Starting phenix.real_space_refine on Wed Sep 17 02:59:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9arx_43797/09_2025/9arx_43797.cif Found real_map, /net/cci-nas-00/data/ceres_data/9arx_43797/09_2025/9arx_43797.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9arx_43797/09_2025/9arx_43797.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9arx_43797/09_2025/9arx_43797.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9arx_43797/09_2025/9arx_43797.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9arx_43797/09_2025/9arx_43797.map" } resolution = 3.24 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= -0.000 sd= 0.018 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 12 5.16 5 C 1234 2.51 5 N 291 2.21 5 O 314 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-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 1851 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1838 Classifications: {'peptide': 256} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 9, 'TRANS': 246} Chain breaks: 2 Unresolved non-hydrogen bonds: 182 Unresolved non-hydrogen angles: 223 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 3, 'ASN:plan1': 3, 'TYR:plan': 2, 'PHE:plan': 2, 'ARG:plan': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 80 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'SRO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.66, per 1000 atoms: 0.36 Number of scatterers: 1851 At special positions: 0 Unit cell: (62.48, 69.52, 64.24, 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 12 16.00 O 314 8.00 N 291 7.00 C 1234 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 148 " - pdb=" SG CYS A 227 " 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: 0.26 Conformation dependent library (CDL) restraints added in 135.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 492 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 0 sheets defined 91.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing helix chain 'A' and resid 80 through 102 removed outlier: 3.876A pdb=" N VAL A 84 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ILE A 86 " --> pdb=" O ALA A 82 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE A 93 " --> pdb=" O ILE A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 106 removed outlier: 3.689A pdb=" N GLN A 106 " --> pdb=" O LYS A 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 103 through 106' Processing helix chain 'A' and resid 107 through 127 Processing helix chain 'A' and resid 127 through 137 Processing helix chain 'A' and resid 144 through 146 No H-bonds generated for 'chain 'A' and resid 144 through 146' Processing helix chain 'A' and resid 147 through 179 removed outlier: 3.513A pdb=" N TRP A 151 " --> pdb=" O LEU A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 186 removed outlier: 3.615A pdb=" N PHE A 186 " --> pdb=" O HIS A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 207 removed outlier: 4.091A pdb=" N ALA A 192 " --> pdb=" O SER A 188 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER A 207 " --> pdb=" O SER A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 213 removed outlier: 4.440A pdb=" N VAL A 212 " --> pdb=" O MET A 208 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE A 213 " --> pdb=" O PRO A 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 208 through 213' Processing helix chain 'A' and resid 217 through 221 removed outlier: 3.655A pdb=" N LYS A 220 " --> pdb=" O ASP A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 243 removed outlier: 3.892A pdb=" N ILE A 237 " --> pdb=" O ASN A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 261 removed outlier: 3.856A pdb=" N ILE A 252 " --> pdb=" O THR A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 349 removed outlier: 3.622A pdb=" N GLN A 319 " --> pdb=" O ILE A 315 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS A 320 " --> pdb=" O SER A 316 " (cutoff:3.500A) Proline residue: A 338 - end of helix removed outlier: 3.596A pdb=" N VAL A 347 " --> pdb=" O ASN A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 382 removed outlier: 3.826A pdb=" N VAL A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N TRP A 367 " --> pdb=" O ASN A 363 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER A 372 " --> pdb=" O ILE A 368 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N SER A 373 " --> pdb=" O GLY A 369 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA A 374 " --> pdb=" O TYR A 370 " (cutoff:3.500A) Proline residue: A 377 - end of helix Processing helix chain 'A' and resid 384 through 390 removed outlier: 3.761A pdb=" N ARG A 388 " --> pdb=" O ASN A 384 " (cutoff:3.500A) 149 hydrogen bonds defined for protein. 