.231 1.249 -0.018 2.00e-02 2.50e+03 8.01e-01 bond pdb=" C VAL A 150 " pdb=" O VAL A 150 " ideal model delta sigma weight residual 1.232 1.240 -0.008 8.90e-03 1.26e+04 7.68e-01 bond pdb=" CB PRO A 258 " pdb=" CG PRO A 258 " ideal model delta sigma weight residual 1.492 1.533 -0.041 5.00e-02 4.00e+02 6.66e-01 ... (remaining 2105 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.00: 2723 1.00 - 2.01: 103 2.01 - 3.01: 29 3.01 - 4.02: 3 4.02 - 5.02: 2 Bond angle restraints: 2860 Sorted by residual: angle pdb=" CA LEU A 278 " pdb=" C LEU A 278 " pdb=" O LEU A 278 " ideal model delta sigma weight residual 122.51 118.24 4.27 1.34e+00 5.57e-01 1.01e+01 angle pdb=" CA GLU A 279 " pdb=" C GLU A 279 " pdb=" O GLU A 279 " ideal model delta sigma weight residual 120.80 117.26 3.54 1.70e+00 3.46e-01 4.33e+00 angle pdb=" C GLU A 198 " pdb=" N HIS A 199 " pdb=" CA HIS A 199 " ideal model delta sigma weight residual 122.46 125.10 -2.64 1.41e+00 5.03e-01 3.51e+00 angle pdb=" N HIS A 201 " pdb=" CA HIS A 201 " pdb=" CB HIS A 201 " ideal model delta sigma weight residual 112.78 110.18 2.60 1.53e+00 4.27e-01 2.88e+00 angle pdb=" O LEU A 278 " pdb=" C LEU A 278 " pdb=" N GLU A 279 " ideal model delta sigma weight residual 122.83 124.92 -2.09 1.31e+00 5.83e-01 2.54e+00 ... (remaining 2855 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.40: 1137 16.40 - 32.80: 89 32.80 - 49.20: 24 49.20 - 65.61: 1 65.61 - 82.01: 7 Dihedral angle restraints: 1258 sinusoidal: 505 harmonic: 753 Sorted by residual: dihedral pdb=" CA HIS A 200 " pdb=" C HIS A 200 " pdb=" N HIS A 201 " pdb=" CA HIS A 201 " ideal model delta harmonic sigma weight residual 180.00 153.92 26.08 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA HIS A 199 " pdb=" C HIS A 199 " pdb=" N HIS A 200 " pdb=" CA HIS A 200 " ideal model delta harmonic sigma weight residual 180.00 162.81 17.19 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CG ARG A 103 " pdb=" CD ARG A 103 " pdb=" NE ARG A 103 " pdb=" CZ ARG A 103 " ideal model delta sinusoidal sigma weight residual -90.00 -134.50 44.50 2 1.50e+01 4.44e-03 1.05e+01 ... (remaining 1255 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 198 0.029 - 0.059: 72 0.059 - 0.088: 18 0.088 - 0.117: 19 0.117 - 0.147: 8 Chirality restraints: 315 Sorted by residual: chirality pdb=" CA LEU A 278 " pdb=" N LEU A 278 " pdb=" C LEU A 278 " pdb=" CB LEU A 278 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.38e-01 chirality pdb=" CA ILE A 88 " pdb=" N ILE A 88 " pdb=" C ILE A 88 " pdb=" CB ILE A 88 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.58e-01 chirality pdb=" CA VAL A 246 " pdb=" N VAL A 246 " pdb=" C VAL A 246 " pdb=" CB VAL A 246 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.38e-01 ... (remaining 312 not shown) Planarity restraints: 376 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 277 " -0.009 2.00e-02 2.50e+03 1.85e-02 3.44e+00 pdb=" C THR A 277 " 0.032 2.00e-02 2.50e+03 pdb=" O THR A 277 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU A 278 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 257 " 0.020 5.00e-02 4.00e+02 3.02e-02 1.46e+00 pdb=" N PRO A 258 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 258 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 258 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 186 " -0.019 5.00e-02 4.00e+02 2.84e-02 1.29e+00 pdb=" N PRO A 187 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 187 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 187 " -0.016 5.00e-02 4.00e+02 ... (remaining 373 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 412 2.79 - 3.32: 1733 3.32 - 3.84: 3189 3.84 - 4.37: 3604 4.37 - 4.90: 6338 Nonbonded interactions: 15276 Sorted by model distance: nonbonded pdb=" NH1 ARG A 19 " pdb=" O LEU A 109 " model vdw 2.260 3.120 nonbonded pdb=" N GLY A 159 " pdb=" OE2 GLU A 204 " model vdw 2.333 3.120 nonbonded pdb=" OD1 ASN A 10 " pdb=" NE1 TRP A 17 " model vdw 2.442 3.120 nonbonded pdb=" N GLU A 15 " pdb=" OE1 GLU A 15 " model vdw 2.588 3.120 nonbonded pdb=" O LEU A 278 " pdb=" C GLU A 279 " model vdw 2.623 3.270 ... (remaining 15271 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.570 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:7.