444 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: 0.27 Time building geometry restraints manager: 0.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 546 1.34 - 1.46: 331 1.46 - 1.58: 999 1.58 - 1.69: 1 1.69 - 1.81: 18 Bond restraints: 1895 Sorted by residual: bond pdb=" CD2 SRO A 501 " pdb=" CE2 SRO A 501 " ideal model delta sigma weight residual 1.419 1.367 0.052 2.00e-02 2.50e+03 6.69e+00 bond pdb=" CD1 SRO A 501 " pdb=" NE1 SRO A 501 " ideal model delta sigma weight residual 1.377 1.327 0.050 2.00e-02 2.50e+03 6.26e+00 bond pdb=" C ILE A 210 " pdb=" N PRO A 211 " ideal model delta sigma weight residual 1.334 1.377 -0.043 2.34e-02 1.83e+03 3.42e+00 bond pdb=" CB PRO A 144 " pdb=" CG PRO A 144 " ideal model delta sigma weight residual 1.492 1.579 -0.087 5.00e-02 4.00e+02 3.01e+00 bond pdb=" C ILE A 245 " pdb=" N PRO A 246 " ideal model delta sigma weight residual 1.335 1.355 -0.021 1.28e-02 6.10e+03 2.62e+00 ... (remaining 1890 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 2431 1.49 - 2.99: 138 2.99 - 4.48: 21 4.48 - 5.97: 8 5.97 - 7.46: 6 Bond angle restraints: 2604 Sorted by residual: angle pdb=" CA PRO A 144 " pdb=" N PRO A 144 " pdb=" CD PRO A 144 " ideal model delta sigma weight residual 112.00 105.29 6.71 1.40e+00 5.10e-01 2.30e+01 angle pdb=" N CYS A 337 " pdb=" CA CYS A 337 " pdb=" C CYS A 337 " ideal model delta sigma weight residual 109.81 116.95 -7.14 2.21e+00 2.05e-01 1.04e+01 angle pdb=" CA CYS A 337 " pdb=" C CYS A 337 " pdb=" N PRO A 338 " ideal model delta sigma weight residual 118.44 123.09 -4.65 1.59e+00 3.96e-01 8.55e+00 angle pdb=" CA ASN A 187 " pdb=" C ASN A 187 " pdb=" N SER A 188 " ideal model delta sigma weight residual 114.76 117.92 -3.16 1.14e+00 7.69e-01 7.66e+00 angle pdb=" N ASN A 187 " pdb=" CA ASN A 187 " pdb=" C ASN A 187 " ideal model delta sigma weight residual 109.39 113.64 -4.25 1.59e+00 3.96e-01 7.13e+00 ... (remaining 2599 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.89: 963 16.89 - 33.79: 99 33.79 - 50.68: 16 50.68 - 67.57: 4 67.57 - 84.46: 2 Dihedral angle restraints: 1084 sinusoidal: 332 harmonic: 752 Sorted by residual: dihedral pdb=" CB CYS A 148 " pdb=" SG CYS A 148 " pdb=" SG CYS A 227 " pdb=" CB CYS A 227 " ideal model delta sinusoidal sigma weight residual -86.00 -170.46 84.46 1 1.00e+01 1.00e-02 8.67e+01 dihedral pdb=" CA PRO A 144 " pdb=" C PRO A 144 " pdb=" N SER A 145 " pdb=" CA SER A 145 " ideal model delta harmonic sigma weight residual 180.00 -160.49 -19.51 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA ARG A 140 " pdb=" C ARG A 140 " pdb=" N TRP A 141 " pdb=" CA TRP A 141 " ideal model delta harmonic sigma weight residual -180.00 -161.80 -18.20 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 1081 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 223 0.044 - 0.088: 86 0.088 - 0.132: 16 0.132 - 0.176: 6 0.176 - 0.220: 1 Chirality restraints: 332 Sorted by residual: chirality pdb=" CB VAL A 241 " pdb=" CA VAL A 241 " pdb=" CG1 VAL A 241 " pdb=" CG2 VAL A 241 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA CYS A 337 " pdb=" N CYS A 337 " pdb=" C CYS A 337 " pdb=" CB CYS A 337 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.51e-01 chirality pdb=" CA MET A 208 " pdb=" N MET A 208 " pdb=" C MET A 208 " pdb=" CB MET A 208 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.39e-01 ... (remaining 329 not shown) Planarity restraints: 313 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 143 " -0.049 5.00e-02 4.00e+02 7.10e-02 8.06e+00 pdb=" N PRO A 144 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO A 144 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 144 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 337 " -0.038 5.00e-02 4.00e+02 5.65e-02 5.10e+00 pdb=" N PRO A 338 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 338 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 338 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 245 " -0.036 5.00e-02 4.00e+02 5.42e-02 4.69e+00 pdb=" N PRO A 246 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 246 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 246 " -0.031 5.00e-02 4.00e+02 ... (remaining 310 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 577 2.82 - 3.34: 1744 3.34 - 3.86: 3039 3.86 - 4.38: 3318 4.38 - 4.90: 6009 Nonbonded interactions: 14687 Sorted by model distance: nonbonded pdb=" OD2 ASP A 155 " pdb=" OH TYR A 370 " model vdw 2.302 3.040 nonbonded pdb=" OD1 ASN A 110 " pdb=" OH TYR A 387 " model vdw 2.306 3.040 nonbonded pdb=" O THR A 253 " pdb=" OG1 THR A 257 " model vdw 2.347 3.040 nonbonded pdb=" O ALA A 161 " pdb=" ND1 HIS A 165 " model vdw 2.364 3.120 nonbonded pdb=" O VAL A 199 " pdb=" OG SER A 203 " model vdw 2.365 3.040 ... (remaining 14682 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: 1.820 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: 0.050 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 3.800 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 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 : 0.006 0.087 1896 Z= 0.249 Angle : 0.858 7.463 2606 Z= 0.497 Chirality : 0.049 0.220 332 Planarity : 0.009 0.071 313 Dihedral : 14.131 72.776 589 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.00 % Allowed : 18.64 % 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: -2.03 (0.46), residues: 250 helix: -1.11 (0.30), residues: 205 sheet: None (None), residues: 0 loop : -1.54 (0.95), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 388 TYR 0.010 0.001 TYR A 153 PHE 0.015 0.002 PHE A 244 TRP 0.021 0.002 TRP A 141 HIS 0.005 0.002 HIS A 165 Details of bonding type rmsd covalent geometry : bond 0.00557 ( 1895) covalent geometry : angle 0.85769 ( 2604) SS BOND : bond 0.00151 ( 1) SS BOND : angle 0.97840 ( 2) hydrogen bonds : bond 0.14034 ( 149) hydrogen bonds : angle 6.19686 ( 444) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.073 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.0480 time to fit residues: 1.9382 Evaluate side-chains 30 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 12 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3812 r_free = 0.3812 target = 0.157963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.143622 restraints weight = 2377.142| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 1.40 r_work: 0.3597 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3501 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 1896 Z= 0.152 Angle : 0.545 5.023 2606 Z= 0.285 Chirality : 0.039 0.105 332 Planarity : 0.005 0.040 313 Dihedral : 4.791 27.325 266 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.95 % Allowed : 15.82 % Favored : 80.23 % 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: -0.03 (0.53), residues: 250 helix: 0.29 (0.35), residues: 206 sheet: None (None), residues: 0 loop : -0.95 (1.13), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 173 TYR 0.009 0.001 TYR A 174 PHE 0.012 0.001 PHE A 244 TRP 0.008 0.001 TRP A 141 HIS 0.005 0.002 HIS A 165 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 1895) covalent geometry : angle 0.54517 ( 2604) SS BOND : bond 0.00034 ( 1) SS BOND : angle 0.31237 ( 2) hydrogen bonds : bond 0.04014 ( 149) hydrogen bonds : angle 4.07540 ( 444) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 30 time to evaluate : 0.068 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 36 average time/residue: 0.0392 time to fit residues: 1.7964 Evaluate side-chains 31 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 27 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 386 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 7 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 21 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 = 0.3796 r_free = 0.3796 target = 0.156008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.142298 restraints weight = 2412.923| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 1.32 r_work: 0.3586 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 1896 Z= 0.165 Angle : 0.565 6.548 2606 Z= 0.288 Chirality : 0.040 0.113 332 Planarity : 0.004 0.033 313 Dihedral : 4.745 28.227 266 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 5.65 % Allowed : 15.82 % Favored : 78.53 % 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: 0.68 (0.54), residues: 250 helix: 0.77 (0.35), residues: 206 sheet: None (None), residues: 0 loop : -0.63 (1.13), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 388 TYR 0.007 0.001 TYR A 174 PHE 0.012 0.001 PHE A 244 TRP 0.009 0.001 TRP A 141 HIS 0.004 0.001 HIS A 165 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 1895) covalent geometry : angle 0.56473 ( 2604) SS BOND : bond 0.00101 ( 1) SS BOND : angle 0.37324 ( 2) hydrogen bonds : bond 0.04035 ( 149) hydrogen bonds : angle 4.02993 ( 444) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 26 time to evaluate : 0.097 Fit side-chains REVERT: A 141 TRP cc_start: 0.7386 (OUTLIER) cc_final: 0.6274 (t60) outliers start: 10 outliers final: 6 residues processed: 34 average time/residue: 0.0421 time to fit residues: 1.8231 Evaluate side-chains 32 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 25 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 141 TRP Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 316 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 7 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3788 