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 2110 Z= 0.119 Angle : 0.494 5.020 2860 Z= 0.280 Chirality : 0.043 0.147 315 Planarity : 0.004 0.030 376 Dihedral : 14.214 82.006 776 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.93 % Allowed : 0.47 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 0.80 (0.52), residues: 259 helix: 2.70 (0.56), residues: 87 sheet: -0.34 (0.70), residues: 57 loop : -0.70 (0.51), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 13 TYR 0.004 0.001 TYR A 190 PHE 0.011 0.001 PHE A 92 TRP 0.008 0.001 TRP A 17 HIS 0.006 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00213 ( 2110) covalent geometry : angle 0.49419 ( 2860) hydrogen bonds : bond 0.04838 ( 92) hydrogen bonds : angle 4.76139 ( 261) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 50 time to evaluate : 0.080 Fit side-chains REVERT: A 74 MET cc_start: 0.7655 (mtm) cc_final: 0.7407 (pp-130) REVERT: A 145 ASN cc_start: 0.7392 (m110) cc_final: 0.7191 (m-40) REVERT: A 173 ASN cc_start: 0.8258 (t0) cc_final: 0.7988 (t0) outliers start: 2 outliers final: 0 residues processed: 51 average time/residue: 0.8774 time to fit residues: 45.3200 Evaluate side-chains 41 residues out of total 214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 12 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 1 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 chunk 16 optimal weight: 20.0000 chunk 15 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- 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 = 0.3618 r_free = 0.3618 target = 0.136687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.105858 restraints weight = 2245.392| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.76 r_work: 0.3117 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2110 Z= 0.180 Angle : 0.617 7.614 2860 Z= 0.327 Chirality : 0.048 0.156 315 Planarity : 0.005 0.034 376 Dihedral : 4.643 21.443 292 Min Nonbonded Distance : 2.660 Molprobity Statistics. All-atom Clashscore : 1.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.80 % Allowed : 12.15 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 0.66 (0.51), residues: 259 helix: 2.48 (0.56), residues: 87 sheet: -0.28 (0.71), residues: 56 loop : -0.78 (0.50), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 103 TYR 0.009 0.001 TYR A 131 PHE 0.018 0.002 PHE A 259 TRP 0.009 0.001 TRP A 96 HIS 0.008 0.002 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 2110) covalent geometry : angle 0.61693 ( 2860) hydrogen bonds : bond 0.07343 ( 92) hydrogen bonds : angle 4.62283 ( 261) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.086 Fit side-chains REVERT: A 25 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8273 (tp) REVERT: A 57 GLN cc_start: 0.7821 (OUTLIER) cc_final: 0.6916 (mp10) REVERT: A 74 MET cc_start: 0.8316 (mtm) cc_final: 0.7686 (pp-130) REVERT: A 173 ASN cc_start: 0.8325 (t0) cc_final: 0.7934 (t0) outliers start: 6 outliers final: 2 residues processed: 41 average time/residue: 0.9992 time to fit residues: 41.4541 Evaluate side-chains 43 residues out of total 214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 57 GLN Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 244 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 24 optimal weight: 7.9990 chunk 20 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 chunk 8 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 5 optimal weight: 20.0000 chunk 12 optimal weight: 0.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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 = 0.3637 r_free = 0.3637 target = 0.138128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.107773 restraints weight = 2271.258| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.77 r_work: 0.3143 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2110 Z= 0.140 Angle : 0.539 7.655 2860 Z= 0.288 Chirality : 0.045 0.132 315 Planarity : 0.004 0.032 376 Dihedral : 4.373 17.246 292 Min Nonbonded Distance : 2.654 Molprobity Statistics. All-atom Clashscore : 1.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.80 % Allowed : 14.49 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 0.60 (0.51), residues: 259 helix: 2.56 (0.56), residues: 87 sheet: -0.68 (0.68), residues: 60 loop : -0.69 (0.50), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 254 TYR 0.006 0.001 TYR A 131 PHE 0.014 0.002 PHE A 259 TRP 0.007 0.001 TRP A 96 HIS 0.005 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 2110) covalent geometry : angle 0.53939 ( 2860) hydrogen bonds : bond 0.05829 ( 92) hydrogen bonds : angle 4.38030 ( 261) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.087 Fit side-chains REVERT: A 19 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7544 (ttp-110) REVERT: A 57 GLN cc_start: 0.7825 (OUTLIER) cc_final: 0.6803 (mp10) REVERT: A 74 MET cc_start: 0.8299 (mtm) cc_final: 0.7661 (pp-130) REVERT: A 173 ASN cc_start: 0.8353 (t0) cc_final: 0.7991 (t0) REVERT: A 254 ARG cc_start: 0.6970 (mpt90) cc_final: 0.6713 (mmp-170) outliers start: 6 outliers final: 2 residues processed: 39 average time/residue: 1.0078 time to fit residues: 39.7991 Evaluate side-chains 40 residues out of total 214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ARG Chi-restraints excluded: chain A residue 57 GLN Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 244 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 23 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 12 optimal weight: 0.4980 chunk 1 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 14 optimal weight: 20.0000 chunk 2 optimal weight: 7.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- 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 = 0.3650 r_free = 0.3650 target = 0.139180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.108951 restraints weight = 2286.802| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.76 r_work: 0.3163 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 2110 Z= 0.125 Angle : 0.511 8.034 2860 Z= 0.271 Chirality : 0.044 0.132 315 Planarity : 0.004 0.031 376 Dihedral : 4.166 13.734 292 Min Nonbonded Distance : 2.653 Molprobity Statistics. All-atom Clashscore : 1.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.80 % Allowed : 15.89 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 0.72 (0.51), residues: 259 helix: 2.74 (0.57), residues: 87 sheet: -0.67 (0.68), residues: 60 loop : -0.67 (0.49), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 30 TYR 0.006 0.001 TYR A 131 PHE 0.012 0.002 PHE A 259 TRP 0.008 0.001 TRP A 96 HIS 0.005 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 2110) covalent geometry : angle 0.51067 ( 2860) hydrogen bonds : bond 0.05235 ( 92) hydrogen bonds : angle 4.21771 ( 261) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.101 Fit side-chains REVERT: A 25 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.8274 (tp) REVERT: A 57 GLN cc_start: 0.7815 (OUTLIER) cc_final: 0.6935 (mp10) REVERT: A 74 MET cc_start: 0.8317 (mtm) cc_final: 0.7716 (pp-130) REVERT: A 173 ASN cc_start: 0.8359 (t0) cc_final: 0.8024 (t0) REVERT: A 199 HIS cc_start: 0.5692 (p-80) cc_final: 0.4422 (t70) outliers start: 6 outliers final: 3 residues processed: 39 average time/residue: 0.9230 time to fit residues: 36.4496 Evaluate side-chains 42 residues out of total 214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 57 GLN Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 278 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 6 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 21 optimal weight: 8.9990 chunk 5 optimal weight: 20.0000 chunk 19 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 12 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 = 0.3599 r_free = 0.3599 target = 0.134818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.104557 restraints weight = 2267.349| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.74 r_work: 0.3102 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2110 Z= 0.205 Angle : 0.644 8.426 2860 Z= 0.343 Chirality : 0.049 0.147 315 Planarity : 0.005 0.035 376 Dihedral : 4.662 15.802 292 Min Nonbonded Distance : 2.653 Molprobity Statistics. All-atom Clashscore : 0.