r_free = 0.3788 target = 0.155108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.141616 restraints weight = 2387.977| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 1.30 r_work: 0.3582 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3489 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 1896 Z= 0.169 Angle : 0.570 5.301 2606 Z= 0.288 Chirality : 0.040 0.115 332 Planarity : 0.004 0.032 313 Dihedral : 4.704 27.845 266 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.52 % Allowed : 15.25 % Favored : 80.23 % 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: 0.95 (0.55), residues: 250 helix: 0.96 (0.36), residues: 206 sheet: None (None), residues: 0 loop : -0.62 (1.14), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 388 TYR 0.007 0.001 TYR A 174 PHE 0.013 0.001 PHE A 244 TRP 0.010 0.001 TRP A 141 HIS 0.004 0.001 HIS A 165 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 1895) covalent geometry : angle 0.56975 ( 2604) SS BOND : bond 0.00103 ( 1) SS BOND : angle 0.55317 ( 2) hydrogen bonds : bond 0.04027 ( 149) hydrogen bonds : angle 4.04447 ( 444) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.071 Fit side-chains REVERT: A 141 TRP cc_start: 0.7535 (OUTLIER) cc_final: 0.6432 (t60) outliers start: 8 outliers final: 6 residues processed: 34 average time/residue: 0.0415 time to fit residues: 1.7908 Evaluate side-chains 33 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 26 time to evaluate : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 141 TRP Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 316 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 0.1980 chunk 19 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.156763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.142712 restraints weight = 2363.900| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 1.40 r_work: 0.3591 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3497 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 1896 Z= 0.144 Angle : 0.538 5.070 2606 Z= 0.273 Chirality : 0.039 0.128 332 Planarity : 0.004 0.030 313 Dihedral : 4.713 30.990 266 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 5.08 % Allowed : 16.95 % Favored : 77.97 % 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: 1.24 (0.55), residues: 250 helix: 1.18 (0.36), residues: 206 sheet: None (None), residues: 0 loop : -0.61 (1.15), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 388 TYR 0.006 0.001 TYR A 174 PHE 0.012 0.001 PHE A 244 TRP 0.011 0.001 TRP A 141 HIS 0.003 0.001 HIS A 165 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 1895) covalent geometry : angle 0.53831 ( 2604) SS BOND : bond 0.00133 ( 1) SS BOND : angle 0.55076 ( 2) hydrogen bonds : bond 0.03754 ( 149) hydrogen bonds : angle 3.97354 ( 444) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 29 time to evaluate : 0.070 Fit side-chains REVERT: A 141 TRP cc_start: 0.7445 (OUTLIER) cc_final: 0.6445 (t60) outliers start: 9 outliers final: 7 residues processed: 36 average time/residue: 0.0401 time to fit residues: 1.8301 Evaluate side-chains 33 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 25 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 141 TRP Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 316 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 17 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3794 r_free = 0.3794 target = 0.155635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.141502 restraints weight = 2384.068| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 1.42 r_work: 0.3579 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3483 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 1896 Z= 0.152 Angle : 0.541 5.121 2606 Z= 0.275 Chirality : 0.040 0.128 332 Planarity : 0.004 0.031 313 Dihedral : 4.646 29.283 266 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 6.21 % Allowed : 15.25 % Favored : 78.53 % 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: 1.29 (0.55), residues: 250 helix: 1.23 (0.36), residues: 206 sheet: None (None), residues: 0 loop : -0.68 (1.14), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 388 TYR 0.007 0.001 TYR A 174 PHE 0.012 0.001 PHE A 244 TRP 0.011 0.002 TRP A 141 HIS 0.004 0.001 HIS A 165 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 1895) covalent geometry : angle 0.54110 ( 2604) SS BOND : bond 0.00153 ( 1) SS BOND : angle 0.54395 ( 2) hydrogen bonds : bond 0.03824 ( 149) hydrogen bonds : angle 3.98143 ( 444) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 27 time to evaluate : 0.068 Fit side-chains REVERT: A 141 TRP cc_start: 0.7497 (OUTLIER) cc_final: 0.6557 (t60) outliers start: 11 outliers final: 7 residues processed: 36 average time/residue: 0.0395 time to fit residues: 1.8371 Evaluate side-chains 33 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 25 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 141 TRP Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 316 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 24 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 4 optimal weight: 0.2980 chunk 2 optimal weight: 0.0870 overall best weight: 0.4558 ------------------------------------------------------------------------------- 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 = 0.3823 r_free = 0.3823 target = 0.158484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.144827 restraints weight = 2365.127| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 1.31 r_work: 0.3619 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3526 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 1896 Z= 0.120 Angle : 0.503 5.058 2606 Z= 0.256 Chirality : 0.039 0.135 332 Planarity : 0.004 0.030 313 Dihedral : 4.751 35.250 266 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 4.52 % Allowed : 17.51 % Favored : 77.97 % 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: 1.58 (0.55), residues: 250 helix: 1.45 (0.36), residues: 206 sheet: None (None), residues: 0 loop : -0.68 (1.13), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 388 TYR 0.006 0.001 TYR A 153 PHE 0.013 0.001 PHE A 244 TRP 0.010 0.001 TRP A 141 HIS 0.004 0.001 HIS A 165 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 1895) covalent geometry : angle 0.50306 ( 2604) SS BOND : bond 0.00127 ( 1) SS BOND : angle 0.48893 ( 2) hydrogen bonds : bond 0.03417 ( 149) hydrogen bonds : angle 3.83852 ( 444) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.068 Fit side-chains REVERT: A 141 TRP cc_start: 0.7353 (OUTLIER) cc_final: 0.6513 (t60) outliers start: 8 outliers final: 5 residues processed: 34 average time/residue: 0.0399 time to fit residues: 1.7202 Evaluate side-chains 34 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 28 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 141 TRP Chi-restraints excluded: chain A residue 248 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 8 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 24 optimal weight: 0.0370 chunk 4 optimal weight: 0.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- 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 = 0.3815 r_free = 0.3815 target = 0.157650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.143960 restraints weight = 2367.106| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 1.32 r_work: 0.3611 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3518 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 1896 Z= 0.129 Angle : 0.512 5.096 2606 Z= 0.260 Chirality : 0.039 0.138 332 Planarity : 0.004 0.030 313 Dihedral : 4.604 31.918 266 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.95 % Allowed : 19.21 % Favored : 76.84 % 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: 1.65 (0.55), residues: 250 helix: 1.50 (0.36), residues: 206 sheet: None (None), residues: 0 loop : -0.67 (1.14), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 388 TYR 0.006 0.001 TYR A 174 PHE 0.012 0.001 PHE A 244 TRP 0.010 0.001 TRP A 141 HIS 0.004 0.001 HIS A 165 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 1895) covalent geometry : angle 0.51200 ( 2604) SS BOND : bond 0.00146 ( 1) SS BOND : angle 0.48132 ( 2) hydrogen bonds : bond 0.03535 ( 149) hydrogen bonds : angle 3.84687 ( 444) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 30 time to evaluate : 0.068 Fit side-chains REVERT: A 141 TRP cc_start: 0.7378 (OUTLIER) cc_final: 0.6554 (t60) outliers start: 7 outliers final: 6 residues processed: 35 average time/residue: 0.0391 time to fit residues: 1.7396 Evaluate side-chains 35 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 28 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 141 TRP Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 248 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 20 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 7 optimal weight: 0.3980 chunk 23 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 10 optimal weight: 0.0870 chunk 2 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- 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 = 0.3826 r_free = 0.3826 target = 0.158753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.145195 restraints weight = 2368.508| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 1.31 r_work: 0.3616 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3524 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 