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.74 % Allowed : 15.42 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 0.50 (0.51), residues: 259 helix: 2.42 (0.57), residues: 87 sheet: -0.43 (0.69), residues: 56 loop : -0.91 (0.48), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 103 TYR 0.010 0.002 TYR A 131 PHE 0.019 0.002 PHE A 259 TRP 0.008 0.001 TRP A 96 HIS 0.006 0.002 HIS A 7 Details of bonding type rmsd covalent geometry : bond 0.00441 ( 2110) covalent geometry : angle 0.64351 ( 2860) hydrogen bonds : bond 0.08052 ( 92) hydrogen bonds : angle 4.67264 ( 261) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.102 Fit side-chains REVERT: A 25 ILE cc_start: 0.8702 (OUTLIER) cc_final: 0.8257 (tp) REVERT: A 57 GLN cc_start: 0.7789 (OUTLIER) cc_final: 0.6967 (mp10) REVERT: A 74 MET cc_start: 0.8319 (mtm) cc_final: 0.7697 (pp-130) REVERT: A 173 ASN cc_start: 0.8352 (t0) cc_final: 0.7979 (t0) REVERT: A 199 HIS cc_start: 0.5825 (p-80) cc_final: 0.4206 (t70) outliers start: 8 outliers final: 4 residues processed: 43 average time/residue: 0.9948 time to fit residues: 43.2657 Evaluate side-chains 44 residues out of total 214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 57 GLN Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 278 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 20 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 21 optimal weight: 9.9990 chunk 13 optimal weight: 8.9990 chunk 18 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 = 0.3628 r_free = 0.3628 target = 0.137216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.107296 restraints weight = 2242.052| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.74 r_work: 0.3140 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2110 Z= 0.143 Angle : 0.547 8.500 2860 Z= 0.291 Chirality : 0.045 0.133 315 Planarity : 0.004 0.034 376 Dihedral : 4.335 14.632 292 Min Nonbonded Distance : 2.658 Molprobity Statistics. All-atom Clashscore : 1.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.27 % Allowed : 15.89 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 0.62 (0.51), residues: 259 helix: 2.60 (0.57), residues: 87 sheet: -0.42 (0.69), residues: 56 loop : -0.87 (0.48), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 30 TYR 0.007 0.001 TYR A 131 PHE 0.014 0.002 PHE A 259 TRP 0.008 0.001 TRP A 96 HIS 0.005 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 2110) covalent geometry : angle 0.54665 ( 2860) hydrogen bonds : bond 0.06035 ( 92) hydrogen bonds : angle 4.40170 ( 261) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.091 Fit side-chains REVERT: A 25 ILE cc_start: 0.8705 (OUTLIER) cc_final: 0.8243 (tp) REVERT: A 57 GLN cc_start: 0.7798 (OUTLIER) cc_final: 0.6912 (mp10) REVERT: A 74 MET cc_start: 0.8311 (mtm) cc_final: 0.7696 (pp-130) REVERT: A 173 ASN cc_start: 0.8336 (t0) cc_final: 0.8022 (t0) outliers start: 7 outliers final: 5 residues processed: 40 average time/residue: 0.8185 time to fit residues: 33.1808 Evaluate side-chains 43 residues out of total 214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 57 GLN Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 278 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 17 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 = 0.3617 r_free = 0.3617 target = 0.136318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.106294 restraints weight = 2262.528| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.74 r_work: 0.3125 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2110 Z= 0.159 Angle : 0.575 8.820 2860 Z= 0.305 Chirality : 0.046 0.137 315 Planarity : 0.004 0.034 376 Dihedral : 4.402 15.156 292 Min Nonbonded Distance : 2.660 Molprobity Statistics. All-atom Clashscore : 0.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.27 % Allowed : 15.89 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 0.54 (0.51), residues: 259 helix: 2.54 (0.57), residues: 87 sheet: -0.51 (0.68), residues: 56 loop : -0.90 (0.48), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 103 TYR 0.008 0.001 TYR A 131 PHE 0.016 0.002 PHE A 259 TRP 0.009 0.001 TRP A 96 HIS 0.004 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 2110) covalent geometry : angle 0.57531 ( 2860) hydrogen bonds : bond 0.06766 ( 92) hydrogen bonds : angle 4.48518 ( 261) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.055 Fit side-chains REVERT: A 25 ILE cc_start: 0.8715 (OUTLIER) cc_final: 0.8239 (tp) REVERT: A 57 GLN cc_start: 0.7783 (OUTLIER) cc_final: 0.6968 (mp10) REVERT: A 74 MET cc_start: 0.8305 (mtm) cc_final: 0.7691 (pp-130) REVERT: A 173 ASN cc_start: 0.8334 (t0) cc_final: 0.7999 (t0) REVERT: A 254 ARG cc_start: 0.6923 (mpt90) cc_final: 0.6674 (mmp-170) outliers start: 7 outliers final: 4 residues processed: 40 average time/residue: 0.6095 time to fit residues: 24.6697 Evaluate side-chains 43 residues out of total 214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 57 GLN Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 278 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 18 optimal weight: 6.9990 chunk 13 optimal weight: 8.9990 chunk 21 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 overall best weight: 3.9788 ------------------------------------------------------------------------------- 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 = 0.3608 r_free = 0.3608 target = 0.135470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.105805 restraints weight = 2250.280| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.72 r_work: 0.3117 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2110 Z= 0.169 Angle : 0.596 9.409 2860 Z= 0.315 Chirality : 0.046 0.137 315 Planarity : 0.005 0.035 376 Dihedral : 4.482 15.473 292 Min Nonbonded Distance : 2.662 Molprobity Statistics. All-atom Clashscore : 1.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.74 % Allowed : 15.42 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 0.51 (0.51), residues: 259 helix: 2.54 (0.57), residues: 87 sheet: -0.54 (0.68), residues: 56 loop : -0.93 (0.48), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 103 TYR 0.008 0.001 TYR A 131 PHE 0.017 0.002 PHE A 259 TRP 0.009 0.001 TRP A 96 HIS 0.005 0.001 HIS A 7 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 2110) covalent geometry : angle 0.59639 ( 2860) hydrogen bonds : bond 0.07058 ( 92) hydrogen bonds : angle 4.52942 ( 261) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.048 Fit side-chains REVERT: A 25 ILE cc_start: 0.8712 (OUTLIER) cc_final: 0.8258 (tp) REVERT: A 57 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.6923 (mp10) REVERT: A 74 MET cc_start: 0.8294 (mtm) cc_final: 0.7678 (pp-130) REVERT: A 173 ASN cc_start: 0.8340 (t0) cc_final: 0.8002 (t0) outliers start: 8 outliers final: 4 residues processed: 40 average time/residue: 0.5711 time to fit residues: 23.1339 Evaluate side-chains 43 residues out of total 214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 57 GLN Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 278 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 11 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 14 optimal weight: 20.0000 chunk 20 optimal weight: 3.9990 chunk 5 optimal weight: 0.0770 chunk 7 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 overall best weight: 2.3744 ------------------------------------------------------------------------------- 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 = 0.3634 r_free = 0.3634 target = 0.137813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.108319 restraints weight = 2246.850| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.72 r_work: 0.3152 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2110 Z= 0.132 Angle : 0.541 9.004 2860 Z= 0.285 Chirality : 0.044 0.132 315 Planarity : 0.004 0.040 376 Dihedral : 4.180 14.550 292 Min Nonbonded Distance : 2.656 Molprobity Statistics. All-atom Clashscore : 1.