1896 Z= 0.123 Angle : 0.505 5.085 2606 Z= 0.257 Chirality : 0.039 0.138 332 Planarity : 0.004 0.030 313 Dihedral : 4.647 33.195 266 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.52 % Allowed : 19.21 % Favored : 76.27 % 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: 1.68 (0.55), residues: 250 helix: 1.52 (0.36), residues: 206 sheet: None (None), residues: 0 loop : -0.68 (1.13), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 388 TYR 0.008 0.001 TYR A 153 PHE 0.013 0.001 PHE A 244 TRP 0.010 0.001 TRP A 141 HIS 0.004 0.001 HIS A 165 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 1895) covalent geometry : angle 0.50516 ( 2604) SS BOND : bond 0.00149 ( 1) SS BOND : angle 0.50182 ( 2) hydrogen bonds : bond 0.03443 ( 149) hydrogen bonds : angle 3.83209 ( 444) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.073 Fit side-chains REVERT: A 141 TRP cc_start: 0.7325 (OUTLIER) cc_final: 0.6516 (t60) outliers start: 8 outliers final: 6 residues processed: 35 average time/residue: 0.0380 time to fit residues: 1.7074 Evaluate side-chains 35 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 28 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 141 TRP Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 248 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 11 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 10 optimal weight: 0.2980 chunk 0 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 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 = 0.3809 r_free = 0.3809 target = 0.156971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.143500 restraints weight = 2354.331| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 1.31 r_work: 0.3599 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3506 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 1896 Z= 0.141 Angle : 0.524 5.132 2606 Z= 0.267 Chirality : 0.039 0.141 332 Planarity : 0.004 0.031 313 Dihedral : 4.570 29.956 266 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 4.52 % Allowed : 19.21 % Favored : 76.27 % 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: 1.55 (0.55), residues: 250 helix: 1.44 (0.36), residues: 206 sheet: None (None), residues: 0 loop : -0.72 (1.13), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 388 TYR 0.008 0.001 TYR A 153 PHE 0.012 0.001 PHE A 244 TRP 0.010 0.002 TRP A 141 HIS 0.004 0.001 HIS A 165 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 1895) covalent geometry : angle 0.52449 ( 2604) SS BOND : bond 0.00172 ( 1) SS BOND : angle 0.53220 ( 2) hydrogen bonds : bond 0.03656 ( 149) hydrogen bonds : angle 3.89972 ( 444) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.068 Fit side-chains REVERT: A 141 TRP cc_start: 0.7407 (OUTLIER) cc_final: 0.6587 (t60) outliers start: 8 outliers final: 7 residues processed: 35 average time/residue: 0.0401 time to fit residues: 1.7891 Evaluate side-chains 37 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 141 TRP Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 248 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 9 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 16 optimal weight: 0.2980 chunk 22 optimal weight: 0.9990 chunk 14 optimal weight: 0.0670 chunk 23 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 overall best weight: 0.4518 ------------------------------------------------------------------------------- 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 = 0.3830 r_free = 0.3830 target = 0.158937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.145325 restraints weight = 2354.094| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 1.31 r_work: 0.3623 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3531 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 1896 Z= 0.119 Angle : 0.500 5.076 2606 Z= 0.254 Chirality : 0.039 0.143 332 Planarity : 0.004 0.030 313 Dihedral : 4.684 34.515 266 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.52 % Allowed : 19.77 % Favored : 75.71 % 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: 1.74 (0.55), residues: 250 helix: 1.57 (0.36), residues: 206 sheet: None (None), residues: 0 loop : -0.70 (1.13), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 185 TYR 0.006 0.001 TYR A 153 PHE 0.013 0.001 PHE A 244 TRP 0.009 0.001 TRP A 141 HIS 0.004 0.001 HIS A 165 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 1895) covalent geometry : angle 0.50030 ( 2604) SS BOND : bond 0.00132 ( 1) SS BOND : angle 0.49338 ( 2) hydrogen bonds : bond 0.03370 ( 149) hydrogen bonds : angle 3.82114 ( 444) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 751.97 seconds wall clock time: 14 minutes 21.63 seconds (861.63 seconds total)