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.74 % Allowed : 15.42 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 0.73 (0.51), residues: 259 helix: 2.80 (0.56), residues: 87 sheet: -0.47 (0.69), residues: 56 loop : -0.85 (0.49), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 30 TYR 0.006 0.001 TYR A 131 PHE 0.012 0.001 PHE A 259 TRP 0.007 0.001 TRP A 96 HIS 0.005 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 2110) covalent geometry : angle 0.54074 ( 2860) hydrogen bonds : bond 0.05431 ( 92) hydrogen bonds : angle 4.26760 ( 261) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.051 Fit side-chains REVERT: A 25 ILE cc_start: 0.8693 (OUTLIER) cc_final: 0.8224 (tp) REVERT: A 57 GLN cc_start: 0.7800 (OUTLIER) cc_final: 0.6910 (mp10) REVERT: A 74 MET cc_start: 0.8283 (mtm) cc_final: 0.7655 (pp-130) REVERT: A 173 ASN cc_start: 0.8362 (t0) cc_final: 0.8063 (t0) outliers start: 8 outliers final: 4 residues processed: 41 average time/residue: 0.6764 time to fit residues: 28.0639 Evaluate side-chains 42 residues out of total 214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 57 GLN Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 278 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 5 optimal weight: 0.1980 chunk 24 optimal weight: 9.9990 chunk 7 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 21 optimal weight: 9.9990 chunk 12 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- 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 = 0.3614 r_free = 0.3614 target = 0.136009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.106450 restraints weight = 2281.390| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.73 r_work: 0.3126 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2110 Z= 0.155 Angle : 0.585 9.210 2860 Z= 0.307 Chirality : 0.045 0.137 315 Planarity : 0.004 0.034 376 Dihedral : 4.321 15.021 292 Min Nonbonded Distance : 2.660 Molprobity Statistics. All-atom Clashscore : 0.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.80 % Allowed : 15.89 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 0.61 (0.51), residues: 259 helix: 2.68 (0.56), residues: 87 sheet: -0.52 (0.68), residues: 56 loop : -0.90 (0.49), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 30 TYR 0.008 0.001 TYR A 131 PHE 0.015 0.002 PHE A 259 TRP 0.009 0.001 TRP A 96 HIS 0.004 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 2110) covalent geometry : angle 0.58480 ( 2860) hydrogen bonds : bond 0.06493 ( 92) hydrogen bonds : angle 4.40603 ( 261) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.087 Fit side-chains REVERT: A 16 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7569 (mt-10) REVERT: A 25 ILE cc_start: 0.8690 (OUTLIER) cc_final: 0.8231 (tp) REVERT: A 57 GLN cc_start: 0.7800 (OUTLIER) cc_final: 0.6919 (mp10) REVERT: A 74 MET cc_start: 0.8296 (mtm) cc_final: 0.7693 (pp-130) REVERT: A 173 ASN cc_start: 0.8386 (t0) cc_final: 0.8071 (t0) outliers start: 6 outliers final: 4 residues processed: 40 average time/residue: 0.7827 time to fit residues: 31.7064 Evaluate side-chains 43 residues out of total 214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 57 GLN Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 278 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 24 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 17 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 16 optimal weight: 8.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 = 0.3638 r_free = 0.3638 target = 0.137931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.108716 restraints weight = 2289.704| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.72 r_work: 0.3156 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2110 Z= 0.126 Angle : 0.536 9.060 2860 Z= 0.280 Chirality : 0.043 0.131 315 Planarity : 0.004 0.032 376 Dihedral : 4.091 14.449 292 Min Nonbonded Distance : 2.655 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.27 % Allowed : 15.42 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 0.80 (0.51), residues: 259 helix: 2.88 (0.56), residues: 87 sheet: -0.42 (0.70), residues: 56 loop : -0.82 (0.49), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 30 TYR 0.005 0.001 TYR A 131 PHE 0.012 0.001 PHE A 259 TRP 0.007 0.001 TRP A 96 HIS 0.004 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 2110) covalent geometry : angle 0.53642 ( 2860) hydrogen bonds : bond 0.05206 ( 92) hydrogen bonds : angle 4.21857 ( 261) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1343.78 seconds wall clock time: 23 minutes 40.78 seconds (1420.78 seconds total)